Mercurial > repos > nick > duplex

annotate mafft/core/MSalign11.c @ 18:e4d75f9efb90 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
1 #include "mltaln.h"
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
2 #include "dp.h"
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
3
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
4 #define DEBUG 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
5 #define XXXXXXX 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
6 #define USE_PENALTY_EX 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
7
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
8 static void extendmseq( char **mseq1, char **mseq2, char **seq1, char **seq2, int i, int j, int prevhiti, int prevhitj )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
9 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
10 // char gap[] = "-";
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
11 char *gap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
12 gap = newgapstr;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
13 int l;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
14
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
15 fprintf( stderr, "i=%d, prevhiti=%d\n", i, prevhiti );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
16 fprintf( stderr, "j=%d, prevhitj=%d\n", j, prevhitj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
17 l = prevhiti - i - 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
18 fprintf( stderr, "l=%d\n", l );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
19 while( l>0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
20 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
21 *--mseq1[0] = seq1[0][i+l--];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
22 *--mseq2[0] = *gap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
23 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
24 l= prevhitj - j - 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
25 fprintf( stderr, "l=%d\n", l );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
26 while( l>0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
27 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
28 *--mseq1[0] = *gap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
29 *--mseq2[0] = seq2[0][j+l--];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
30 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
31 if( i < 0 || j < 0 ) return;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
32 *--mseq1[0] = seq1[0][i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
33 *--mseq2[0] = seq2[0][j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
34 fprintf( stderr, "added %c to mseq1, mseq1 = %s \n", seq1[0][i], mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
35 fprintf( stderr, "added %c to mseq2, mseq2 = %s \n", seq2[0][j], mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
36 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
37
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
38 static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
39 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
40 char tmpc = s1[0][i1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
41 char *seq2 = s2[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
42
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
43 while( lgth2-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
44 *match++ = amino_dis[(int)tmpc][(int)*seq2++];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
45 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
46
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
47 static float Atracking( float *lasthorizontalw, float *lastverticalw,
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
48 char **seq1, char **seq2,
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
49 char **mseq1, char **mseq2,
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
50 float **cpmx1, float **cpmx2,
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
51 int **ijp )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
52 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
53 int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
54 // char gap[] = "-";
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
55 char *gap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
56 gap = newgapstr;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
57 lgth1 = strlen( seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
58 lgth2 = strlen( seq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
59
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
60
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
61 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
62 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
63 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
64 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
65 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
66 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
67
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
68 for( i=0; i<lgth1+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
69 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
70 ijp[i][0] = i + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
71 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
72 for( j=0; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
73 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
74 ijp[0][j] = -( j + 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
75 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
76
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
77
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
78 mseq1[0] += lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
79 *mseq1[0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
80 mseq2[0] += lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
81 *mseq2[0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
82 iin = lgth1; jin = lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
83 limk = lgth1+lgth2 + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
84 for( k=0; k<limk; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
85 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
86 if( ijp[iin][jin] < 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
87 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
88 ifi = iin-1; jfi = jin+ijp[iin][jin];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
89 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
90 else if( ijp[iin][jin] > 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
91 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
92 ifi = iin-ijp[iin][jin]; jfi = jin-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
93 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
94 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
95 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
96 ifi = iin-1; jfi = jin-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
97 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
98 l = iin - ifi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
99 while( --l )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
100 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
101 *--mseq1[0] = seq1[0][ifi+l];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
102 *--mseq2[0] = *gap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
103 k++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
104 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
105 l= jin - jfi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
106 while( --l )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
107 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
108 *--mseq1[0] = *gap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
109 *--mseq2[0] = seq2[0][jfi+l];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
110 k++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
111 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
112 if( iin <= 0 || jin <= 0 ) break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
113 *--mseq1[0] = seq1[0][ifi];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
114 *--mseq2[0] = seq2[0][jfi];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
115 k++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
116 iin = ifi; jin = jfi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
117 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
118 return( 0.0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
119 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
120
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
121 void backdp( float **WMMTX, float wmmax, float *maxinw, float *maxinh, int lgth1, int lgth2, int alloclen, float *w1, float *w2, float *initverticalw, float *m, int *mp, int iin, int jin, char **seq1, char **seq2, char **mseq1, char **mseq2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
122 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
123 register int i, j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
124 int prevhiti, prevhitj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
125 // int lasti, lastj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
126 float g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
127 float fpenalty = (float)penalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
128 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
129 float fpenalty_ex = (float)penalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
130 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
131 float *currentw, *previousw, *wtmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
132 float mi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
133 int mpi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
134 int *mpjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
135 float *mjpt, *prept, *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
136 float wm = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
137 float forwwm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
138
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
139 currentw = w1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
140 previousw = w2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
141
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
142 match_calc( initverticalw, seq2, seq1, lgth2-1, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
143 match_calc( currentw, seq1, seq2, lgth1-1, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
144
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
145
