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annotate mafft/core/tbfast.c @ 18:e4d75f9efb90 draft

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planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
parents
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18
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1 #include "mltaln.h"
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2
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3 #define DEBUG 0
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4 #define IODEBUG 0
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5 #define SCOREOUT 0
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6
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7 static int nadd;
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8 static int treein;
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9 static int topin;
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10 static int treeout;
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11 static int distout;
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12 static int noalign;
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13 static int multidist;
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14 static int subalignment;
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15 static int subalignmentoffset;
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16
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17 #ifdef enablemultithread
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18 typedef struct _jobtable
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19 {
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20 int i;
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21 int j;
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22 } Jobtable;
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23
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24 typedef struct _distancematrixthread_arg
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25 {
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26 int njob;
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27 int thread_no;
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28 float *selfscore;
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29 float **iscore;
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30 char **seq;
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31 int **skiptable;
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32 Jobtable *jobpospt;
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33 pthread_mutex_t *mutex;
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34 } distancematrixthread_arg_t;
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35
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36 typedef struct _treebasethread_arg
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37 {
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38 int thread_no;
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39 int *nrunpt;
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40 int njob;
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41 int *nlen;
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42 int *jobpospt;
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43 int ***topol;
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44 Treedep *dep;
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45 char **aseq;
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46 double *effarr;
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47 int *alloclenpt;
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48 LocalHom **localhomtable;
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49 RNApair ***singlerna;
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50 double *effarr_kozo;
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51 int *fftlog;
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52 char *mergeoralign;
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53 pthread_mutex_t *mutex;
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54 pthread_cond_t *treecond;
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55 } treebasethread_arg_t;
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56 #endif
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57
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58 void arguments( int argc, char *argv[] )
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59 {
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60 int c;
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61
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62 nthread = 1;
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63 outnumber = 0;
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64 scoreout = 0;
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65 spscoreout = 0;
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66 treein = 0;
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67 topin = 0;
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68 rnaprediction = 'm';
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69 rnakozo = 0;
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70 nevermemsave = 0;
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71 inputfile = NULL;
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72 addfile = NULL;
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73 addprofile = 1;
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74 fftkeika = 0;
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75 constraint = 0;
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76 nblosum = 62;
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77 fmodel = 0;
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78 calledByXced = 0;
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79 devide = 0;
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80 use_fft = 0; // chuui
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81 force_fft = 0;
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82 fftscore = 1;
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83 fftRepeatStop = 0;
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84 fftNoAnchStop = 0;
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85 weight = 3;
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86 utree = 1;
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87 tbutree = 1;
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88 refine = 0;
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89 check = 1;
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90 cut = 0.0;
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91 disp = 0;
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92 outgap = 1;
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93 alg = 'A';
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94 mix = 0;
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95 tbitr = 0;
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96 scmtd = 5;
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97 tbweight = 0;
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98 tbrweight = 3;
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99 checkC = 0;
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100 treemethod = 'X';
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101 sueff_global = 0.1;
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102 contin = 0;
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103 scoremtx = 1;
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104 kobetsubunkatsu = 0;
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105 dorp = NOTSPECIFIED;
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106 ppenalty_dist = NOTSPECIFIED;
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107 ppenalty = NOTSPECIFIED;
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108 penalty_shift_factor = 1000.0;
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109 ppenalty_ex = NOTSPECIFIED;
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110 poffset = NOTSPECIFIED;
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111 kimuraR = NOTSPECIFIED;
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112 pamN = NOTSPECIFIED;
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113 geta2 = GETA2;
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114 fftWinSize = NOTSPECIFIED;
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115 fftThreshold = NOTSPECIFIED;
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116 RNAppenalty = NOTSPECIFIED;
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117 RNAppenalty_ex = NOTSPECIFIED;
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118 RNApthr = NOTSPECIFIED;
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119 TMorJTT = JTT;
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120 consweight_multi = 1.0;
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121 consweight_rna = 0.0;
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122 multidist = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
123 subalignment = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
124 subalignmentoffset = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
125 legacygapcost = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
126 specificityconsideration = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
127
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
128 while( --argc > 0 && (*++argv)[0] == '-' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
129 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
130 while ( ( c = *++argv[0] ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
131 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
132 switch( c )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
133 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
134 case 'i':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
135 inputfile = *++argv;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
136 fprintf( stderr, "inputfile = %s\n", inputfile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
137 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
138 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
139 case 'I':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
140 nadd = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
141 fprintf( stderr, "nadd = %d\n", nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
142 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
143 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
144 case 'e':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
145 RNApthr = (int)( atof( *++argv ) * 1000 - 0.5 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
146 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
147 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
148 case 'o':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
149 RNAppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
150 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
151 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
152 case 'V':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
153 ppenalty_dist = (int)( atof( *++argv ) * 1000 - 0.5 );
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nick
parents:
diff changeset
154 // fprintf( stderr, "ppenalty = %d\n", ppenalty );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
155 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
156 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
157 case 'f':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
158 ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
159 // fprintf( stderr, "ppenalty = %d\n", ppenalty );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
160 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
161 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
162 case 'Q':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
163 penalty_shift_factor = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
164 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
165 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
166 case 'g':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
167 ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
168 fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
169 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
170 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
171 case 'h':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
172 poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
173 // fprintf( stderr, "poffset = %d\n", poffset );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
174 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
175 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
176 case 'k':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
177 kimuraR = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
178 fprintf( stderr, "kappa = %d\n", kimuraR );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
179 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
180 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
181 case 'b':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
182 nblosum = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
183 scoremtx = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
184 fprintf( stderr, "blosum %d / kimura 200\n", nblosum );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
185 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
186 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
187 case 'j':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
188 pamN = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
189 scoremtx = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
190 TMorJTT = JTT;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
191 fprintf( stderr, "jtt/kimura %d\n", pamN );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
192 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
193 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
194 case 'm':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
195 pamN = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
196 scoremtx = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
197 TMorJTT = TM;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
198 fprintf( stderr, "tm %d\n", pamN );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
199 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
200 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
201 case 'l':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
202 fastathreshold = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
203 constraint = 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
204 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
205 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
206 case 'r':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
207 consweight_rna = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
208 rnakozo = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
209 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
210 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
211 case 'c':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
212 consweight_multi = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
213 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
214 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
215 case 'C':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
216 nthread = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
217 fprintf( stderr, "nthread = %d\n", nthread );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
218 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
219 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
220 case 's':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
221 specificityconsideration = (double)myatof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
222 // fprintf( stderr, "specificityconsideration = %f\n", specificityconsideration );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
223 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
224 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
225 case 'R':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
226 rnaprediction = 'r';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
227 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
228 case 'a':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
229 fmodel = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
230 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
231 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
232 case 'K':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
233 addprofile = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
234 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
235 case 'y':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
236 distout = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
237 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
238 case 't':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
239 treeout = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
240 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
241 case 'T':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
242 noalign = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
243 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
244 case 'D':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
245 dorp = 'd';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
246 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
247 case 'P':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
248 dorp = 'p';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
249 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
250 case 'L':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
251 legacygapcost = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
252 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
253 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
254 case 'O':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
255 outgap = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
256 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
257 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
258 case 'O':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
259 fftNoAnchStop = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
260 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
261 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
262 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
263 case 'S' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
264 scoreout = 1; // for checking parallel calculation
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
265 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
266 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
267 case 'S' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
268 spscoreout = 1; // 2014/Dec/30, sp score
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
269 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
270 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
271 case 'H':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
272 subalignment = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
273 subalignmentoffset = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
274 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
275 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
276 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
277 case 'e':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
278 fftscore = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
279 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
280 case 'r':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
281 fmodel = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
282 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
283 case 'R':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
284 fftRepeatStop = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
285 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
286 case 's':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
287 treemethod = 's';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
288 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
289 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
290 case 'X':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
291 treemethod = 'X';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
292 sueff_global = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
293 fprintf( stderr, "sueff_global = %f\n", sueff_global );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
294 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
295 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
296 case 'E':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
297 treemethod = 'E';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
298 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
299 case 'q':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
300 treemethod = 'q';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
301 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
302 case 'n' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
303 outnumber = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
304 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
305 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
306 case 'a':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
307 alg = 'a';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
308 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
309 case 'H':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
310 alg = 'H';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
311 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
312 case 'Q':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
313 alg = 'Q';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
314 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
315 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
316 case 'A':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
317 alg = 'A';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
318 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
319 case 'M':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
320 alg = 'M';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
321 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
322 case 'N':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
323 nevermemsave = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
324 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
325 case 'B': // hitsuyou! memopt -M -B no tame
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
326 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
327 case 'F':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
328 use_fft = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
329 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
330 case 'G':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
331 force_fft = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
332 use_fft = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
333 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
334 case 'U':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
335 treein = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
336 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
337 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
338 case 'V':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
339 topin = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
340 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
341 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
342 case 'u':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
343 tbrweight = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
344 weight = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
345 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
346 case 'v':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
347 tbrweight = 3;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
348 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
349 case 'd':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
350 multidist = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
351 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
352 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
353 case 'd':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
354 disp = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
355 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
356 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
357 /* Modified 01/08/27, default: user tree */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
358 case 'J':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
359 tbutree = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
