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annotate mafft/core/dvtditr.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 /* Tree-dependent-iteration */
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2 /* Devide to segments */
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3
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4 #include "mltaln.h"
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5
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6 extern char **seq_g;
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7 extern char **res_g;
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8 static int subalignment;
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9 static int subalignmentoffset;
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10
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11 static int intop;
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12 static int intree;
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13 static double autosubalignment;
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14
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15
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16 static void calcmaxdistclass( void )
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17 {
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18 int c;
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19 float rep;
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20 for( c=0; c<ndistclass; c++ )
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21 {
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22 rep = (double) 2 * c / ndistclass; // dist:0-2 for dist2offset
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23 // fprintf( stderr, "c=%d, rep=%f, offset=%f\n", c, rep, dist2offset( rep ) );
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24 if( dist2offset( rep ) == 0.0 )
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25 break;
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26 }
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27 fprintf( stderr, "ndistclass = %d, maxdistclass = %d\n", ndistclass, c+1 );
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28 maxdistclass = c + 1;
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29 // maxdistclass = ndistclass; // CHUUI!!!!
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30 return;
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31 }
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32
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33 void arguments( int argc, char *argv[] )
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34 {
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35 int c;
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36 char *argkey;
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37
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38 outnumber = 0;
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39 nthread = 1;
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40 randomseed = 0;
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41 scoreout = 0;
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42 spscoreout = 0;
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43 parallelizationstrategy = BAATARI1;
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44 intop = 0;
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45 intree = 0;
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46 inputfile = NULL;
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47 rnakozo = 0;
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48 rnaprediction = 'm';
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49 nevermemsave = 0;
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50 score_check = 1;
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51 fftkeika = 1;
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52 constraint = 0;
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53 fmodel = 0;
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54 kobetsubunkatsu = 1;
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55 bunkatsu = 1;
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56 nblosum = 62;
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57 niter = 100;
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58 calledByXced = 0;
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59 devide = 1;
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60 divWinSize = 20; /* 70 */
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61 divThreshold = 65;
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62 fftscore = 1;
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63 fftRepeatStop = 0;
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64 fftNoAnchStop = 0;
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65 scmtd = 5;
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66 cooling = 1;
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67 weight = 4;
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68 utree = 1;
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69 refine = 1;
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70 check = 1;
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71 cut = 0.0;
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72 disp = 0;
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73 outgap = 1;
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74 use_fft = 0; // CHUUI dochira demo mafft.tmpl deha F
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75 force_fft = 0;
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76 alg = 'A'; /* chuui */
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77 mix = 0;
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78 checkC = 0;
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79 tbitr = 0;
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80 treemethod = 'X';
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81 sueff_global = 0.1;
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82 scoremtx = 1;
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83 dorp = NOTSPECIFIED;
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84 ppenalty = NOTSPECIFIED;
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85 penalty_shift_factor = 1000.0;
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86 ppenalty_ex = NOTSPECIFIED;
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87 poffset = NOTSPECIFIED;
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88 kimuraR = NOTSPECIFIED;
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89 pamN = NOTSPECIFIED;
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90 geta2 = GETA2;
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91 fftWinSize = NOTSPECIFIED;
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92 fftThreshold = NOTSPECIFIED;
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93 RNAppenalty = NOTSPECIFIED;
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94 RNAppenalty_ex = NOTSPECIFIED;
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95 RNApthr = NOTSPECIFIED;
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96 TMorJTT = JTT;
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97 consweight_multi = 1.0;
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98 consweight_rna = 0.0;
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99 subalignment = 0;
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100 subalignmentoffset = 0;
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101 legacygapcost = 0;
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102 specificityconsideration = 0.0;
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103 autosubalignment = 0.0;
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104
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105 while( --argc > 0 && (*++argv)[0] == '-' )
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106 {
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107 while ( (c = *++argv[0]) )
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108 {
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109 switch( c )
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110 {
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111 case 'i':
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112 inputfile = *++argv;
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113 fprintf( stderr, "inputfile = %s\n", inputfile );
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114 --argc;
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115 goto nextoption;
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116 case 'I':
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117 niter = myatoi( *++argv );
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118 fprintf( stderr, "niter = %d\n", niter );
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119 --argc;
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120 goto nextoption;
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nick
parents:
diff changeset
121 case 'e':
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nick
parents:
diff changeset
122 RNApthr = (int)( atof( *++argv ) * 1000 - 0.5 );
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nick
parents:
diff changeset
123 --argc;
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nick
parents:
diff changeset
124 goto nextoption;
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nick
parents:
diff changeset
125 case 'o':
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nick
parents:
diff changeset
126 RNAppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
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nick
parents:
diff changeset
127 --argc;
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nick
parents:
diff changeset
128 goto nextoption;
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nick
parents:
diff changeset
129 case 'f':
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parents:
diff changeset
130 ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
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nick
parents:
diff changeset
131 // fprintf( stderr, "ppenalty = %d\n", ppenalty );
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parents:
diff changeset
132 --argc;
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nick
parents:
diff changeset
133 goto nextoption;
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nick
parents:
diff changeset
134 case 'Q':
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parents:
diff changeset
135 penalty_shift_factor = atof( *++argv );
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nick
parents:
diff changeset
136 if( penalty_shift_factor < 100.0 && penalty_shift_factor != 2.0 )
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parents:
diff changeset
137 {
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parents:
diff changeset
138 fprintf( stderr, "%f, penalty_shift is fixed to penalty x 2 in the iterative refinement phase.\n", penalty_shift_factor );
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parents:
diff changeset
139 penalty_shift_factor = 2.0;
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parents:
diff changeset
140 }
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nick
parents:
diff changeset
141 --argc;
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nick
parents:
diff changeset
142 goto nextoption;
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parents:
diff changeset
143 case 'g':
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parents:
diff changeset
144 ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
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parents:
diff changeset
145 // fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
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nick
parents:
diff changeset
146 --argc;
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nick
parents:
diff changeset
147 goto nextoption;
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parents:
diff changeset
148 case 'h':
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parents:
diff changeset
149 poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
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nick
parents:
diff changeset
150 fprintf( stderr, "poffset = %d\n", poffset );
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nick
parents:
diff changeset
151 --argc;
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nick
parents:
diff changeset
152 goto nextoption;
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nick
parents:
diff changeset
153 case 'k':
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parents:
diff changeset
154 kimuraR = myatoi( *++argv );
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nick
parents:
diff changeset
155 fprintf( stderr, "kappa = %d\n", kimuraR );
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nick
parents:
diff changeset
156 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
157 goto nextoption;
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parents:
diff changeset
158 case 'b':
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parents:
diff changeset
159 nblosum = myatoi( *++argv );
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nick
parents:
diff changeset
160 scoremtx = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
161 fprintf( stderr, "blosum %d / kimura 200\n", nblosum );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
162 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
163 goto nextoption;
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parents:
diff changeset
164 case 'j':
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parents:
diff changeset
165 pamN = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
166 scoremtx = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
167 TMorJTT = JTT;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
168 fprintf( stderr, "jtt/kimura %d\n", pamN );
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nick
parents:
diff changeset
169 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
170 goto nextoption;
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parents:
diff changeset
171 case 'm':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
172 pamN = myatoi( *++argv );
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parents:
diff changeset
173 scoremtx = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
174 TMorJTT = TM;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
175 fprintf( stderr, "tm %d\n", pamN );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
176 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
177 goto nextoption;
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parents:
diff changeset
178 case 'l':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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179 fastathreshold = atof( *++argv );
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parents:
diff changeset
180 constraint = 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
181 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
182 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
183 case 'r':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
184 consweight_rna = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
185 rnakozo = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
186 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
187 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
188 case 'c':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
189 consweight_multi = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
190 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
191 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
192 case 'C':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
193 nthread = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
194 fprintf( stderr, "nthread = %d\n", nthread );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
195 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
196 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
197 case 'H':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
198 subalignment = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
199 subalignmentoffset = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
200 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
201 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
202 case 't':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
203 randomseed = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
204 fprintf( stderr, "randomseed = %d\n", randomseed );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
205 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
206 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
207 case 'p':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
208 argkey = *++argv;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
209 if( !strcmp( argkey, "BESTFIRST" ) ) parallelizationstrategy = BESTFIRST;
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parents:
diff changeset
210 else if( !strcmp( argkey, "BAATARI0" ) ) parallelizationstrategy = BAATARI0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
211 else if( !strcmp( argkey, "BAATARI1" ) ) parallelizationstrategy = BAATARI1;
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parents:
diff changeset
212 else if( !strcmp( argkey, "BAATARI2" ) ) parallelizationstrategy = BAATARI2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
213 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
214 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
215 fprintf( stderr, "Unknown parallelization strategy, %s\n", argkey );
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parents:
diff changeset
216 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
217 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
218 // exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
219 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
220 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
221 case 's':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
222 specificityconsideration = (double)myatof( *++argv );
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parents:
diff changeset
223 // fprintf( stderr, "specificityconsideration = %f\n", specificityconsideration );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
224 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
225 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
226 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
227 case 'S' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
228 scoreout = 1; // for checking parallel calculation
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
229 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
230 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
231 case 'S' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
232 spscoreout = 1; // 2014/Dec/30, sp score
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
233 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
234 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
235 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
236 case 's' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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parents:
diff changeset
237 RNAscoremtx = 'r';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
238 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
239 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
240 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
241 case 'a':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
242 fmodel = 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 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
245 case 'N':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
246 nevermemsave = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
247 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
248 case 'D':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
249 dorp = 'd';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
250 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
251 case 'P':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
252 dorp = 'p';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
253 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
254 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
255 case 'Q':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
256 alg = 'Q';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
257 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
258 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
259 case 'R':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
260 rnaprediction = 'r';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
261 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
262 case 'O':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
263 fftNoAnchStop = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
264 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
265 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
266 case 'e':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
267 fftscore = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
268 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
269 case 'r':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
270 fmodel = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
271 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
272 case 'R':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
273 fftRepeatStop = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
274 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
275 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
276 case 'T':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
277 kobetsubunkatsu = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
278 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
279 case 'B':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
280 bunkatsu = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
281 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
282 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
283 case 'c':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
284 cooling = 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 'a':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