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
146 prevhiti = iin;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
147 prevhitj = jin;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
148 fprintf( stderr, "prevhiti = %d, lgth1 = %d\n", prevhiti, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
149 fprintf( stderr, "prevhitj = %d, lgth2 = %d\n", prevhitj, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
150 extendmseq( mseq1, mseq2, seq1, seq2, prevhiti, prevhitj, lgth1, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
151
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
152 for( i=0; i<lgth1-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
153 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
154 initverticalw[i] += fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
155 WMMTX[i][lgth2-1] += fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
156 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
157 for( j=0; j<lgth2-1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
158 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
159 currentw[j] += fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
160 WMMTX[lgth1-1][j] += fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
161 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
162
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
163
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
164 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
165 fprintf( stderr, "initverticalw = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
166 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
167 fprintf( stderr, "% 8.2f", initverticalw[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
168 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
169 fprintf( stderr, "currentw = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
170 for( i=0; i<lgth2; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
171 fprintf( stderr, "% 8.2f", currentw[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
172 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
173 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
174
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
175 for( j=lgth2-1; j>0; --j )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
176 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
177 m[j-1] = currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
178 mp[j] = 0; // iranai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
179 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
180
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
181 for( j=0; j<lgth2; j++ ) m[j] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
182 //m[lgth2-1] ga, irunoka iranainoka irahai.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
183
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
184 for( i=lgth1-2; i>-1; i-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
185 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
186 wtmp = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
187 previousw = currentw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
188 currentw = wtmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
189
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
190 previousw[lgth2-1] = initverticalw[i+1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
191
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
192 match_calc( currentw, seq1, seq2, i, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
193
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
194 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
195 fprintf( stderr, "i=%d, currentw = \n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
196 for( j=0; j<lgth2; j++ ) fprintf( stderr, "% 8.2f", currentw[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
197 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
198 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
199
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
200 currentw[lgth2-1] = initverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
201
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
202 mi = previousw[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
203 mpi = lgth2-1; //iranai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
204
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
205
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
206 mjpt = m + lgth2 - 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
207 prept = previousw + lgth2 - 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
208 curpt = currentw + lgth2 - 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
209 mpjpt = mp + lgth2 - 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
210
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
211 for( j=lgth2-2; j>-1; j-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
212 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
213
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
214 // fprintf( stderr, "i,j=%d,%d %c-%c ", i, j, seq1[0][i], seq2[0][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
215 wm = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
216 g = mi + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
217 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
218 fprintf( stderr, "%5.0f?", g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
219 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
220 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
221 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
222 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
223 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
224 g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
225 if( g >= mi )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
226 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
227 mi = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
228 mpi = j+1; //iranai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
229 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
230 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
231 mi += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
232 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
233
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
234 g = *mjpt + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
235 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
236 fprintf( stderr, "%5.0f?", g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
237 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
238 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
239 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
240 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
241 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
242 g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
243 if( g >= *mjpt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
244 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
245 *mjpt = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
246 *mpjpt = i-1; //iranai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
247 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
248 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
249 m[j] += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
250 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
251
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
252 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
253 fprintf( stderr, "*curpt = %5.0f \n", *curpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
254 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
255
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
256 // forwwm = wm + MIN( maxinw[i], maxinh[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
257 forwwm = wm + MIN( maxinw[i], maxinh[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
258 WMMTX[i][j] = forwwm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
259 if( forwwm == wmmax && i<prevhiti && j<prevhitj )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
260 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
261 fprintf( stderr, "hit!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
262 extendmseq( mseq1, mseq2, seq1, seq2, i, j, prevhiti, prevhitj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
263 if( forwwm == wmmax )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
264 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
265 *--mseq1[0] = 'u';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
266 *--mseq2[0] = 'u';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
267 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
268 prevhiti = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
269 prevhitj = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
270 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
271 *curpt += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
272
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
273 mjpt--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
274 prept--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
275 mpjpt--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
276 curpt--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
277 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
278 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
279 extendmseq( mseq1, mseq2, seq1, seq2, -1, -1, prevhiti, prevhitj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
280 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
281
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
282
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
283 float MSalign11( char **seq1, char **seq2, int alloclen )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
284 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
285 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
286 // int k;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
287 register int i, j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
288 int lasti, lastj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
289 int iin = 0, jin = 0; // by Mathog, a guess
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
290 int lgth1, lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
291 int resultlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
292 float wm = 0.0; /* int ?????? */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
293 float g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
294 float *currentw, *previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
295 float fpenalty = (float)penalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