360 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
361 /* modification end. */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
362 case 'z':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
363 fftThreshold = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
364 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
365 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
366 case 'w':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
367 fftWinSize = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
368 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
369 goto nextoption;
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370 case 'Z':
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371 checkC = 1;
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372 break;
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373 default:
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374 fprintf( stderr, "illegal option %c\n", c );
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375 argc = 0;
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376 break;
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377 }
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378 }
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379 nextoption:
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380 ;
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381 }
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382 if( argc == 1 )
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383 {
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384 cut = atof( (*argv) );
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385 argc--;
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386 }
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387 if( argc != 0 )
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388 {
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389 fprintf( stderr, "options: Check source file !\n" );
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390 exit( 1 );
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391 }
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392 if( tbitr == 1 && outgap == 0 )
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393 {
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394 fprintf( stderr, "conflicting options : o, m or u\n" );
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395 exit( 1 );
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396 }
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397 if( alg == 'C' && outgap == 0 )
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398 {
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399 fprintf( stderr, "conflicting options : C, o\n" );
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400 exit( 1 );
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401 }
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402 }
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403
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404 #if 0
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405 static void *distancematrixthread2( void *arg )
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406 {
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407 distancematrixthread_arg_t *targ = (distancematrixthread_arg_t *)arg;
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408 int njob = targ->njob;
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409 int thread_no = targ->thread_no;
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410 float *selfscore = targ->selfscore;
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411 float **iscore = targ->iscore;
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412 char **seq = targ->seq;
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413 Jobtable *jobpospt = targ->jobpospt;
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414
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415 float ssi, ssj, bunbo;
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416 int i, j;
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417
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418 while( 1 )
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419 {
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420 pthread_mutex_lock( targ->mutex );
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421 i = jobpospt->i;
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422 i++;
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423 if( i == njob-1 )
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424 {
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425 pthread_mutex_unlock( targ->mutex );
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426 return( NULL );
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427 }
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428 jobpospt->i = i;
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429 pthread_mutex_unlock( targ->mutex );
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430
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431 ssi = selfscore[i];
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432 if( i % 10 == 0 ) fprintf( stderr, "\r% 5d / %d (thread %4d)", i, njob, thread_no );
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433 for( j=i+1; j<njob; j++ )
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434 {
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435 ssj = selfscore[j];
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436 bunbo = MIN( ssi, ssj );
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437 if( bunbo == 0.0 )
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438 iscore[i][j-i] = 1.0;
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439 else
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440 iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty_dist ) / bunbo;
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441 }
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442 }
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443 }
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444 #endif
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445
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446 #ifdef enablemultithread
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447 static void *distancematrixthread( void *arg ) // v7.2 ijou deha tsukawanaihazu
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448 {
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449 distancematrixthread_arg_t *targ = (distancematrixthread_arg_t *)arg;
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450 int njob = targ->njob;
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451 int thread_no = targ->thread_no;
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452 float *selfscore = targ->selfscore;
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453 float **iscore = targ->iscore;
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454 char **seq = targ->seq;
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455 int **skiptable = targ->skiptable;
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456 Jobtable *jobpospt = targ->jobpospt;
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457
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458 float ssi, ssj, bunbo;
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459 int i, j;
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460
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461 while( 1 )
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462 {
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463 pthread_mutex_lock( targ->mutex );
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464 j = jobpospt->j;
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465 i = jobpospt->i;
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466 j++;
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467 if( j == njob )
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468 {
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469 i++;
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470 j = i + 1;
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471 if( i == njob-1 )
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472 {
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473 pthread_mutex_unlock( targ->mutex );
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474 return( NULL );
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475 }
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476 }
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477 jobpospt->j = j;
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478 jobpospt->i = i;
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479 pthread_mutex_unlock( targ->mutex );
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480
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481
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482 if( j==i+1 && i % 10 == 0 ) fprintf( stderr, "\r% 5d / %d (thread %4d)", i, njob, thread_no );
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483 ssi = selfscore[i];
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484 ssj = selfscore[j];
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485 bunbo = MIN( ssi, ssj );
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486 if( bunbo == 0.0 )
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487 iscore[i][j-i] = 2.0; // 2013/Oct/17
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488 else
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489 // iscore[i][j-i] = ( 1.0 - naivepairscore11( seq[i], seq[j], penalty_dist ) / bunbo ) * 2.0; // 2013/Oct/17
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490 iscore[i][j-i] = ( 1.0 - naivepairscorefast( seq[i], seq[j], skiptable[i], skiptable[j], penalty_dist ) / bunbo ) * 2.0; // 2014/Aug/15 fast
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491 if( iscore[i][j-i] > 10 ) iscore[i][j-i] = 10.0; // 2015/Mar/17
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492 }
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493 }
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494
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495 static void *treebasethread( void *arg )
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496 {
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497 treebasethread_arg_t *targ = (treebasethread_arg_t *)arg;
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498 int *nrunpt = targ->nrunpt;
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499 int thread_no = targ->thread_no;
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500 int njob = targ->njob;
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501 int *nlen = targ->nlen;
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502 int *jobpospt = targ->jobpospt;
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503 int ***topol = targ->topol;
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504 Treedep *dep = targ->dep;
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505 char **aseq = targ->aseq;
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506 double *effarr = targ->effarr;
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507 int *alloclen = targ->alloclenpt;
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508 LocalHom **localhomtable = targ->localhomtable;
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509 RNApair ***singlerna = targ->singlerna;
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510 double *effarr_kozo = targ->effarr_kozo;
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511 int *fftlog = targ->fftlog;
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512 char *mergeoralign = targ->mergeoralign;
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513
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514 char **mseq1, **mseq2;
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515 char **localcopy;
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516 int i, j, l;
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517 int len1, len2;
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518 int clus1, clus2;
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519 float pscore;
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520 char *indication1, *indication2;
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521 double *effarr1 = NULL;
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522 double *effarr2 = NULL;
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523 double *effarr1_kozo = NULL;
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524 double *effarr2_kozo = NULL;
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525 LocalHom ***localhomshrink = NULL;
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526 int m1, m2;
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527 float dumfl = 0.0;
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528 int ffttry;
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529 RNApair ***grouprna1 = NULL, ***grouprna2 = NULL;
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530 double **dynamicmtx;
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531
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532
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533 mseq1 = AllocateCharMtx( njob, 0 );
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534 mseq2 = AllocateCharMtx( njob, 0 );
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535 localcopy = calloc( njob, sizeof( char * ) );
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536 dynamicmtx = AllocateDoubleMtx( nalphabets, nalphabets );
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537
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538 if( rnakozo && rnaprediction == 'm' )
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539 {
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540 grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
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541 grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
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542 }
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543 else
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544 {
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545 grouprna1 = grouprna2 = NULL;
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546 }
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547
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548 effarr1 = AllocateDoubleVec( njob );
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549 effarr2 = AllocateDoubleVec( njob );
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550 indication1 = AllocateCharVec( 150 );
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551 indication2 = AllocateCharVec( 150 );
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552 #if 0
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553 #else
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554 if( constraint )
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555 {
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556 localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
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557 for( i=0; i<njob; i++ )
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558 localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
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559 }
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560 #endif
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561 effarr1_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
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562 effarr2_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
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563 for( i=0; i<njob; i++ ) effarr1_kozo[i] = 0.0;
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564 for( i=0; i<njob; i++ ) effarr2_kozo[i] = 0.0;
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565
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566
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567 #if 0
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568 #endif
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569
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570 #if 0
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571 for( i=0; i<njob; i++ )
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572 fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
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573 #endif
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574
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575 #if 0 //-> main thread
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576 if( constraint )
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577 calcimportance( njob, effarr, aseq, localhomtable );
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578 #endif
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579
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580
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581 // writePre( njob, name, nlen, aseq, 0 );
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582
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583
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584 // for( l=0; l<njob-1; l++ )
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585 while( 1 )
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586 {
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587
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588 pthread_mutex_lock( targ->mutex );
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589 l = *jobpospt;
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590 if( l == njob-1 )
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591 {
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592 pthread_mutex_unlock( targ->mutex );
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593 if( commonIP ) FreeIntMtx( commonIP );
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594 commonIP = NULL;
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595 Falign( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
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596 Falign_udpari_long( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL );
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597 A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
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598 free( mseq1 );
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599 free( mseq2 );
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600 free( localcopy );
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601 free( effarr1 );
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602 free( effarr2 );
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603 free( effarr1_kozo );
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604 free( effarr2_kozo );
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605 free( indication1 );
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606 free( indication2 );
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607 FreeDoubleMtx( dynamicmtx );
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608 if( rnakozo && rnaprediction == 'm' )
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609 {
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610 if( grouprna1 ) free( grouprna1 ); // nakami ha?
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611 if( grouprna2 ) free( grouprna2 ); // nakami ha?
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612 grouprna1 = grouprna2 = NULL;
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613 }
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614 if( constraint )
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615 {
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616 if( localhomshrink ) // nen no tame
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617 {
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618 for( i=0; i<njob; i++ )
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619 {
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620 free( localhomshrink[i] );
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621 localhomshrink[i] = NULL;
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622 }
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623 free( localhomshrink );
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624 localhomshrink = NULL;
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625 }
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626 }
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627 return( NULL );
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628 }
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629 *jobpospt = l+1;
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630
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631 if( dep[l].child0 != -1 )
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632 {
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633 while( dep[dep[l].child0].done == 0 )
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634 pthread_cond_wait( targ->treecond, targ->mutex );
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635 }
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636 if( dep[l].child1 != -1 )
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637 {
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638 while( dep[dep[l].child1].done == 0 )
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639 pthread_cond_wait( targ->treecond, targ->mutex );
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640 }
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641 // while( *nrunpt >= nthread )
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642 // pthread_cond_wait( targ->treecond, targ->mutex );
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643 (*nrunpt)++;
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644
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645 // pthread_mutex_unlock( targ->mutex );
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646
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647 if( mergeoralign[l] == 'n' )
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648 {
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649 // fprintf( stderr, "SKIP!\n" );
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650 dep[l].done = 1;
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651 (*nrunpt)--;
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652 pthread_cond_broadcast( targ->treecond );
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653 free( topol[l][0] );
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654 free( topol[l][1] );
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655 free( topol[l] );
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656 pthread_mutex_unlock( targ->mutex );
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657 continue;
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658 }
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659
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660
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661
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662 m1 = topol[l][0][0];
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663 m2 = topol[l][1][0];
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664
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665 // fprintf( stderr, "\ndistfromtip = %f\n", dep[l].distfromtip );
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666 // makedynamicmtx( dynamicmtx, n_dis_consweight_multi, dep[l].distfromtip - 0.5 );
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667 makedynamicmtx( dynamicmtx, n_dis_consweight_multi, dep[l].distfromtip );
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668
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669 // pthread_mutex_lock( targ->mutex );
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670
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671
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672
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673 len1 = strlen( aseq[m1] );
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674 len2 = strlen( aseq[m2] );
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675 if( *alloclen <= len1 + len2 )
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676 {
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677 fprintf( stderr, "\nReallocating (by thread %d) ..", thread_no );
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678 *alloclen = ( len1 + len2 ) + 1000;
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679 ReallocateCharMtx( aseq, njob, *alloclen + 10 );
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680 fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