287 alg = 'a';
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 case 's' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
290 treemethod = 's';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
291 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
292 case 'H':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
293 alg = 'H';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
294 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
295 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
296 case 'A':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
297 alg = 'A';
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 'M':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
300 alg = 'M';
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 'F':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
303 use_fft = 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 't':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
307 weight = 4;
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 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
310 case 'u':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
311 weight = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
312 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
313 case 'U':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
314 intree = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
315 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
316 case 'V':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
317 intop = 1;
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 'J':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
320 utree = 0;
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 'd':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
323 disp = 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 'Z':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
326 score_check = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
327 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
328 case 'Y':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
329 score_check = 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
330 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
331 case 'L':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
332 legacygapcost = 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 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
335 case 'n' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
336 treemethod = 'n';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
337 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
338 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
339 case 'n' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
340 outnumber = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
341 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
342 case 'X':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
343 treemethod = 'X';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
344 sueff_global = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
345 fprintf( stderr, "sueff_global = %f\n", sueff_global );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
346 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
347 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
348 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
349 case 'E' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
350 treemethod = 'E';
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 case 'q' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
353 treemethod = 'q';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
354 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
355 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
356 case 'E':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
357 autosubalignment = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
358 fprintf( stderr, "autosubalignment = %f\n", autosubalignment );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
359 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
360 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
361 case 'z':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
362 fftThreshold = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
363 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
364 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
365 case 'w':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
366 fftWinSize = myatoi( *++argv );
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367 --argc;
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368 goto nextoption;
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369 default:
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370 fprintf( stderr, "illegal option %c\n", c );
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371 argc = 0;
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372 break;
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373 }
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374 }
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375 nextoption:
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376 ;
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377 }
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378 if( argc == 1 )
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379 {
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380 cut = atof( (*argv) );
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381 argc--;
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382 }
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383 if( argc != 0 )
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384 {
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385 fprintf( stderr, "options : Check source file!\n" );
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386 exit( 1 );
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387 }
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388 #if 0
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389 if( alg == 'A' && weight == 0 )
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390 ErrorExit( "ERROR : Algorithm A+ and un-weighted\n" );
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391 #endif
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392 }
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393
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394
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395 int main( int argc, char *argv[] )
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396 {
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397 int identity;
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398 static int nlen[M];
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399 static char **name, **seq, **aseq, **bseq;
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400 static Segment *segment = NULL;
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401 static int anchors[MAXSEG];
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402 int i, j;
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403 int iseg, nseg;
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404 int ***topol;
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405 double **len;
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406 double **eff;
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407 FILE *prep;
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408 FILE *infp;
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409 FILE *orderfp;
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410 int alloclen;
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411 int returnvalue;
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412 char c;
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413 int ocut;
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414 char **seq_g_bk;
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415 LocalHom **localhomtable = NULL; // by D.Mathog
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416 RNApair ***singlerna;
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417 int nogaplen;
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418 static char **nogap1seq;
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419 static char *kozoarivec;
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420 int nkozo;
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421 int alignmentlength;
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422 int **skipthisbranch;
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423 int foundthebranch;
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424 int nsubalignments, maxmem;
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425 int **subtable;
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426 int *insubtable;
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427 int *preservegaps;
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428 char ***subalnpt;
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429
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430 arguments( argc, argv );
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431 #ifndef enablemultithread
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432 nthread = 0;
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433 #endif
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434 if( fastathreshold < 0.0001 ) constraint = 0;
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435
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436 if( inputfile )
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437 {
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438 infp = fopen( inputfile, "r" );
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439 if( !infp )
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440 {
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441 fprintf( stderr, "Cannot open %s\n", inputfile );
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442 exit( 1 );
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443 }
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444 }
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445 else
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446 infp = stdin;
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447
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448 #if 0
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449 PreRead( stdin, &njob, &nlenmax );
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450 #else
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451 getnumlen( infp );
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452 #endif
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453 rewind( infp );
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454
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455 nkozo = 0;
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456
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457 if( njob < 2 )
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458 {
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459 fprintf( stderr, "At least 2 sequences should be input!\n"