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681 }
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682
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683 for( i=0; (j=topol[l][0][i])!=-1; i++ )
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684 {
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685 localcopy[j] = calloc( *alloclen, sizeof( char ) );
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686 strcpy( localcopy[j], aseq[j] );
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687 }
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688 for( i=0; (j=topol[l][1][i])!=-1; i++ )
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689 {
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690 localcopy[j] = calloc( *alloclen, sizeof( char ) );
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691 strcpy( localcopy[j], aseq[j] );
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692 }
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693
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694 pthread_mutex_unlock( targ->mutex );
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695
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696
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697
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698 if( effarr_kozo )
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699 {
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700 clus1 = fastconjuction_noname_kozo( topol[l][0], localcopy, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
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701 clus2 = fastconjuction_noname_kozo( topol[l][1], localcopy, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
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702 }
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703 else
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704 {
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705 clus1 = fastconjuction_noname( topol[l][0], localcopy, mseq1, effarr1, effarr, indication1, 0.0 );
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706 clus2 = fastconjuction_noname( topol[l][1], localcopy, mseq2, effarr2, effarr, indication2, 0.0 );
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707 }
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708
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709
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710
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711 #if 1
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712 fprintf( stderr, "\rSTEP % 5d /%d (thread %4d) ", l+1, njob-1, thread_no );
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713 #else
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714 fprintf( stderr, "STEP %d /%d (thread %d) \n", l+1, njob-1, thread_no );
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715 fprintf( stderr, "group1 = %.66s", indication1 );
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716 if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
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717 fprintf( stderr, ", child1 = %d\n", dep[l].child0 );
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718 fprintf( stderr, "group2 = %.66s", indication2 );
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719 if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
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720 fprintf( stderr, ", child2 = %d\n", dep[l].child1 );
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721
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722 fprintf( stderr, "Group1's lengths = " );
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nick
parents:
diff changeset
723 for( i=0; i<clus1; i++ ) fprintf( stderr, "%d ", strlen( mseq1[i] ) );
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diff changeset
724 fprintf( stderr, "\n" );
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nick
parents:
diff changeset
725 fprintf( stderr, "Group2's lengths = " );
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nick
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diff changeset
726 for( i=0; i<clus2; i++ ) fprintf( stderr, "%d ", strlen( mseq2[i] ) );
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nick
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diff changeset
727 fprintf( stderr, "\n" );
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nick
parents:
diff changeset
728
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diff changeset
729 #endif
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diff changeset
730
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nick
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diff changeset
731
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nick
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diff changeset
732
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diff changeset
733 // for( i=0; i<clus1; i++ ) fprintf( stderr, "## STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
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nick
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diff changeset
734
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diff changeset
735 if( constraint )
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diff changeset
736 {
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diff changeset
737 fastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
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nick
parents:
diff changeset
738 // msfastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
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nick
parents:
diff changeset
739 // fprintf( stderr, "localhomshrink =\n" );
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diff changeset
740 // outlocalhompt( localhomshrink, clus1, clus2 );
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diff changeset
741 // weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink );
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diff changeset
742 // fprintf( stderr, "after weight =\n" );
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nick
parents:
diff changeset
743 // outlocalhompt( localhomshrink, clus1, clus2 );
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diff changeset
744 }
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diff changeset
745 if( rnakozo && rnaprediction == 'm' )
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diff changeset
746 {
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diff changeset
747 makegrouprna( grouprna1, singlerna, topol[l][0] );
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nick
parents:
diff changeset
748 makegrouprna( grouprna2, singlerna, topol[l][1] );
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diff changeset
749 }
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diff changeset
750
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diff changeset
751
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diff changeset
752 /*
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diff changeset
753 fprintf( stderr, "before align all\n" );
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nick
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diff changeset
754 display( localcopy, njob );
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nick
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diff changeset
755 fprintf( stderr, "\n" );
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nick
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diff changeset
756 fprintf( stderr, "before align 1 %s \n", indication1 );
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diff changeset
757 display( mseq1, clus1 );
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nick
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diff changeset
758 fprintf( stderr, "\n" );
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diff changeset
759 fprintf( stderr, "before align 2 %s \n", indication2 );
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nick
parents:
diff changeset
760 display( mseq2, clus2 );
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nick
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diff changeset
761 fprintf( stderr, "\n" );
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diff changeset
762 */
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diff changeset
763
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diff changeset
764 if( !nevermemsave && ( constraint != 2 && alg != 'M' && ( len1 > 30000 || len2 > 30000 ) ) )
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diff changeset
765 {
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diff changeset
766 fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
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nick
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diff changeset
767 alg = 'M';
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diff changeset
768 if( commonIP ) FreeIntMtx( commonIP );
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diff changeset
769 commonIP = NULL;
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diff changeset
770 commonAlloc1 = 0;
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diff changeset
771 commonAlloc2 = 0;
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diff changeset
772 }
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diff changeset
773
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nick
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diff changeset
774
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775 // if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
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diff changeset
776 if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );
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777 else ffttry = 0;
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diff changeset
778 // ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000 ); // v6.708
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diff changeset
779 // fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (float)len1/fftlog[m1], clus1, (float)len2/fftlog[m2], clus2 );
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diff changeset
780 // fprintf( stderr, "f=%d, clus1=%d, fftlog[m1]=%d, clus2=%d, fftlog[m2]=%d\n", ffttry, clus1, fftlog[m1], clus2, fftlog[m2] );
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diff changeset
781 if( constraint == 2 )
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diff changeset
782 {
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diff changeset
783 if( alg == 'M' )
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diff changeset
784 {
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785 fprintf( stderr, "\n\nMemory saving mode is not supported.\n\n" );
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786 exit( 1 );
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787 }
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diff changeset
788 fprintf( stderr, "c" );
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nick
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diff changeset
789 if( alg == 'A' )
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diff changeset
790 {
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791 imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
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792 if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
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diff changeset
793 pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
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diff changeset
794 }
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diff changeset
795 else if( alg == 'Q' )
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diff changeset
796 {
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797 fprintf( stderr, "Not supported\n" );
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798 exit( 1 );
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799 }
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800 }
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801 else if( force_fft || ( use_fft && ffttry ) )
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diff changeset
802 {
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803 fprintf( stderr, "f" );
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diff changeset
804 if( alg == 'M' )
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diff changeset
805 {
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806 fprintf( stderr, "m" );
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807 pscore = Falign_udpari_long( NULL, NULL, dynamicmtx, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, *alloclen, fftlog+m1 );
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diff changeset
808 }
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diff changeset
809 else
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810 pscore = Falign( NULL, NULL, dynamicmtx, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, *alloclen, fftlog+m1, NULL, 0, NULL );
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811 }
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812 else
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diff changeset
813 {
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814 fprintf( stderr, "d" );
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diff changeset
815 fftlog[m1] = 0;
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diff changeset
816 switch( alg )
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817 {
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818 case( 'a' ):
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
819 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
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diff changeset
820 break;
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diff changeset
821 case( 'M' ):
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822 fprintf( stderr, "m" );
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823 pscore = MSalignmm( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
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824 break;
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diff changeset
825 case( 'A' ):
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
826 pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
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827 break;
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828 default:
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829 ErrorExit( "ERROR IN SOURCE FILE" );
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diff changeset
830 }
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831 }
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832
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833 nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
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834
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835 #if SCOREOUT
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836 fprintf( stderr, "score = %10.2f\n", pscore );
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837 #endif
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838
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839 /*
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840 fprintf( stderr, "after align 1 %s \n", indication1 );
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841 display( mseq1, clus1 );
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842 fprintf( stderr, "\n" );
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843 fprintf( stderr, "after align 2 %s \n", indication2 );
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844 display( mseq2, clus2 );
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845 fprintf( stderr, "\n" );
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846 */
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847
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848 // writePre( njob, name, nlen, localcopy, 0 );
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849
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850 if( disp ) display( localcopy, njob );
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851
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852 pthread_mutex_lock( targ->mutex );
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853 dep[l].done = 1;
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854 (*nrunpt)--;
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855 pthread_cond_broadcast( targ->treecond );
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856
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857 // pthread_mutex_unlock( targ->mutex );
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858 // pthread_mutex_lock( targ->mutex );
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859
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860 for( i=0; (j=topol[l][0][i])!=-1; i++ )
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861 strcpy( aseq[j], localcopy[j] );
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862 for( i=0; (j=topol[l][1][i])!=-1; i++ )
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863 strcpy( aseq[j], localcopy[j] );
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864 pthread_mutex_unlock( targ->mutex );
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865
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866 for( i=0; (j=topol[l][0][i])!=-1; i++ )
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867 free( localcopy[j] );
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868 for( i=0; (j=topol[l][1][i])!=-1; i++ )
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869 free( localcopy[j] );
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870 free( topol[l][0] );
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871 free( topol[l][1] );
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872 free( topol[l] );
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873
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874 }
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875 }
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876 #endif
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877
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878 void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq1, char **mseq2, int ***topol, Treedep *dep, double *effarr, int *alloclen, LocalHom **localhomtable, RNApair ***singlerna, double *effarr_kozo )
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879 {
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880 int i, l, m;
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881 int len1nocommongap, len2nocommongap;
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882 int len1, len2;
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883 int clus1, clus2;
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884 float pscore, tscore;
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885 static char *indication1, *indication2;
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886 static double *effarr1 = NULL;
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887 static double *effarr2 = NULL;
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888 static double *effarr1_kozo = NULL;
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889 static double *effarr2_kozo = NULL;
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890 static LocalHom ***localhomshrink = NULL;
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891 static int *fftlog;
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892 int m1, m2;
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893 static int *gaplen;
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894 static int *gapmap;
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895 static int *alreadyaligned;
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896 float dumfl = 0.0;
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897 int ffttry;
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898 RNApair ***grouprna1 = NULL, ***grouprna2 = NULL;
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899 static double **dynamicmtx;
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900
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901 if( rnakozo && rnaprediction == 'm' )
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902 {
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903 grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
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904 grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
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905 }
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906 else
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907 {
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908 grouprna1 = grouprna2 = NULL;
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909 }
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910
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911 if( effarr1 == NULL )
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912 {
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913 fftlog = AllocateIntVec( njob );
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914 effarr1 = AllocateDoubleVec( njob );
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915 effarr2 = AllocateDoubleVec( njob );
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916 indication1 = AllocateCharVec( 150 );
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917 indication2 = AllocateCharVec( 150 );
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918 gaplen = AllocateIntVec( *alloclen+10 );
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919 gapmap = AllocateIntVec( *alloclen+10 );
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920 alreadyaligned = AllocateIntVec( njob );
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921 dynamicmtx = AllocateDoubleMtx( nalphabets, nalphabets );
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922 #if 0
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923 #else
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924 if( constraint )
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925 {
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926 localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
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927 for( i=0; i<njob; i++ )
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928 localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
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929 }
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930 #endif
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931 effarr1_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
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932 effarr2_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
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933 for( i=0; i<njob; i++ ) effarr1_kozo[i] = 0.0;
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934 for( i=0; i<njob; i++ ) effarr2_kozo[i] = 0.0;
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935 }
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936
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937 for( i=0; i<njob-nadd; i++ ) alreadyaligned[i] = 1;
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938 for( i=njob-nadd; i<njob; i++ ) alreadyaligned[i] = 0;
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939
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940 for( l=0; l<njob; l++ ) fftlog[l] = 1;
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941
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942 #if 0
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943 fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
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944 #endif
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945
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946 #if 0
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947 for( i=0; i<njob; i++ )
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948 fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
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949 #endif
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950
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diff changeset
951
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952 if( constraint )
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953 calcimportance( njob, effarr, aseq, localhomtable );
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954 // dontcalcimportance( njob, effarr, aseq, localhomtable ); // CHUUIII!!!!!
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955
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956
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957 // writePre( njob, name, nlen, aseq, 0 );
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958
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959 tscore = 0.0;
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960 for( l=0; l<njob-1; l++ )
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961 {
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962 // fprintf( stderr, "\ndistfromtip = %f\n", dep[l].distfromtip );
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963 makedynamicmtx( dynamicmtx, n_dis_consweight_multi, dep[l].distfromtip );
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964 // makedynamicmtx( dynamicmtx, n_dis_consweight_multi, ( dep[l].distfromtip - 0.2 ) * 3 );
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965 if( mergeoralign[l] == 'n' )
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966 {
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967 // fprintf( stderr, "SKIP!\n" );
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968 free( topol[l][0] );
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969 free( topol[l][1] );
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970 free( topol[l] );
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971 continue;
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972 }
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973
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974 m1 = topol[l][0][0];
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975 m2 = topol[l][1][0];
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976 len1 = strlen( aseq[m1] );
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977 len2 = strlen( aseq[m2] );
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978 if( *alloclen < len1 + len2 )
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979 {
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980 fprintf( stderr, "\nReallocating.." );
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981 *alloclen = ( len1 + len2 ) + 1000;
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982 ReallocateCharMtx( aseq, njob, *alloclen + 10 );
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983 gaplen = realloc( gaplen, ( *alloclen + 10 ) * sizeof( int ) );
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984 if( gaplen == NULL )
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985 {
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986 fprintf( stderr, "Cannot realloc gaplen\n" );
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987 exit( 1 );
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988 }
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989 gapmap = realloc( gapmap, ( *alloclen + 10 ) * sizeof( int ) );
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990 if( gapmap == NULL )
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991 {
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992 fprintf( stderr, "Cannot realloc gapmap\n" );
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993 exit( 1 );
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994 }
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995 fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
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996 }
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997
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998 if( effarr_kozo )
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999 {
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1000 clus1 = fastconjuction_noname_kozo( topol[l][0], aseq, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
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1001 clus2 = fastconjuction_noname_kozo( topol[l][1], aseq, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
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1002 }
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1003 else
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1004 {
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1005 clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1, 0.0 );
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1006 clus2 = fastconjuction_noname( topol[l][1], aseq, mseq2, effarr2, effarr, indication2, 0.0 );
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1007 }
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1008
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1009 if( mergeoralign[l] == '1' || mergeoralign[l] == '2' ) // only in serial version
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1010 {
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1011 newgapstr = "=";
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1012 }
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1013 else
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1014 newgapstr = "-";
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1015
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1016
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1017 len1nocommongap = len1;
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1018 len2nocommongap = len2;
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1019 if( mergeoralign[l] == '1' ) // nai
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1020 {
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1021 findcommongaps( clus2, mseq2, gapmap );
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1022 commongappick( clus2, mseq2 );
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1023 len2nocommongap = strlen( mseq2[0] );
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1024 }
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1025 else if( mergeoralign[l] == '2' )
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1026 {
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1027 findcommongaps( clus1, mseq1, gapmap );
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1028 commongappick( clus1, mseq1 );
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1029 len1nocommongap = strlen( mseq1[0] );
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1030 }
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1031
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1032
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1033 fprintf( trap_g, "\nSTEP-%d\n", l );
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1034 fprintf( trap_g, "group1 = %s\n", indication1 );
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1035 fprintf( trap_g, "group2 = %s\n", indication2 );
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1036
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1037 #if 1
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1038 fprintf( stderr, "\rSTEP % 5d /%d ", l+1, njob-1 );
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1039 fflush( stderr );
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1040 #else
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1041 fprintf( stdout, "STEP %d /%d\n", l+1, njob-1 );
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1042 fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
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1043 fprintf( stderr, "group1 = %.66s", indication1 );
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1044 if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
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1045 fprintf( stderr, "\n" );
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1046 fprintf( stderr, "group2 = %.66s", indication2 );
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1047 if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
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1048 fprintf( stderr, "\n" );
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1049 #endif
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1050
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1051
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1052
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1053 // for( i=0; i<clus1; i++ ) fprintf( stderr, "## STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
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1054
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1055 if( constraint )
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1056 {
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1057 fastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
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1058 // msfastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
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1059 // fprintf( stderr, "localhomshrink =\n" );
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1060 // outlocalhompt( localhomshrink, clus1, clus2 );
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1061 // weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink );
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1062 // fprintf( stderr, "after weight =\n" );
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1063 // outlocalhompt( localhomshrink, clus1, clus2 );
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1064 }
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1065 if( rnakozo && rnaprediction == 'm' )
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1066 {
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1067 makegrouprna( grouprna1, singlerna, topol[l][0] );
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1068 makegrouprna( grouprna2, singlerna, topol[l][1] );
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1069 }
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1070
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1071
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1072 /*
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1073 fprintf( stderr, "before align all\n" );
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1074 display( aseq, njob );
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1075 fprintf( stderr, "\n" );
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1076 fprintf( stderr, "before align 1 %s \n", indication1 );
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1077 display( mseq1, clus1 );
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1078 fprintf( stderr, "\n" );
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1079 fprintf( stderr, "before align 2 %s \n", indication2 );
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1080 display( mseq2, clus2 );
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1081 fprintf( stderr, "\n" );
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1082 */
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1083
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1084 if( !nevermemsave && ( constraint != 2 && alg != 'M' && ( len1 > 30000 || len2 > 30000 ) ) )
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1085 {
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1086 fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
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1087 alg = 'M';
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1088 if( commonIP ) FreeIntMtx( commonIP );
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1089 commonIP = NULL;
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1090 commonAlloc1 = 0;
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1091 commonAlloc2 = 0;
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1092 }
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1093
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1094
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1095 // if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
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1096 if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );
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1097 else ffttry = 0;
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1098 // ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000 ); // v6.708
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1099 // fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (float)len1/fftlog[m1], clus1, (float)len2/fftlog[m2], clus2 );
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1100 // fprintf( stderr, "f=%d, clus1=%d, fftlog[m1]=%d, clus2=%d, fftlog[m2]=%d\n", ffttry, clus1, fftlog[m1], clus2, fftlog[m2] );
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1101 if( constraint == 2 )
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1102 {
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1103 if( alg == 'M' )
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1104 {
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1105 fprintf( stderr, "\n\nMemory saving mode is not supported.\n\n" );
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1106 exit( 1 );
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1107 }
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1108 fprintf( stderr, "c" );
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1109 if( alg == 'A' )
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1110 {
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1111 imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
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1112 if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
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1113 pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
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1114 }
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1115 else if( alg == 'Q' )
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1116 {
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1117 fprintf( stderr, "Not supported\n" );
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1118 exit( 1 );
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1119 }
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1120 }
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1121 else if( force_fft || ( use_fft && ffttry ) )
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1122 {
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1123 fprintf( stderr, "f" );
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1124 if( alg == 'M' )
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1125 {
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1126 fprintf( stderr, "m" );
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1127 pscore = Falign_udpari_long( NULL, NULL, dynamicmtx, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, *alloclen, fftlog+m1 );
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1128 }
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1129 else
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1130 pscore = Falign( NULL, NULL, dynamicmtx, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, *alloclen, fftlog+m1, NULL, 0, NULL );
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1131 }
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1132 else
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1133 {
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1134 fprintf( stderr, "d" );
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1135 fftlog[m1] = 0;
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1136 switch( alg )
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1137 {
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1138 case( 'a' ):
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1139 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
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1140 break;
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1141 case( 'M' ):
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1142 fprintf( stderr, "m" );
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1143 pscore = MSalignmm( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
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1144 break;
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1145 case( 'A' ):
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1146 pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
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1147 break;
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1148 default:
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1149 ErrorExit( "ERROR IN SOURCE FILE" );
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1150 }
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1151 }
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1152
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1153 nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
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1154
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1155 #if SCOREOUT
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1156 fprintf( stderr, "score = %10.2f\n", pscore );
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1157 #endif
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1158 tscore += pscore;
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1159 /*
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1160 fprintf( stderr, "after align 1 %s \n", indication1 );
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1161 display( mseq1, clus1 );
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1162 fprintf( stderr, "\n" );
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1163 fprintf( stderr, "after align 2 %s \n", indication2 );
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1164 display( mseq2, clus2 );
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1165 fprintf( stderr, "\n" );
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1166 */
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1167
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1168 // writePre( njob, name, nlen, aseq, 0 );
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1169
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1170 if( disp ) display( aseq, njob );
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diff changeset
1171
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diff changeset
1172 if( mergeoralign[l] == '1' ) // jissainiha nai. atarashii hairetsu ha saigo dakara.
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diff changeset
1173 {
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diff changeset
1174 adjustgapmap( strlen( mseq2[0] )-len2nocommongap+len2, gapmap, mseq2[0] );
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diff changeset
1175 restorecommongaps( njob, aseq, topol[l][0], topol[l][1], gapmap, *alloclen, '-' );
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diff changeset
1176 findnewgaps( clus2, 0, mseq2, gaplen );
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diff changeset
1177 insertnewgaps( njob, alreadyaligned, aseq, topol[l][1], topol[l][0], gaplen, gapmap, *alloclen, alg, '-' );
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diff changeset
1178 for( i=0; i<njob; i++ ) eq2dash( aseq[i] );
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diff changeset
1179 for( i=0; (m=topol[l][0][i])>-1; i++ ) alreadyaligned[m] = 1;
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diff changeset
1180 }
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diff changeset
1181 if( mergeoralign[l] == '2' )
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diff changeset
1182 {
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1183 // fprintf( stderr, ">mseq1[0] = \n%s\n", mseq1[0] );
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diff changeset
1184 // fprintf( stderr, ">mseq2[0] = \n%s\n", mseq2[0] );
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diff changeset
1185 adjustgapmap( strlen( mseq1[0] )-len1nocommongap+len1, gapmap, mseq1[0] );
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diff changeset
1186 restorecommongaps( njob, aseq, topol[l][0], topol[l][1], gapmap, *alloclen, '-' );
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diff changeset
1187 findnewgaps( clus1, 0, mseq1, gaplen );
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diff changeset
1188 insertnewgaps( njob, alreadyaligned, aseq, topol[l][0], topol[l][1], gaplen, gapmap, *alloclen, alg, '-' );
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diff changeset
1189 #if 0
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1190 for( i=0; i<njob; i++ ) eq2dash( aseq[i] );
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diff changeset
1191 for( i=0; i<clus1; i++ ) eq2dash( mseq1[i] );
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diff changeset
1192 for( i=0; i<clus2; i++ ) eq2dash( mseq2[i] );
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diff changeset
1193 #else
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1194 eq2dashmatometehayaku( mseq1, clus1 );
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diff changeset
1195 eq2dashmatometehayaku( mseq2, clus2 );
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diff changeset
1196 #endif
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1197 for( i=0; (m=topol[l][1][i])>-1; i++ ) alreadyaligned[m] = 1;
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1198 }
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1199
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1200 free( topol[l][0] );
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diff changeset
1201 free( topol[l][1] );
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diff changeset
1202 free( topol[l] );
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1203 }
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1204 #if SCOREOUT
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1205 fprintf( stderr, "totalscore = %10.2f\n\n", tscore );
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1206 #endif
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1207 if( rnakozo && rnaprediction == 'm' )
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1208 {
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1209 if( grouprna1 ) free( grouprna1 ); // nakami ha?
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1210 if( grouprna2 ) free( grouprna2 ); // nakami ha?