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460 "Only %d sequence found.\n", njob );
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461 exit( 1 );
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462 }
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463
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464
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465 if( subalignment )
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466 {
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467 readsubalignmentstable( njob, NULL, NULL, &nsubalignments, &maxmem );
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468 fprintf( stderr, "nsubalignments = %d\n", nsubalignments );
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469 fprintf( stderr, "maxmem = %d\n", maxmem );
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470 subtable = AllocateIntMtx( nsubalignments, maxmem+1 );
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471 insubtable = AllocateIntVec( njob );
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472 preservegaps = AllocateIntVec( njob );
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473 for( i=0; i<njob; i++ ) insubtable[i] = 0;
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474 for( i=0; i<njob; i++ ) preservegaps[i] = 0;
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475 subalnpt = AllocateCharCub( nsubalignments, maxmem, 0 );
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476 readsubalignmentstable( njob, subtable, preservegaps, NULL, NULL );
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477 for( i=0; i<nsubalignments; i++ ) for( j=0; j<insubtable[i]; j++ )
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478 {
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479 if( subtable[i][j] < 0 )
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480 {
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481 fprintf( stderr, "Not supported in the iterative refinmenment mode.\n" );
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482 fprintf( stderr, "Please use a positive number to represent a sequence.\n" );
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483 }
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484 }
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485 }
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486
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487 ocut = cut;
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488
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489 segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
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490 // if( treemethod == 'X' || treemethod == 'E' || treemethod == 'q' )
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diff changeset
491 topol = AllocateIntCub( njob, 2, njob );
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diff changeset
492 len = AllocateDoubleMtx( njob, 2 );
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diff changeset
493 eff = AllocateDoubleMtx( njob, njob );
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diff changeset
494 seq = AllocateCharMtx( njob, nlenmax*9+1 );
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diff changeset
495 name = AllocateCharMtx( njob, B+1 );
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diff changeset
496 seq_g = AllocateCharMtx( njob, nlenmax*9+1 );
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497 res_g = AllocateCharMtx( njob, nlenmax*9+1 );
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498 aseq = AllocateCharMtx( njob, nlenmax*9+1 );
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499 bseq = AllocateCharMtx( njob, nlenmax*9+1 );
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500 nogap1seq = AllocateCharMtx( 1, nlenmax*1+1 );
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501 alloclen = nlenmax * 9;
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diff changeset
502 seq_g_bk = AllocateCharMtx( njob, 0 );
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diff changeset
503 for( i=0; i<njob; i++ ) seq_g_bk[i] = seq_g[i];
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504 kozoarivec = AllocateCharVec( njob );
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505 skipthisbranch = AllocateIntMtx( njob, 2 );
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506 for( i=0; i<njob; i++ ) skipthisbranch[i][0] = skipthisbranch[i][1] = 0;
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507
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508 if( constraint )
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509 {
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510 localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
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511 for( i=0; i<njob; i++)
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512 {
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513 localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
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514 for( j=0; j<njob; j++)
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515 {
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516 localhomtable[i][j].start1 = -1;
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517 localhomtable[i][j].end1 = -1;
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518 localhomtable[i][j].start2 = -1;
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519 localhomtable[i][j].end2 = -1;
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520 localhomtable[i][j].overlapaa = -1.0;
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521 localhomtable[i][j].opt = -1.0;
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522 localhomtable[i][j].importance = -1.0;
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diff changeset
523 localhomtable[i][j].next = NULL;
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diff changeset
524 localhomtable[i][j].nokori = 0;
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diff changeset
525 localhomtable[i][j].extended = -1;
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526 localhomtable[i][j].last = localhomtable[i]+j;
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diff changeset
527 localhomtable[i][j].korh = 'h';
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528 }
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529 }
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530 fprintf( stderr, "Loading 'hat3' ... " );
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diff changeset
531 fflush( stderr );
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532 prep = fopen( "hat3", "r" );
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533 if( prep == NULL ) ErrorExit( "Make hat3." );
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534 readlocalhomtable2( prep, njob, localhomtable, kozoarivec );
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diff changeset
535 fclose( prep );
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diff changeset
536 // for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
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537 // fprintf( stdout, "%d %d %d %d %d %d %d\n", i, j, localhomtable[i][j].opt, localhomtable[i][j].start1, localhomtable[i][j].end1, localhomtable[i][j].start2, localhomtable[i][j].end2 );
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538 fprintf( stderr, "done.\n" );
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539 fflush( stderr );
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540 #if 0
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541 fprintf( stderr, "Extending localhom ... " );
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542 extendlocalhom( njob, localhomtable );
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543 fprintf( stderr, "done.\n" );
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544 #endif
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diff changeset
545 nkozo = 0;
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diff changeset
546 for( i=0; i<njob; i++ ) if( kozoarivec[i] ) nkozo++;
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547 }
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548
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diff changeset
549
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550 // if( nlenmax > 30000 )
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551 if( nlenmax > 50000 ) // version >= 6.823
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552 {
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553 #if 0
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diff changeset
554 if( constraint )
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555 {
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556 fprintf( stderr, "\nnlenmax=%d, nagasugi!\n", nlenmax );
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557 exit( 1 );
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diff changeset
558 }
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diff changeset
559 if( nevermemsave )
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diff changeset
560 {
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561 fprintf( stderr, "\nnevermemsave=1, nlenmax=%d, nagasugi!\n", nlenmax );
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562 exit( 1 );
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563 }
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diff changeset
564 #endif
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565 if( !constraint && !nevermemsave && alg != 'M' )
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diff changeset
566 {
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567 fprintf( stderr, "\nnlenmax=%d, Switching to the memsave mode\n", nlenmax );
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568 alg = 'M';
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569 }
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diff changeset
570 }
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571
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diff changeset
572 #if 0
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573 Read( name, nlen, seq_g );
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diff changeset
574 #else
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575 readData_pointer( infp, name, nlen, seq_g );
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576 #endif
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577 fclose( infp );
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578
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579 if( specificityconsideration ) calcmaxdistclass();
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580
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581 for( i=0; i<njob; i++ )
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diff changeset
582 {
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583 res_g[i][0] = 0;
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584 }
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585
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586 identity = 1;
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587 for( i=0; i<njob; i++ )