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1211 grouprna1 = grouprna2 = NULL;
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1212 }
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1213 if( constraint )
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1214 {
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1215 if( localhomshrink ) // nen no tame
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1216 {
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1217 for( i=0; i<njob; i++ )
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1218 {
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1219 free( localhomshrink[i] );
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1220 localhomshrink[i] = NULL;
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1221 }
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diff changeset
1222 free( localhomshrink );
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1223 localhomshrink = NULL;
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diff changeset
1224 }
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diff changeset
1225 }
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1226 }
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1227
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1228 static void WriteOptions( FILE *fp )
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1229 {
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1230
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1231 if( dorp == 'd' ) fprintf( fp, "DNA\n" );
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1232 else
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1233 {
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1234 if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
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1235 else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
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1236 else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
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1237 }
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1238 fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
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diff changeset
1239 if( use_fft ) fprintf( fp, "FFT on\n" );
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1240
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1241 fprintf( fp, "tree-base method\n" );
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1242 if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
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1243 else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
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1244 if( tbitr || tbweight )
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1245 {
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1246 fprintf( fp, "iterate at each step\n" );
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1247 if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
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1248 if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
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1249 if( tbweight ) fprintf( fp, " weighted\n" );
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1250 fprintf( fp, "\n" );
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1251 }
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1252
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1253 fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
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1254
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1255 if( alg == 'a' )
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1256 fprintf( fp, "Algorithm A\n" );
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1257 else if( alg == 'A' )
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1258 fprintf( fp, "Algorithm A+\n" );
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1259 else if( alg == 'C' )
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diff changeset
1260 fprintf( fp, "Apgorithm A+/C\n" );
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1261 else
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1262 fprintf( fp, "Unknown algorithm\n" );
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1263
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1264 if( treemethod == 'X' )
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1265 fprintf( fp, "Tree = UPGMA (mix).\n" );
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diff changeset
1266 else if( treemethod == 'E' )
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diff changeset
1267 fprintf( fp, "Tree = UPGMA (average).\n" );
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diff changeset
1268 else if( treemethod == 'q' )
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diff changeset
1269 fprintf( fp, "Tree = Minimum linkage.\n" );
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1270 else
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1271 fprintf( fp, "Unknown tree.\n" );
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diff changeset
1272
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1273 if( use_fft )
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1274 {
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1275 fprintf( fp, "FFT on\n" );
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1276 if( dorp == 'd' )
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1277 fprintf( fp, "Basis : 4 nucleotides\n" );
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1278 else
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1279 {
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1280 if( fftscore )
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diff changeset
1281 fprintf( fp, "Basis : Polarity and Volume\n" );
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parents:
diff changeset
1282 else
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diff changeset
1283 fprintf( fp, "Basis : 20 amino acids\n" );
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parents:
diff changeset
1284 }
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diff changeset
1285 fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
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parents:
diff changeset
1286 fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
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diff changeset
1287 }
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diff changeset
1288 else
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diff changeset
1289 fprintf( fp, "FFT off\n" );
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diff changeset
1290 fflush( fp );
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1291 }
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diff changeset
1292
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diff changeset
1293
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diff changeset
1294 int main( int argc, char *argv[] )
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1295 {
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diff changeset
1296 static int *nlen;
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diff changeset
1297 static float *selfscore;
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diff changeset
1298 int nogaplen;
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1299 static char **name, **seq;
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diff changeset
1300 static char **mseq1, **mseq2;
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diff changeset
1301 static char **bseq;
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1302 static float **iscore, **iscore_kozo;
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diff changeset
1303 int **skiptable;
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diff changeset
1304 static double *eff, *eff_kozo, *eff_kozo_mapped = NULL;
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diff changeset
1305 int i, j, ien, ik, jk;
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diff changeset
1306 static int ***topol, ***topol_kozo;
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diff changeset
1307 static int *addmem;
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diff changeset
1308 static Treedep *dep;
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diff changeset
1309 static float **len, **len_kozo;
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diff changeset
1310 FILE *prep;
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diff changeset
1311 FILE *infp;
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diff changeset
1312 FILE *orderfp;
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diff changeset
1313 FILE *hat2p;
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parents:
diff changeset
1314 double unweightedspscore;
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diff changeset
1315 int alignmentlength;
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diff changeset
1316 char *mergeoralign;
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diff changeset
1317 int foundthebranch;
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diff changeset
1318 int nsubalignments, maxmem;
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diff changeset
1319 int **subtable;
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1320 int *insubtable;
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diff changeset
1321 int *preservegaps;
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diff changeset
1322 char ***subalnpt;
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1323
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1324 char c;
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diff changeset
1325 int alloclen;
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diff changeset
1326 LocalHom **localhomtable = NULL;
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diff changeset
1327 RNApair ***singlerna = NULL;
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diff changeset
1328 float ssi, ssj, bunbo;
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diff changeset
1329 static char *kozoarivec;
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diff changeset
1330 int nkozo;
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1331
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1332 arguments( argc, argv );
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diff changeset
1333 #ifndef enablemultithread
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1334 nthread = 0;
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1335 #endif
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1336
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1337 if( fastathreshold < 0.0001 ) constraint = 0;
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1338
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diff changeset
1339 if( inputfile )
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1340 {
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1341 infp = fopen( inputfile, "r" );
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1342 if( !infp )
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1343 {
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1344 fprintf( stderr, "Cannot open %s\n", inputfile );
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1345 exit( 1 );
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1346 }
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1347 }
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1348 else
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1349 infp = stdin;
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1350
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1351 getnumlen( infp );
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1352 rewind( infp );
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1353
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nick
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diff changeset
1354
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1355 nkozo = 0;
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1356
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1357 if( njob < 2 )
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1358 {
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1359 fprintf( stderr, "At least 2 sequences should be input!\n"
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1360 "Only %d sequence found.\n", njob );
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1361 exit( 1 );
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1362 }
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1363
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1364 if( subalignment )
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1365 {
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1366 readsubalignmentstable( njob, NULL, NULL, &nsubalignments, &maxmem );
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diff changeset
1367 fprintf( stderr, "nsubalignments = %d\n", nsubalignments );
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diff changeset
1368 fprintf( stderr, "maxmem = %d\n", maxmem );
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parents:
diff changeset
1369 subtable = AllocateIntMtx( nsubalignments, maxmem+1 );
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parents:
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1370 insubtable = AllocateIntVec( njob );
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1371 for( i=0; i<njob; i++ ) insubtable[i] = 0;
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parents:
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1372 preservegaps = AllocateIntVec( njob );
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parents:
diff changeset
1373 for( i=0; i<njob; i++ ) preservegaps[i] = 0;
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parents:
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1374 subalnpt = AllocateCharCub( nsubalignments, maxmem, 0 );
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parents:
diff changeset
1375 readsubalignmentstable( njob, subtable, preservegaps, NULL, NULL );
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1376 }
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1377
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diff changeset
1378 seq = AllocateCharMtx( njob, nlenmax+1 );
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parents:
diff changeset
1379 mseq1 = AllocateCharMtx( njob, 0 );
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parents:
diff changeset
1380 mseq2 = AllocateCharMtx( njob, 0 );
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parents:
diff changeset
1381
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diff changeset
1382 name = AllocateCharMtx( njob, B+1 );
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nick
parents:
diff changeset
1383 nlen = AllocateIntVec( njob );
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parents:
diff changeset
1384 selfscore = AllocateFloatVec( njob );
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parents:
diff changeset
1385
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diff changeset
1386 topol = AllocateIntCub( njob, 2, 0 );
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parents:
diff changeset
1387 len = AllocateFloatMtx( njob, 2 );
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parents:
diff changeset
1388 iscore = AllocateFloatHalfMtx( njob );
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parents:
diff changeset
1389 eff = AllocateDoubleVec( njob );
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parents:
diff changeset
1390 kozoarivec = AllocateCharVec( njob );
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parents:
diff changeset
1391
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1392 mergeoralign = AllocateCharVec( njob );
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parents:
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1393
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1394 dep = (Treedep *)calloc( njob, sizeof( Treedep ) );
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diff changeset
1395 if( nadd ) addmem = AllocateIntVec( nadd+1 );
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1396
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diff changeset
1397 if( constraint )
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1398 {
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1399 localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
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1400 for( i=0; i<njob; i++ )
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1401 {
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1402 localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
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1403 for( j=0; j<njob; j++ )
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1404 {
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1405 localhomtable[i][j].start1 = -1;
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diff changeset
1406 localhomtable[i][j].end1 = -1;
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1407 localhomtable[i][j].start2 = -1;
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diff changeset
1408 localhomtable[i][j].end2 = -1;
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diff changeset
1409 localhomtable[i][j].overlapaa = -1.0;
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diff changeset
1410 localhomtable[i][j].opt = -1.0;
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diff changeset
1411 localhomtable[i][j].importance = -1.0;
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diff changeset
1412 localhomtable[i][j].next = NULL;
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diff changeset
1413 localhomtable[i][j].korh = 'h';
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1414 }
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1415 }
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1416
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1417 fprintf( stderr, "Loading 'hat3' ... " );
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1418 prep = fopen( "hat3", "r" );
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1419 if( prep == NULL ) ErrorExit( "Make hat3." );
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1420 readlocalhomtable( prep, njob, localhomtable, kozoarivec );
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1421 fclose( prep );
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1422 fprintf( stderr, "\ndone.\n" );
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diff changeset
1423
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diff changeset
1424
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1425 nkozo = 0;
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diff changeset
1426 for( i=0; i<njob; i++ )
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1427 {
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1428 // fprintf( stderr, "kozoarivec[%d] = %d\n", i, kozoarivec[i] );
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diff changeset
1429 if( kozoarivec[i] ) nkozo++;
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1430 }
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1431 if( nkozo )
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1432 {
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1433 topol_kozo = AllocateIntCub( nkozo, 2, 0 );
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diff changeset
1434 len_kozo = AllocateFloatMtx( nkozo, 2 );
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diff changeset
1435 iscore_kozo = AllocateFloatHalfMtx( nkozo );
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diff changeset
1436 eff_kozo = AllocateDoubleVec( nkozo );
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diff changeset
1437 eff_kozo_mapped = AllocateDoubleVec( njob );
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1438 }
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diff changeset
1439
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diff changeset
1440
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1441 // outlocalhom( localhomtable, njob );
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1442
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1443 #if 0
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1444 fprintf( stderr, "Extending localhom ... " );
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1445 extendlocalhom2( njob, localhomtable );
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1446 fprintf( stderr, "done.\n" );
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1447 #endif
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diff changeset
1448 }
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diff changeset
1449
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diff changeset
1450 #if 0
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1451 readData( infp, name, nlen, seq );
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1452 #else
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1453 readData_pointer( infp, name, nlen, seq );
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diff changeset
1454 fclose( infp );
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diff changeset
1455 #endif
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diff changeset
1456
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1457 constants( njob, seq );
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1458
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diff changeset
1459 #if 0
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1460 fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
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diff changeset
1461 #endif
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1462
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1463 initSignalSM();
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1464
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1465 initFiles();
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1466
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1467 WriteOptions( trap_g );
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1468
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1469 c = seqcheck( seq );
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1470 if( c )
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1471 {
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1472 fprintf( stderr, "Illegal character %c\n", c );
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1473 exit( 1 );
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1474 }
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1475
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1476 // writePre( njob, name, nlen, seq, 0 );
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1477
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1478 if( treein )
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1479 {
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1480 #if 0
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1481 if( nkozo )
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1482 {
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1483 fprintf( stderr, "Both structure and user tree have been given. Not yet supported!\n" );
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1484 exit( 1 );
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1485 }
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1486 #endif
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1487 fprintf( stderr, "Loading a tree ... " );
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1488 loadtree( njob, topol, len, name, nlen, dep );
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1489 // loadtop( njob, topol, len, name, NULL, dep ); // 2015/Jan/13, not yet checked
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1490 fprintf( stderr, "\ndone.\n\n" );
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1491 }
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1492 else
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1493 {
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1494 if( tbutree == 0 )
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1495 {
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1496 for( i=1; i<njob; i++ )
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1497 {
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1498 if( nlen[i] != nlen[0] )
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1499 {
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1500 fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
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1501 exit( 1 );
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1502 }
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1503 }
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1504
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1505 fprintf( stderr, "Making a distance matrix .. (Should not be used in versions >7.2) \n" );
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1506 fflush( stderr );
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1507 skiptable = AllocateIntMtx( njob, 0 );
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1508 makeskiptable( njob, skiptable, seq ); // allocate suru.