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588 {
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589 identity *= ( nlen[i] == nlen[0] );
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590 }
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591 if( !identity )
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592 {
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593 fprintf( stderr, "Input pre-aligned data\n" );
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594 exit( 1 );
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595 }
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596 constants( njob, seq_g );
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597
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diff changeset
598 #if 0
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599 fprintf( stderr, "penalty = %d\n", penalty );
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600 fprintf( stderr, "penalty_ex = %d\n", penalty_ex );
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601 fprintf( stderr, "offset = %d\n", offset );
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diff changeset
602 #endif
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603
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diff changeset
604 initSignalSM();
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605
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diff changeset
606 initFiles();
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607
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608 #if 0
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609 if( njob == 2 )
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610 {
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611 writePre( njob, name, nlen, seq_g, 1 );
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612 SHOWVERSION;
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613 return( 0 );
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614 }
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615 #else
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616 if( njob == 2 )
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617 {
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618 weight = 0;
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619 niter = 1;
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620 }
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621 #endif
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622
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623 c = seqcheck( seq_g );
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624 if( c )
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625 {
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626 fprintf( stderr, "Illegal character %c\n", c );
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627 exit( 1 );
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628 }
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629 commongappick( njob, seq_g );
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630
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631 if( rnakozo && rnaprediction == 'm' )
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632 {
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633 singlerna = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
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634 prep = fopen( "hat4", "r" );
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635 if( prep == NULL ) ErrorExit( "Make hat4 using mccaskill." );
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636 fprintf( stderr, "Loading 'hat4' ... " );
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637 fflush( stderr );
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638 for( i=0; i<njob; i++ )
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639 {
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640 gappick0( nogap1seq[0], seq_g[i] );
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641 nogaplen = strlen( nogap1seq[0] );
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642 singlerna[i] = (RNApair **)calloc( nogaplen+1, sizeof( RNApair * ) );
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643 for( j=0; j<nogaplen; j++ )
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644 {
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645 singlerna[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
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646 singlerna[i][j][0].bestpos = -1;
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647 singlerna[i][j][0].bestscore = -1.0;
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648 }
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649 singlerna[i][nogaplen] = NULL;
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650 readmccaskill( prep, singlerna[i], nogaplen );
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651 }
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652 fclose( prep );
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653 fprintf( stderr, "\ndone.\n" );
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654 fflush( stderr );
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655 }
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656 else
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657 singlerna = NULL;
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658
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659
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660
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661 if( utree )
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662 {
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663 prep = fopen( "hat2", "r" );
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664 if( !prep ) ErrorExit( "Make hat2." );
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665 readhat2_pointer( prep, njob, name, eff );
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666 fclose( prep );
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667 #if 0
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668 fprintf( stderr, "eff = \n" );
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669 for( i=0; i<njob-1; i++ )
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670 {
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671 for( j=i+1; j<njob; j++ )
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672 {
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673 fprintf( stderr, "%d-%d, %f\n", i, j, eff[i][j] );
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674 }
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675 fprintf( stderr, "\n" );
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676 }
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677 #endif
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678 if( intree )
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679 {
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680 veryfastsupg_double_loadtree( njob, eff, topol, len, name );
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681 #if 0
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682 fprintf( stderr, "eff = \n" );
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683 for( i=0; i<njob-1; i++ )
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684 {
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685 for( j=i+1; j<njob; j++ )
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686 {
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687 fprintf( stderr, "%d-%d, %f\n", i, j, eff[i][j] );
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688 }
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689 fprintf( stderr, "\n" );
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690 }
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691 exit( 1 );
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692 #endif
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693 }
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694 else if( intop ) // v6.528 deha if( intop ) dattanode intree ga mukou datta.
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695 {
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696 fprintf( stderr, "--topin has been disabled\n" );
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697 exit( 1 );
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698 // veryfastsupg_double_loadtop( njob, eff, topol, len );
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699 }
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700 else if( subalignment )
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701 fixed_supg_double_treeout_constrained( njob, eff, topol, len, name, nsubalignments, subtable );
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702 else if( treemethod == 'X' || treemethod == 'E' || treemethod == 'q' )
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703 // veryfastsupg_double_outtree( njob, eff, topol, len, name );
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704 fixed_musclesupg_double_treeout( njob, eff, topol, len, name );
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705 else if( treemethod == 'n' )
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706 nj( njob, eff, topol, len );
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707 else if( treemethod == 's' )
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708 spg( njob, eff, topol, len );
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709 else if( treemethod == 'p' )
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710 upg2( njob, eff, topol, len );
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711 else ErrorExit( "Incorrect treemethod.\n" );
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712 }
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713 #if DEBUG
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714 printf( "utree = %d\n", utree );
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715 #endif
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716
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717 if( autosubalignment > 0.0 && subalignment == 0 )
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718 {
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719 // reporterr( "Computing skipthisbranch..\n" );
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720 insubtable = AllocateIntVec( njob );
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721 preservegaps = AllocateIntVec( njob );
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722 subtable = calloc( 1, sizeof( char * ) );
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723 subtable[0] = NULL; // for FreeIntMtx
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diff changeset
724 for( i=0; i<njob; i++ ) insubtable[i] = 0;
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diff changeset
725 for( i=0; i<njob; i++ ) preservegaps[i] = 0; // tsukawanaikamo
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diff changeset
726 if( generatesubalignmentstable( njob, &subtable, &nsubalignments, &maxmem, topol, len, autosubalignment ) ) // subtable ha allocate sareru.