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1509 ien = njob-1;
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diff changeset
1510 for( i=0; i<njob; i++ )
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1511 {
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1512 // selfscore[i] = naivepairscore11( seq[i], seq[i], penalty_dist );
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1513 selfscore[i] = naivepairscorefast( seq[i], seq[i], skiptable[i], skiptable[i], penalty_dist );
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1514 // fprintf( stderr, "penalty = %d\n", penalty );
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1515 // fprintf( stderr, "penalty_dist = %d\n", penalty_dist );
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1516 }
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1517 #ifdef enablemultithread
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parents:
diff changeset
1518 if( nthread > 0 )
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diff changeset
1519 {
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diff changeset
1520 distancematrixthread_arg_t *targ;
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nick
parents:
diff changeset
1521 Jobtable jobpos;
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parents:
diff changeset
1522 pthread_t *handle;
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parents:
diff changeset
1523 pthread_mutex_t mutex;
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parents:
diff changeset
1524
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diff changeset
1525 jobpos.i = 0;
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parents:
diff changeset
1526 jobpos.j = 0;
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parents:
diff changeset
1527
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diff changeset
1528 targ = calloc( nthread, sizeof( distancematrixthread_arg_t ) );
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parents:
diff changeset
1529 handle = calloc( nthread, sizeof( pthread_t ) );
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parents:
diff changeset
1530 pthread_mutex_init( &mutex, NULL );
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parents:
diff changeset
1531
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diff changeset
1532 for( i=0; i<nthread; i++ )
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parents:
diff changeset
1533 {
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diff changeset
1534 targ[i].thread_no = i;
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parents:
diff changeset
1535 targ[i].njob = njob;
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parents:
diff changeset
1536 targ[i].selfscore = selfscore;
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parents:
diff changeset
1537 targ[i].iscore = iscore;
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parents:
diff changeset
1538 targ[i].seq = seq;
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parents:
diff changeset
1539 targ[i].skiptable = skiptable;
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parents:
diff changeset
1540 targ[i].jobpospt = &jobpos;
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parents:
diff changeset
1541 targ[i].mutex = &mutex;
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parents:
diff changeset
1542
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diff changeset
1543 pthread_create( handle+i, NULL, distancematrixthread, (void *)(targ+i) );
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1544 }
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diff changeset
1545
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parents:
diff changeset
1546 for( i=0; i<nthread; i++ )
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parents:
diff changeset
1547 {
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parents:
diff changeset
1548 pthread_join( handle[i], NULL );
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parents:
diff changeset
1549 }
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parents:
diff changeset
1550 pthread_mutex_destroy( &mutex );
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nick
parents:
diff changeset
1551 free( handle );
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nick
parents:
diff changeset
1552 free( targ );
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parents:
diff changeset
1553 }
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1554 else
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parents:
diff changeset
1555 #endif
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diff changeset
1556 {
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parents:
diff changeset
1557 for( i=0; i<ien; i++ )
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parents:
diff changeset
1558 {
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diff changeset
1559 if( i % 10 == 0 )
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parents:
diff changeset
1560 {
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parents:
diff changeset
1561 fprintf( stderr, "\r% 5d / %d", i, ien );
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parents:
diff changeset
1562 fflush( stderr );
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1563 }
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parents:
diff changeset
1564 ssi = selfscore[i];
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parents:
diff changeset
1565 for( j=i+1; j<njob; j++ )
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parents:
diff changeset
1566 {
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parents:
diff changeset
1567 ssj = selfscore[j];
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parents:
diff changeset
1568 bunbo = MIN( ssi, ssj );
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nick
parents:
diff changeset
1569 if( bunbo == 0.0 )
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parents:
diff changeset
1570 iscore[i][j-i] = 2.0; // 2013/Oct/17 2bai
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1571 else
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parents:
diff changeset
1572 // iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty_dist ) / MIN( selfscore[i], selfscore[j] );
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diff changeset
1573 // iscore[i][j-i] = ( 1.0 - naivepairscore11( seq[i], seq[j], penalty_dist ) / bunbo ) * 2.0; // 2013/Oct/17 2bai
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parents:
diff changeset
1574 iscore[i][j-i] = ( 1.0 - naivepairscorefast( seq[i], seq[j], skiptable[i], skiptable[j], penalty_dist ) / bunbo ) * 2.0; // 2014/Aug/15 fast
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parents:
diff changeset
1575 if( iscore[i][j-i] > 10 ) iscore[i][j-i] = 10.0; // 2015/Mar/17
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diff changeset
1576 //exit( 1 );
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parents:
diff changeset
1577
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diff changeset
1578 #if 0
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diff changeset
1579 fprintf( stderr, "### ssj = %f\n", ssj );
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parents:
diff changeset
1580 fprintf( stderr, "### selfscore[i] = %f\n", selfscore[i] );
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parents:
diff changeset
1581 fprintf( stderr, "### selfscore[j] = %f\n", selfscore[j] );
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parents:
diff changeset
1582 fprintf( stderr, "### rawscore = %f\n", naivepairscore11( seq[i], seq[j], penalty_dist ) );
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1583 #endif
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1584 }
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diff changeset
1585 }
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diff changeset
1586 }
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diff changeset
1587 fprintf( stderr, "\ndone.\n\n" );
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parents:
diff changeset
1588 FreeIntMtx( skiptable );
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nick
parents:
diff changeset
1589 fflush( stderr );
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parents:
diff changeset
1590 }
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diff changeset
1591 else
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diff changeset
1592 {
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diff changeset
1593 if( multidist )
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diff changeset
1594 {
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diff changeset
1595 fprintf( stderr, "Loading 'hat2n' (aligned sequences - new sequences) ... " );
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nick
parents:
diff changeset
1596 prep = fopen( "hat2n", "r" );
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parents:
diff changeset
1597 if( prep == NULL ) ErrorExit( "Make hat2." );
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parents:
diff changeset
1598 readhat2_floathalf_pointer( prep, njob, name, iscore );
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parents:
diff changeset
1599 fclose( prep );
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1600 fprintf( stderr, "done.\n" );
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diff changeset
1601
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1602 fprintf( stderr, "Loading 'hat2i' (aligned sequences) ... " );
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parents:
diff changeset
1603 prep = fopen( "hat2i", "r" );
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parents:
diff changeset
1604 if( prep == NULL ) ErrorExit( "Make hat2i." );
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parents:
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1605 readhat2_floathalf_pointer( prep, njob-nadd, name, iscore );
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parents:
diff changeset
1606 fclose( prep );
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parents:
diff changeset
1607 fprintf( stderr, "done.\n" );
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diff changeset
1608 }
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1609 else
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diff changeset
1610 {
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1611 fprintf( stderr, "Loading 'hat2' ... " );
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parents:
diff changeset
1612 prep = fopen( "hat2", "r" );
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parents:
diff changeset
1613 if( prep == NULL ) ErrorExit( "Make hat2." );
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parents:
diff changeset
1614 readhat2_floathalf_pointer( prep, njob, name, iscore );
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parents:
diff changeset
1615 fclose( prep );
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parents:
diff changeset
1616 fprintf( stderr, "done.\n" );
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parents:
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1617 }
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1618 }
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1619 #if 1
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1620 if( distout )
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1621 {
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1622 hat2p = fopen( "hat2", "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1623 WriteFloatHat2_pointer_halfmtx( hat2p, njob, name, iscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
1624 fclose( hat2p );
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parents:
diff changeset
1625 }
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parents:
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1626 #endif
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parents:
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1627 if( nkozo )
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parents:
diff changeset
1628 {
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parents:
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1629 ien = njob-1;
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nick
parents:
diff changeset
1630 ik = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1631 for( i=0; i<ien; i++ )
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nick
parents:
diff changeset
1632 {
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diff changeset
1633 jk = ik+1;
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parents:
diff changeset
1634 for( j=i+1; j<njob; j++ )
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1635 {
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diff changeset
1636 if( kozoarivec[i] && kozoarivec[j] )
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1637 {
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diff changeset
1638 iscore_kozo[ik][jk-ik] = iscore[i][j-i];
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1639 }
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1640 if( kozoarivec[j] ) jk++;
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1641 }
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1642 if( kozoarivec[i] ) ik++;
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1643 }
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1644 }
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1645
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1646 fprintf( stderr, "Constructing a UPGMA tree ... " );
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parents:
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1647 fflush( stderr );
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1648 if( topin )
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1649 {
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1650 fprintf( stderr, "--topin has been disabled\n" );
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parents:
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1651 exit( 1 );
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parents:
diff changeset
1652 // fprintf( stderr, "Loading a topology ... " );
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parents:
diff changeset
1653 // loadtop( njob, iscore, topol, len );
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parents:
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1654 // fprintf( stderr, "\ndone.\n\n" );
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1655 }
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1656 else if( subalignment ) // merge error no tame
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1657 {
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1658 fixed_supg_float_realloc_nobk_halfmtx_treeout_constrained( njob, iscore, topol, len, name, nlen, dep, nsubalignments, subtable, 1 );
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1659 }
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1660 else if( treeout ) // merge error no tame
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1661 {
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1662 fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( njob, iscore, topol, len, name, nlen, dep, 1 );
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1663 }
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1664 else
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1665 {
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1666 fixed_musclesupg_float_realloc_nobk_halfmtx( njob, iscore, topol, len, dep, 1, 1 );
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1667 }
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1668 // else
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parents:
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1669 // ErrorExit( "Incorrect tree\n" );
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1670
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1671 if( nkozo )
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1672 {
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1673 // for( i=0; i<nkozo-1; i++ )
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parents:
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1674 // for( j=i+1; j<nkozo; j++ )
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parents:
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1675 // fprintf( stderr, "iscore_kozo[%d][%d] =~ %f\n", i, j, iscore_kozo[i][j-i] );
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parents:
diff changeset
1676 fixed_musclesupg_float_realloc_nobk_halfmtx( nkozo, iscore_kozo, topol_kozo, len_kozo, NULL, 1, 1 );
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1677 }
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1678 fprintf( stderr, "\ndone.\n\n" );
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parents:
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1679 fflush( stderr );
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1680 }
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diff changeset
1681
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1682
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1683 orderfp = fopen( "order", "w" );
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parents:
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1684 if( !orderfp )
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1685 {
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1686 fprintf( stderr, "Cannot open 'order'\n" );
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parents:
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1687 exit( 1 );
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1688 }
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1689 for( i=0; (j=topol[njob-2][0][i])!=-1; i++ )
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1690 {
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1691 fprintf( orderfp, "%d\n", j );
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1692 }
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diff changeset
1693 for( i=0; (j=topol[njob-2][1][i])!=-1; i++ )
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1694 {
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1695 fprintf( orderfp, "%d\n", j );
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1696 }
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1697 fclose( orderfp );
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diff changeset
1698
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1699 if( treeout && noalign )
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1700 {
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1701 writeData_pointer( prep_g, njob, name, nlen, seq );
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parents:
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1702 fprintf( stderr, "\n" );
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diff changeset
1703 SHOWVERSION;
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1704 return( 0 );
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1705 }
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1706
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1707 // countnode( njob, topol, node0 );
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1708 if( tbrweight )
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1709 {
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1710 weight = 3;
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diff changeset
1711 #if 0
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1712 utree = 0; counteff( njob, topol, len, eff ); utree = 1;
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1713 #else
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1714 counteff_simple_float_nostatic( njob, topol, len, eff );
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1715 for( i=njob-nadd; i<njob; i++ ) eff[i] /= (double)100;
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1716 #if 0
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1717 fprintf( stderr, "###### WEIGHT = \n" );
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parents:
diff changeset
1718 for( i=0; i<njob; i++ )
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1719 {
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1720 fprintf( stderr, "w[%d] = %f\n", i, eff[i] );
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1721 }
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1722 exit( 1 );
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parents:
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1723 #endif
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1724 if( nkozo )
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1725 {
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1726 // counteff_simple_float( nkozo, topol_kozo, len_kozo, eff_kozo ); // single weight nanode iranai
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1727 for( i=0,j=0; i<njob; i++ )
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1728 {
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1729 if( kozoarivec[i] )
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1730 {
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1731 // eff_kozo_mapped[i] = eff_kozo[j]; //
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parents:
diff changeset
1732 eff_kozo_mapped[i] = eff[i]; // single weight
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parents:
diff changeset
1733 j++;
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1734 }
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1735 else
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1736 eff_kozo_mapped[i] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
1737 // fprintf( stderr, "eff_kozo_mapped[%d] = %f\n", i, eff_kozo_mapped[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
1738 // fprintf( stderr, " eff[%d] = %f\n", i, eff[i] );
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diff changeset
1739 }
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1740 }
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1741
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1742
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1743 #endif
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1744 }
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1745 else
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1746 {
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1747 for( i=0; i<njob; i++ ) eff[i] = 1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
1748 if( nkozo )
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diff changeset
1749 {
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nick
parents:
diff changeset
1750 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1751 {
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nick
parents:
diff changeset
1752 if( kozoarivec[i] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1753 eff_kozo_mapped[i] = 1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1754 else
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nick
parents:
diff changeset
1755 eff_kozo_mapped[i] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1756 }
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nick
parents:
diff changeset
1757 }
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nick
parents:
diff changeset
1758 }
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nick
parents:
diff changeset
1759
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nick
parents:
diff changeset
1760 FreeFloatHalfMtx( iscore, njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1761 FreeFloatMtx( len );
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nick
parents:
diff changeset
1762
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nick
parents:
diff changeset
1763 alloclen = nlenmax*2+1; //chuui!
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1764 bseq = AllocateCharMtx( njob, alloclen );
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nick
parents:
diff changeset
1765
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nick
parents:
diff changeset
1766
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nick
parents:
diff changeset
1767 if( nadd )
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nick
parents:
diff changeset
1768 {
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nick
parents:
diff changeset
1769 alignmentlength = strlen( seq[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1770 for( i=0; i<njob-nadd; i++ )
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nick
parents:
diff changeset
1771 {
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nick
parents:
diff changeset
1772 if( alignmentlength != strlen( seq[i] ) )
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nick
parents:
diff changeset
1773 {
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nick
parents:
diff changeset
1774 fprintf( stderr, "#################################################################################\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1775 fprintf( stderr, "# ERROR! #\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1776 fprintf( stderr, "# The original%4d sequences must be aligned #\n", njob-nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1777 fprintf( stderr, "#################################################################################\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1778 exit( 1 );
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nick
parents:
diff changeset
1779 }
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nick
parents:
diff changeset
1780 }
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nick
parents:
diff changeset
1781 if( addprofile )
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nick
parents:
diff changeset
1782 {
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nick
parents:
diff changeset
1783 alignmentlength = strlen( seq[njob-nadd] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1784 for( i=njob-nadd; i<njob; i++ )
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nick
parents:
diff changeset
1785 {
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nick
parents:
diff changeset
1786 if( alignmentlength != strlen( seq[i] ) )
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nick
parents:
diff changeset
1787 {
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nick
parents:
diff changeset
1788 fprintf( stderr, "###############################################################################\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1789 fprintf( stderr, "# ERROR! #\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1790 fprintf( stderr, "# The%4d additional sequences must be aligned #\n", nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1791 fprintf( stderr, "# Otherwise, try the '--add' option, instead of '--addprofile' option. #\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1792 fprintf( stderr, "###############################################################################\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1793 exit( 1 );
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nick
parents:
diff changeset
1794 }
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nick
parents:
diff changeset
1795 }
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nick
parents:
diff changeset
1796 for( i=0; i<nadd; i++ ) addmem[i] = njob-nadd+i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1797 addmem[nadd] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1798 foundthebranch = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1799 for( i=0; i<njob-1; i++ )
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nick
parents:
diff changeset
1800 {
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nick
parents:
diff changeset
1801 if( samemember( topol[i][0], addmem ) ) // jissainiha nai
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nick
parents:
diff changeset
1802 {
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nick
parents:
diff changeset
1803 mergeoralign[i] = '1';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1804 foundthebranch = 1;
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nick
parents:
diff changeset
1805 }
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nick
parents:
diff changeset
1806 else if( samemember( topol[i][1], addmem ) ) // samemembern ni henkou kanou
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nick
parents:
diff changeset
1807 {
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nick
parents:
diff changeset
1808 mergeoralign[i] = '2';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1809 foundthebranch = 1;
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nick
parents:
diff changeset
1810 }
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nick
parents:
diff changeset
1811 else
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nick
parents:
diff changeset
1812 {
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nick
parents:
diff changeset
1813 mergeoralign[i] = 'n';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1814 }
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nick
parents:
diff changeset
1815 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1816 if( !foundthebranch )
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nick
parents:
diff changeset
1817 {
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nick
parents:
diff changeset
1818 fprintf( stderr, "###############################################################################\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1819 fprintf( stderr, "# ERROR! #\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1820 fprintf( stderr, "# There is no appropriate position to add the%4d sequences in the guide tree.#\n", nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1821 fprintf( stderr, "# Check whether the%4d sequences form a monophyletic cluster. #\n", nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1822 fprintf( stderr, "# If not, try the '--add' option, instead of the '--addprofile' option. #\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1823 fprintf( stderr, "############################################################################### \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1824 exit( 1 );
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nick
parents:
diff changeset
1825 }
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nick
parents:
diff changeset
1826 commongappick( nadd, seq+njob-nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1827 for( i=njob-nadd; i<njob; i++ ) strcpy( bseq[i], seq[i] );
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nick
parents:
diff changeset
1828 }
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diff changeset
1829 else
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parents:
diff changeset
1830 {
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nick
parents:
diff changeset
1831 for( i=0; i<njob-1; i++ ) mergeoralign[i] = 'n';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1832 for( j=njob-nadd; j<njob; j++ )
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nick
parents:
diff changeset
1833 {
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nick
parents:
diff changeset
1834 addmem[0] = j;
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nick
parents:
diff changeset
1835 addmem[1] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1836 for( i=0; i<njob-1; i++ )
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nick
parents:
diff changeset
1837 {
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nick
parents:
diff changeset
1838 if( samemembern( topol[i][0], addmem, 1 ) ) // arieru
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nick
parents:
diff changeset
1839 {
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nick
parents:
diff changeset
1840 // fprintf( stderr, "HIT!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1841 if( mergeoralign[i] != 'n' ) mergeoralign[i] = 'w';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1842 else mergeoralign[i] = '1';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1843 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1844 else if( samemembern( topol[i][1], addmem, 1 ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1845 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1846 // fprintf( stderr, "HIT!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1847 if( mergeoralign[i] != 'n' ) mergeoralign[i] = 'w';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1848 else mergeoralign[i] = '2';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1849 }
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nick
parents:
diff changeset
1850 }
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nick
parents:
diff changeset
1851 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1852
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1853 for( i=0; i<nadd; i++ ) addmem[i] = njob-nadd+i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1854 addmem[nadd] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1855 for( i=0; i<njob-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1856 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1857 if( includemember( topol[i][0], addmem ) && includemember( topol[i][1], addmem ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1858 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1859 mergeoralign[i] = 'w';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1860 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1861 else if( includemember( topol[i][0], addmem ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1862 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1863 mergeoralign[i] = '1';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1864 }
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nick
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1865 else if( includemember( topol[i][1], addmem ) )
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1866 {
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1867 mergeoralign[i] = '2';
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1868 }
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1869 }
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1870 #if 0
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1871 for( i=0; i<njob-1; i++ )
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1872 {
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1873 fprintf( stderr, "mem0 = " );
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1874 for( j=0; topol[i][0][j]>-1; j++ ) fprintf( stderr, "%d ", topol[i][0][j] );
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1875 fprintf( stderr, "\n" );
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1876 fprintf( stderr, "mem1 = " );
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1877 for( j=0; topol[i][1][j]>-1; j++ ) fprintf( stderr, "%d ", topol[i][1][j] );
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1878 fprintf( stderr, "\n" );
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1879 fprintf( stderr, "i=%d, mergeoralign[] = %c\n", i, mergeoralign[i] );
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1880 }
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1881 #endif
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1882 for( i=njob-nadd; i<njob; i++ ) gappick0( bseq[i], seq[i] );
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1883 }
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1884
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1885 commongappick( njob-nadd, seq );
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1886 for( i=0; i<njob-nadd; i++ ) strcpy( bseq[i], seq[i] );
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1887 }
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1888 //--------------- kokokara ----
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1889 else if( subalignment )
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1890 {
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1891 for( i=0; i<njob-1; i++ ) mergeoralign[i] = 'a';
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1892 for( i=0; i<nsubalignments; i++ )
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1893 {
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1894 fprintf( stderr, "Checking subalignment %d:\n", i+1 );
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1895 alignmentlength = strlen( seq[subtable[i][0]] );
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1896 // for( j=0; subtable[i][j]!=-1; j++ )
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1897 // fprintf( stderr, " %d. %-30.30s\n", subtable[i][j]+1, name[subtable[i][j]]+1 );
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1898 for( j=0; subtable[i][j]!=-1; j++ )
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1899 {
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1900 if( subtable[i][j] >= njob )
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1901 {
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1902 fprintf( stderr, "No such sequence, %d.\n", subtable[i][j]+1 );
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1903 exit( 1 );
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1904 }
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1905 if( alignmentlength != strlen( seq[subtable[i][j]] ) )
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1906 {
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1907 fprintf( stderr, "\n" );
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1908 fprintf( stderr, "###############################################################################\n" );
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1909 fprintf( stderr, "# ERROR!\n" );
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1910 fprintf( stderr, "# Subalignment %d must be aligned.\n", i+1 );
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1911 fprintf( stderr, "# Please check the alignment lengths of following sequences.\n" );
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1912 fprintf( stderr, "#\n" );
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1913 fprintf( stderr, "# %d. %-10.10s -> %d letters (including gaps)\n", subtable[i][0]+1, name[subtable[i][0]]+1, alignmentlength );
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1914 fprintf( stderr, "# %d. %-10.10s -> %d letters (including gaps)\n", subtable[i][j]+1, name[subtable[i][j]]+1, (int)strlen( seq[subtable[i][j]] ) );
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1915 fprintf( stderr, "#\n" );
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1916 fprintf( stderr, "# See http://mafft.cbrc.jp/alignment/software/merge.html for details.\n" );
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1917 if( subalignmentoffset )
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1918 {
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1919 fprintf( stderr, "#\n" );
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1920 fprintf( stderr, "# You specified seed alignment(s) consisting of %d sequences.\n", subalignmentoffset );
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1921 fprintf( stderr, "# In this case, the rule of numbering is:\n" );
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1922 fprintf( stderr, "# The aligned seed sequences are numbered as 1 .. %d\n", subalignmentoffset );
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1923 fprintf( stderr, "# The input sequences to be aligned are numbered as %d .. %d\n", subalignmentoffset+1, subalignmentoffset+njob );
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1924 }
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1925 fprintf( stderr, "###############################################################################\n" );
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1926 fprintf( stderr, "\n" );
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1927 exit( 1 );
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1928 }
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1929 insubtable[subtable[i][j]] = 1;
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1930 }
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1931 for( j=0; j<njob-1; j++ )
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1932 {
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1933 if( includemember( topol[j][0], subtable[i] ) && includemember( topol[j][1], subtable[i] ) )
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1934 {
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1935 mergeoralign[j] = 'n';
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1936 }
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1937 }
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1938 foundthebranch = 0;
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1939 for( j=0; j<njob-1; j++ )
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1940 {
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1941 if( samemember( topol[j][0], subtable[i] ) || samemember( topol[j][1], subtable[i] ) )
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1942 {
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1943 foundthebranch = 1;
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1944 fprintf( stderr, " -> OK\n" );
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1945 break;
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1946 }
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1947 }
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1948 if( !foundthebranch )
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1949 {
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1950 system( "cp infile.tree GuideTree" ); // tekitou
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1951 fprintf( stderr, "\n" );
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1952 fprintf( stderr, "###############################################################################\n" );
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1953 fprintf( stderr, "# ERROR!\n" );
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1954 fprintf( stderr, "# Subalignment %d does not form a monophyletic cluster\n", i+1 );
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1955 fprintf( stderr, "# in the guide tree ('GuideTree' in this directory) internally computed.\n" );
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1956 fprintf( stderr, "# If you really want to use this subalignment, pelase give a tree with --treein \n" );