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727 {
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728 reporterr( "################################################################################################ \n" );
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729 reporterr( "#\n" );
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diff changeset
730 reporterr( "# WARNING: Iterative refinment was not done because you gave a large --fix value (%6.3f).\n", autosubalignment );
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diff changeset
731 reporterr( "#\n" );
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diff changeset
732 reporterr( "################################################################################################ \n" );
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733 writePre( njob, name, nlen, seq_g, 1 );
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734
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diff changeset
735 FreeCharMtx( seq_g_bk );
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diff changeset
736 FreeIntCub( topol );
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diff changeset
737 FreeDoubleMtx( len );
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diff changeset
738 FreeDoubleMtx( eff );
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diff changeset
739 FreeIntMtx( skipthisbranch );
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diff changeset
740 FreeIntMtx( subtable );
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diff changeset
741 free( preservegaps );
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diff changeset
742 free( insubtable );
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743 SHOWVERSION;
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744 return( 0 );
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745 }
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746 // subtable = AllocateIntMtx( nsubalignments, maxmem+1 );
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747 fprintf( stderr, "nsubalignments = %d, maxmem = %d\n", nsubalignments, maxmem );
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diff changeset
748 subalnpt = AllocateCharCub( nsubalignments, maxmem, 0 );
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749 #if 0
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diff changeset
750 for( i=0; i<nsubalignments; i++ )
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751 {
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752 reporterr( "subalignment %d\n", i );
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diff changeset
753 for( j=0; subtable[i][j]!=-1; j++ )
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754 {
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755 reporterr( "%5d", subtable[i][j] );
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756 }
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757 reporterr( "\n" );
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758 }
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759 #endif
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760 #if 0 // wakaran
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761 for( i=0; i<nsubalignments; i++ ) for( j=0; j<insubtable[i]; j++ )
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762 {
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763 if( subtable[i][j] < 0 )
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764 {
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765 fprintf( stderr, "Not supported in the iterative refinmenment mode.\n" );
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766 fprintf( stderr, "Please use a positive number to represent a sequence.\n" );
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767 }
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768 }
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769 #endif
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770 // reporterr( "done.\n" );
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771 }
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772
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773
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774 orderfp = fopen( "order", "w" );
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775 if( !orderfp )
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776 {
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777 fprintf( stderr, "Cannot open 'order'\n" );
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778 exit( 1 );
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779 }
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780 for( i=0; (j=topol[njob-2][0][i])!=-1; i++ )
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781 {
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782 fprintf( orderfp, "%d\n", j );
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783 }
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784 for( i=0; (j=topol[njob-2][1][i])!=-1; i++ )
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785 {
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786 fprintf( orderfp, "%d\n", j );
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787 }
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788 fclose( orderfp );
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789
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790
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791
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792 fprintf( stderr, "\n" );
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793 if( ( !utree && kobetsubunkatsu ) || constraint || !bunkatsu )
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794 {
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795 nseg = 0;
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796 anchors[0] =0;
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797 anchors[1] =strlen( seq_g[0] );
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798 nseg += 2;
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799 }
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800 else
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801 {
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802 nseg = searchAnchors( njob, seq_g, segment );
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803 #if 0
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804 fprintf( stderr, "### nseg = %d\n", nseg );
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805 fprintf( stderr, "### seq_g[0] = %s\n", seq_g[0] );
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806 fprintf( stderr, "### nlenmax = %d\n", nlenmax );
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807 fprintf( stderr, "### len = %d\n", strlen( seq_g[0] ) );
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808
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809 #endif
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810
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811 anchors[0] = 0;
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812 for( i=0; i<nseg; i++ ) anchors[i+1] = segment[i].center;
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813 anchors[nseg+1] = strlen( seq_g[0] );
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814 nseg +=2;
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815
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816 #if 0
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817 for( i=0; i<nseg; i++ )
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818 fprintf( stderr, "anchor[%d] = %d\n", i, anchors[i] );
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819 #endif
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820 }
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821
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822
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823 //--------------- kokokara ----
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824 if( subalignment || autosubalignment )
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825 {
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826 for( i=0; i<nsubalignments; i++ )
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827 {
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828 fprintf( stderr, "\nChecking subalignment %d:\n", i+1 );
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829 alignmentlength = strlen( seq[subtable[i][0]] );
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830 for( j=0; subtable[i][j]!=-1; j++ )
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831 fprintf( stderr, " %d ", subtable[i][j]+1 );
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832 // fprintf( stderr, " ##### %d-%d. %-30.30s\n", i, subtable[i][j]+1, name[subtable[i][j]]+1 );
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833 fprintf( stderr, "\n" );
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834 for( j=0; subtable[i][j]!=-1; j++ )
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835 {
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836 if( subtable[i][j] >= njob )
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837 {
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838 fprintf( stderr, "No such sequence, %d.\n", subtable[i][j]+1 );
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839 exit( 1 );
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840 }
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diff changeset
841 if( alignmentlength != strlen( seq[subtable[i][j]] ) )
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842 {
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diff changeset
843 fprintf( stderr, "\n" );
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diff changeset
844 fprintf( stderr, "###############################################################################\n" );
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diff changeset
845 fprintf( stderr, "# ERROR!\n" );
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diff changeset
846 fprintf( stderr, "# Subalignment %d must be aligned.\n", i+1 );
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diff changeset
847 fprintf( stderr, "# Please check the alignment lengths of following sequences.\n" );
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diff changeset
848 fprintf( stderr, "#\n" );
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diff changeset
849 fprintf( stderr, "# %d. %-10.10s -> %d letters (including gaps)\n", subtable[i][0]+1, name[subtable[i][0]]+1, alignmentlength );
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diff changeset
850 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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diff changeset
851 fprintf( stderr, "#\n" );
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diff changeset
852 fprintf( stderr, "# See http://mafft.cbrc.jp/alignment/software/merge.html for details.\n" );
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diff changeset
853 if( subalignmentoffset )
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diff changeset
854 {
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diff changeset
855 fprintf( stderr, "#\n" );
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diff changeset
856 fprintf( stderr, "# You specified seed alignment(s) consisting of %d sequences.\n", subalignmentoffset );
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diff changeset
857 fprintf( stderr, "# In this case, the rule of numbering is:\n" );
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diff changeset
858 fprintf( stderr, "# The aligned seed sequences are numbered as 1 .. %d\n", subalignmentoffset );
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859 fprintf( stderr, "# The input sequences to be aligned are numbered as %d .. %d\n", subalignmentoffset+1, subalignmentoffset+njob );
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860 }
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diff changeset
861 fprintf( stderr, "###############################################################################\n" );
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diff changeset
862 fprintf( stderr, "\n" );
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863 exit( 1 );
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864 }
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865 insubtable[subtable[i][j]] = 1;
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866 }
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diff changeset
867 for( j=0; j<njob-1; j++ )
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868 {
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diff changeset
869 #if 0
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870 int k;
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871 reporterr( "#### STEP%d\n", j );
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diff changeset
872 for( k=0; topol[j][0][k]!=-1; k++ ) reporterr( "%3d ", topol[j][0][k] );
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diff changeset
873 reporterr( "len=%f\n", len[j][0] );
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diff changeset
874 for( k=0; topol[j][1][k]!=-1; k++ ) reporterr( "%3d ", topol[j][1][k] );
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diff changeset
875 reporterr( "len=%f\n", len[j][1] );
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diff changeset
876 reporterr( "\n" );
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diff changeset
877 #endif
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878 if( includemember( topol[j][0], subtable[i] ) && !samemember( topol[j][0], subtable[i] ) )
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879 {
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880 skipthisbranch[j][0] = 1;
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881 // reporterr( "SKIP 0 !!!!!!\n" );
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diff changeset
882 }
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883 if( includemember( topol[j][1], subtable[i] ) && !samemember( topol[j][1], subtable[i] ) )
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884 {
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diff changeset
885 skipthisbranch[j][1] = 1;
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diff changeset
886 // reporterr( "SKIP 1 !!!!!!\n" );
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diff changeset
887 }
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diff changeset
888 }
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889 foundthebranch = 0;
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diff changeset
890 for( j=0; j<njob-1; j++ )
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diff changeset
891 {
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892 if( samemember( topol[j][0], subtable[i] ) || samemember( topol[j][1], subtable[i] ) )
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diff changeset
893 {
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894 foundthebranch = 1;
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diff changeset
895 fprintf( stderr, " -> OK\n" );
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896 break;
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diff changeset
897 }
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diff changeset
898 }
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899 if( !foundthebranch )
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diff changeset
900 {
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901 system( "cp infile.tree GuideTree" ); // tekitou
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diff changeset
902 fprintf( stderr, "\n" );
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diff changeset
903 fprintf( stderr, "###############################################################################\n" );
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diff changeset
904 fprintf( stderr, "# ERROR!\n" );
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diff changeset
905 fprintf( stderr, "# Subalignment %d does not seem to form a monophyletic cluster\n", i+1 );
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diff changeset
906 fprintf( stderr, "# in the guide tree ('GuideTree' in this directory) internally computed.\n" );
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diff changeset
907 fprintf( stderr, "# If you really want to use this subalignment, pelase give a tree with --treein \n" );
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diff changeset
908 fprintf( stderr, "# http://mafft.cbrc.jp/alignment/software/treein.html\n" );
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diff changeset
909 fprintf( stderr, "# http://mafft.cbrc.jp/alignment/software/merge.html\n" );
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diff changeset
910 if( subalignmentoffset )
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diff changeset
911 {
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diff changeset
912 fprintf( stderr, "#\n" );
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913 fprintf( stderr, "# You specified seed alignment(s) consisting of %d sequences.\n", subalignmentoffset );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
914 fprintf( stderr, "# In this case, the rule of numbering is:\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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diff changeset
915 fprintf( stderr, "# The aligned seed sequences are numbered as 1 .. %d\n", subalignmentoffset );
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diff changeset
916 fprintf( stderr, "# The input sequences to be aligned are numbered as %d .. %d\n", subalignmentoffset+1, subalignmentoffset+njob );
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diff changeset
917 }
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918 fprintf( stderr, "############################################################################### \n" );
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diff changeset
919 fprintf( stderr, "\n" );
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diff changeset
920 exit( 1 );
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921 }
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922 // commongappick( seq[subtable[i]], subalignment[i] ); // irukamo
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923 }
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diff changeset
924 #if 0
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diff changeset
925 for( i=0; i<njob-1; i++ )
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diff changeset
926 {
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927 fprintf( stderr, "STEP %d\n", i+1 );
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928 fprintf( stderr, "group1 = " );
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diff changeset
929 for( j=0; topol[i][0][j] != -1; j++ )
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parents:
diff changeset
930 fprintf( stderr, "%d ", topol[i][0][j]+1 );
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parents:
diff changeset
931 fprintf( stderr, "\n" );
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diff changeset
932 fprintf( stderr, "SKIP -> %d\n\n", skipthisbranch[i][0] );
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diff changeset
933 fprintf( stderr, "group2 = " );
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diff changeset
934 for( j=0; topol[i][1][j] != -1; j++ )
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diff changeset
935 fprintf( stderr, "%d ", topol[i][1][j]+1 );
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parents:
diff changeset
936 fprintf( stderr, "\n" );
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937 fprintf( stderr, "SKIP -> %d\n\n", skipthisbranch[i][1] );
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938 }
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939 #endif
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940
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941 for( i=0; i<njob; i++ )
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diff changeset
942 {
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943 if( insubtable[i] ) strcpy( bseq[i], seq[i] );