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1957 fprintf( stderr, "# http://mafft.cbrc.jp/alignment/software/treein.html\n" );
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1958 fprintf( stderr, "# http://mafft.cbrc.jp/alignment/software/merge.html\n" );
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1959 if( subalignmentoffset )
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1960 {
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1961 fprintf( stderr, "#\n" );
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1962 fprintf( stderr, "# You specified seed alignment(s) consisting of %d sequences.\n", subalignmentoffset );
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1963 fprintf( stderr, "# In this case, the rule of numbering is:\n" );
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1964 fprintf( stderr, "# The aligned seed sequences are numbered as 1 .. %d\n", subalignmentoffset );
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1965 fprintf( stderr, "# The input sequences to be aligned are numbered as %d .. %d\n", subalignmentoffset+1, subalignmentoffset+njob );
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1966 }
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1967 fprintf( stderr, "############################################################################### \n" );
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1968 fprintf( stderr, "\n" );
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1969 exit( 1 );
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1970 }
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1971 // commongappick( seq[subtable[i]], subalignment[i] ); // irukamo
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1972 }
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1973 #if 0
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1974 for( i=0; i<njob-1; i++ )
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1975 {
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1976 fprintf( stderr, "STEP %d\n", i+1 );
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1977 fprintf( stderr, "group1 = " );
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1978 for( j=0; topol[i][0][j] != -1; j++ )
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1979 fprintf( stderr, "%d ", topol[i][0][j]+1 );
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nick
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1980 fprintf( stderr, "\n" );
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nick
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1981 fprintf( stderr, "group2 = " );
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1982 for( j=0; topol[i][1][j] != -1; j++ )
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1983 fprintf( stderr, "%d ", topol[i][1][j]+1 );
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1984 fprintf( stderr, "\n" );
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1985 fprintf( stderr, "%d -> %c\n\n", i, mergeoralign[i] );
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1986 }
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1987 #endif
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1988
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1989 for( i=0; i<njob; i++ )
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1990 {
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1991 if( insubtable[i] ) strcpy( bseq[i], seq[i] );
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1992 else gappick0( bseq[i], seq[i] );
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1993 }
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1994
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1995 for( i=0; i<nsubalignments; i++ )
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1996 {
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1997 for( j=0; subtable[i][j]!=-1; j++ ) subalnpt[i][j] = bseq[subtable[i][j]];
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1998 if( !preservegaps[i] ) commongappick( j, subalnpt[i] );
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1999 }
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2000
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2001 FreeIntMtx( subtable );
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2002 free( insubtable );
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2003 for( i=0; i<nsubalignments; i++ ) free( subalnpt[i] );
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2004 free( subalnpt );
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2005 free( preservegaps );
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2006 }
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2007 //--------------- kokomade ----
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2008 else
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2009 {
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2010 for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
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2011 for( i=0; i<njob-1; i++ ) mergeoralign[i] = 'a';
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2012 }
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2013
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2014 if( rnakozo && rnaprediction == 'm' )
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2015 {
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2016 singlerna = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
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2017 prep = fopen( "hat4", "r" );
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2018 if( prep == NULL ) ErrorExit( "Make hat4 using mccaskill." );
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2019 fprintf( stderr, "Loading 'hat4' ... " );
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2020 for( i=0; i<njob; i++ )
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2021 {
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2022 nogaplen = strlen( bseq[i] );
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2023 singlerna[i] = (RNApair **)calloc( nogaplen+1, sizeof( RNApair * ) );
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2024 for( j=0; j<nogaplen; j++ )
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2025 {
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2026 singlerna[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
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2027 singlerna[i][j][0].bestpos = -1;
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2028 singlerna[i][j][0].bestscore = -1.0;
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diff changeset
2029 }
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2030 singlerna[i][nogaplen] = NULL;
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2031 // fprintf( stderr, "### reading bpp %d ...\n", i );
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2032 readmccaskill( prep, singlerna[i], nogaplen );
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2033 }
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2034 fclose( prep );
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2035 fprintf( stderr, "\ndone.\n" );
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2036 }
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2037 else
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2038 singlerna = NULL;
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2039
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2040
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2041 fprintf( stderr, "Progressive alignment ... \n" );
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2042
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2043 #ifdef enablemultithread
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2044 if( nthread > 0 && nadd == 0 )
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2045 {
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2046 treebasethread_arg_t *targ;
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2047 int jobpos;
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2048 pthread_t *handle;
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2049 pthread_mutex_t mutex;
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2050 pthread_cond_t treecond;
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2051 int *fftlog;
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2052 int nrun;
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2053 int nthread_yoyu;
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diff changeset
2054
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2055 nthread_yoyu = nthread * 1;
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2056 nrun = 0;
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parents:
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2057 jobpos = 0;
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parents:
diff changeset
2058 targ = calloc( nthread_yoyu, sizeof( treebasethread_arg_t ) );
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2059 fftlog = AllocateIntVec( njob );
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diff changeset
2060 handle = calloc( nthread_yoyu, sizeof( pthread_t ) );
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2061 pthread_mutex_init( &mutex, NULL );
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parents:
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2062 pthread_cond_init( &treecond, NULL );
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diff changeset
2063
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parents:
diff changeset
2064 for( i=0; i<njob; i++ ) dep[i].done = 0;
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2065 for( i=0; i<njob; i++ ) fftlog[i] = 1;
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diff changeset
2066
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diff changeset
2067 if( constraint )
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2068 calcimportance( njob, eff, bseq, localhomtable );
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2069 // dontcalcimportance( njob, eff, bseq, localhomtable ); // CHUUUUIIII!!!
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diff changeset
2070
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2071 for( i=0; i<nthread_yoyu; i++ )
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2072 {
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2073 targ[i].thread_no = i;
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2074 targ[i].nrunpt = &nrun;
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2075 targ[i].njob = njob;
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2076 targ[i].nlen = nlen;
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parents:
diff changeset
2077 targ[i].jobpospt = &jobpos;
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parents:
diff changeset
2078 targ[i].topol = topol;
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parents:
diff changeset
2079 targ[i].dep = dep;
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parents:
diff changeset
2080 targ[i].aseq = bseq;
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parents:
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2081 targ[i].effarr = eff;
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2082 targ[i].alloclenpt = &alloclen;
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2083 targ[i].localhomtable = localhomtable;
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2084 targ[i].singlerna = singlerna;
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2085 targ[i].effarr_kozo = eff_kozo_mapped;
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2086 targ[i].fftlog = fftlog;
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2087 targ[i].mergeoralign = mergeoralign;
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2088 targ[i].mutex = &mutex;
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2089 targ[i].treecond = &treecond;
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2090
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2091 pthread_create( handle+i, NULL, treebasethread, (void *)(targ+i) );
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2092 }
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2093
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2094 for( i=0; i<nthread_yoyu; i++ )
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2095 {
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2096 pthread_join( handle[i], NULL );
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2097 }
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2098 pthread_mutex_destroy( &mutex );
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2099 pthread_cond_destroy( &treecond );
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2100 free( handle );
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2101 free( targ );
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2102 free( fftlog );
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2103 }
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2104 else
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2105 #endif
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2106
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2107 treebase( nlen, bseq, nadd, mergeoralign, mseq1, mseq2, topol, dep, eff, &alloclen, localhomtable, singlerna, eff_kozo_mapped );
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2108 fprintf( stderr, "\ndone.\n" );
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2109 if( scoreout )
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2110 {
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2111 unweightedspscore = plainscore( njob, bseq );
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2112 fprintf( stderr, "\nSCORE %s = %.0f, ", "(treebase)", unweightedspscore );
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2113 fprintf( stderr, "SCORE / residue = %f", unweightedspscore / ( njob * strlen( bseq[0] ) ) );
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2114 fprintf( stderr, "\n\n" );
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2115 }
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2116
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2117 #if 0
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2118 if( constraint )
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2119 {
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2120 LocalHom *tmppt1, *tmppt2;
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2121 for( i=0; i<njob; i++ )
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2122 {
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2123 for( j=0; j<njob; j++ )
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2124 {
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2125 tmppt1 = localhomtable[i]+j;
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2126 while( tmppt2 = tmppt1->next )
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2127 {
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2128 free( (void *)tmppt1 );
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2129 tmppt1 = tmppt2;
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2130 }
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2131 free( (void *)tmppt1 );
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2132 }
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2133 free( (void *)(localhomtable[i]+j) );
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2134 }
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2135 free( (void *)localhomtable );
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2136 }
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2137 #endif
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2138
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2139 fprintf( trap_g, "done.\n" );
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2140 fclose( trap_g );
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2141 free( mergeoralign );
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2142 if( rnakozo && rnaprediction == 'm' )
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2143 {
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2144 if( singlerna ) // nen no tame
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2145 {
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2146 for( i=0; i<njob; i++ )
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2147 {
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2148 for( j=0; singlerna[i][j]!=NULL; j++ )
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2149 {
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2150 if( singlerna[i][j] ) free( singlerna[i][j] );
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2151 }
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2152 if( singlerna[i] ) free( singlerna[i] );
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2153 }
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2154 free( singlerna );
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2155 singlerna = NULL;
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2156 }
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2157 }
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2158
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2159 writeData_pointer( prep_g, njob, name, nlen, bseq );
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2160 #if 0
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2161 writeData( stdout, njob, name, nlen, bseq );
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2162 writePre( njob, name, nlen, bseq, !contin );
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2163 writeData_pointer( prep_g, njob, name, nlen, aseq );
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2164 #endif
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2165 #if IODEBUG
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2166 fprintf( stderr, "OSHIMAI\n" );
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2167 #endif
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2168
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2169 if( constraint ) FreeLocalHomTable( localhomtable, njob );
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2170
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2171 if( spscoreout ) reporterr( "Unweighted sum-of-pairs score = %10.5f\n", sumofpairsscore( njob, bseq ) );
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2172
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2173 SHOWVERSION;
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2174 return( 0 );
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2175 }