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diff changeset
944 else gappick0( bseq[i], seq[i] );
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diff changeset
945 }
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946
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947 for( i=0; i<nsubalignments; i++ )
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948 {
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949 for( j=0; subtable[i][j]!=-1; j++ ) subalnpt[i][j] = bseq[subtable[i][j]];
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950 commongappick( j, subalnpt[i] );
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951 }
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952
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953 FreeIntMtx( subtable );
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954 free( insubtable );
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955 for( i=0; i<nsubalignments; i++ ) free( subalnpt[i] );
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956 free( subalnpt );
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957 free( preservegaps );
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958 }
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959 //--------------- kokomade ----
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960
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961
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962
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963
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964 for( i=0; i<njob; i++ ) res_g[i][0] = 0;
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965
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966 for( iseg=0; iseg<nseg-1; iseg++ )
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967 {
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968 int tmplen = anchors[iseg+1]-anchors[iseg];
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969 int pos = strlen( res_g[0] );
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970 for( j=0; j<njob; j++ )
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971 {
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972 strncpy( seq[j], seq_g[j], tmplen );
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973 seq[j][tmplen]= 0;
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974 seq_g[j] += tmplen;
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975
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976 }
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977 fprintf( stderr, "Segment %3d/%3d %4d-%4d\n", iseg+1, nseg-1, pos+1, pos+1+tmplen );
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978 fflush( stderr );
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979 fprintf( trap_g, "Segment %3d/%3d %4d-%4d\n", iseg+1, nseg-1, pos+1, pos+1+tmplen );
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980
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981 cut = ocut;
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982 returnvalue = TreeDependentIteration( njob, name, nlen, seq, bseq, topol, len, eff, skipthisbranch, alloclen, localhomtable, singlerna, nkozo, kozoarivec );
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983
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984 for( i=0; i<njob; i++ )
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985 strcat( res_g[i], bseq[i] );
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986 }
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987 FreeCharMtx( seq_g_bk );
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988 FreeIntCub( topol );
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989 FreeDoubleMtx( len );
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990 FreeDoubleMtx( eff );
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991 FreeIntMtx( skipthisbranch );
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992 free( kozoarivec );
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993 if( constraint ) FreeLocalHomTable( localhomtable, njob );
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994 if( rnakozo && rnaprediction == 'm' )
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995 {
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996 if( singlerna ) // nen no tame
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997 {
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998 for( i=0; i<njob; i++ )
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999 {
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1000 for( j=0; singlerna[i][j]!=NULL; j++ )
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1001 {
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1002 if( singlerna[i][j] ) free( singlerna[i][j] );
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1003 }
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1004 if( singlerna[i] ) free( singlerna[i] );
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1005 }
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1006 free( singlerna );
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1007 singlerna = NULL;
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1008 }
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1009 }
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1010
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1011 #if 0
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1012 Write( stdout, njob, name, nlen, bseq );
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1013 #endif
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1014
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1015 fprintf( stderr, "done\n" );
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1016 fprintf( trap_g, "done\n" );
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1017 fclose( trap_g );
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1018
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1019
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1020 devide = 0;
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1021 writePre( njob, name, nlen, res_g, 1 );
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1022 #if 0
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1023 writeData( stdout, njob, name, nlen, res_g, 1 );
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1024 #endif
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1025
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1026
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1027 if( spscoreout ) reporterr( "Unweighted sum-of-pairs score = %10.5f\n", sumofpairsscore( njob, res_g ) );
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1028
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1029 SHOWVERSION;
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1030 return( 0 );
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1031 }
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1032
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1033 #if 0
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1034 signed int main( int argc, char *argv[] )
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1035 {
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1036 int i, nlen[M];
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1037 char b[B];
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1038 char a[] = "=";
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1039 int value;
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1040
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1041 gets( b ); njob = atoi( b );
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1042
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1043 /*
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1044 scoremtx = 0;
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1045 if( strstr( b, "ayhoff" ) ) scoremtx = 1;
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1046 else if( strstr( b, "dna" ) || strstr( b, "DNA" ) ) scoremtx = -1;
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1047 else if( strstr( b, "M-Y" ) || strstr( b, "iyata" ) ) scoremtx = 2;
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1048 else scoremtx = 0;
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1049 */
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1050 if( strstr( b, "constraint" ) ) cnst = 1;
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1051
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1052 nlenmax = 0;
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1053 i = 0;
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1054 while( i<njob )
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1055 {
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1056 gets( b );
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1057 if( !strncmp( b, a, 1 ) )
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1058 {
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1059 gets( b ); nlen[i] = atoi( b );
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1060 if( nlen[i] > nlenmax ) nlenmax = nlen[i];
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1061 i++;
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1062 }
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1063 }
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1064 if( nlenmax > N || njob > M )
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1065 {
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1066 fprintf( stderr, "ERROR in main\n" );
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1067 exit( 1 );
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1068 }
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1069 /*
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1070 nlenmax = Na;
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1071 */
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1072 rewind( stdin );
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1073 value = main1( nlen, argc, argv );
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1074 exit( 0 );
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1075 }
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1076 #endif