296 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
297 float fpenalty_ex = (float)penalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
298 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
299 float *maxinw = NULL, *maxinwpt = NULL; // by D.Mathog, guess
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
300 float *maxinh = NULL; // by D.Mathog, guess
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
301 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
302 float wmmax;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
303 float *wtmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
304 int *ijppt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
305 float *mjpt, *prept, *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
306 int *mpjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
307 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
308 static float mi, *m;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
309 static int **ijp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
310 static int mpi, *mp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
311 static float *w1, *w2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
312 static float *match;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
313 static float *initverticalw; /* kufuu sureba iranai */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
314 static float *lastverticalw; /* kufuu sureba iranai */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
315 static char **mseq1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
316 static char **mseq2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
317 static char **mseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
318 static float **cpmx1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
319 static float **cpmx2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
320 static int **intwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
321 static float **WMMTX;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
322 static float **floatwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
323 static int orlgth1 = 0, orlgth2 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
324
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
325 if( orlgth1 == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
326 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
327 mseq1 = AllocateCharMtx( njob, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
328 mseq2 = AllocateCharMtx( njob, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
329 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
330
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
331
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
332 lgth1 = strlen( seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
333 lgth2 = strlen( seq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
334
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
335 if( lgth1 > orlgth1 || lgth2 > orlgth2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
336 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
337 int ll1, ll2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
338
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
339 if( orlgth1 > 0 && orlgth2 > 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
340 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
341 FreeFloatVec( w1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
342 FreeFloatVec( w2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
343 FreeFloatVec( match );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
344 FreeFloatVec( initverticalw );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
345 FreeFloatVec( lastverticalw );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
346 FreeFloatVec( maxinw );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
347 FreeFloatVec( maxinh );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
348
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
349 FreeFloatVec( m );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
350 FreeIntVec( mp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
351
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
352 FreeCharMtx( mseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
353
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
354
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
355 FreeFloatMtx( cpmx1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
356 FreeFloatMtx( cpmx2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
357
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
358 FreeFloatMtx( floatwork );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
359 FreeIntMtx( intwork );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
360 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
361
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
362 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
363 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
364
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
365 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
366 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
367 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
368
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
369 w1 = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
370 w2 = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
371 match = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
372
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
373 initverticalw = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
374 lastverticalw = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
375 maxinw = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
376
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
377
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
378 m = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
379 mp = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
380 maxinh = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
381
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
382 mseq = AllocateCharMtx( njob, ll1+ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
383
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
384 cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
385 cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
386
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
387 floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
388 intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
389
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
390 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
391 fprintf( stderr, "succeeded\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
392 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
393
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
394 orlgth1 = ll1 - 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
395 orlgth2 = ll2 - 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
396 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
397
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
398
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
399 mseq1[0] = mseq[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
400 mseq2[0] = mseq[1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
401
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
402
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
403 if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
404 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
405 int ll1, ll2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
406
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
407 if( commonAlloc1 && commonAlloc2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
408 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
409 FreeIntMtx( commonIP );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
410 FreeFloatMtx( WMMTX );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
411 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
412
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
413 ll1 = MAX( orlgth1, commonAlloc1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
414 ll2 = MAX( orlgth2, commonAlloc2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
415
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
416 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
417 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
418 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
419
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
420 commonIP = AllocateIntMtx( ll1+10, ll2+10 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
421 WMMTX = AllocateFloatMtx( ll1+10, ll2+10 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
422
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
423 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
424 fprintf( stderr, "succeeded\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
425 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
426
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
427 commonAlloc1 = ll1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
428 commonAlloc2 = ll2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
429 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
430 ijp = commonIP;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
431
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
432
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
433 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
434 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
435 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
436 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
437
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
438 currentw = w1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
439 previousw = w2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
440
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
441 match_calc( initverticalw, seq2, seq1, 0, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
442
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
443
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
444 match_calc( currentw, seq1, seq2, 0, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
445
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
446 WMMTX[0][0] = initverticalw[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
447
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
448 maxinh[0] = initverticalw[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
449 for( i=1; i<lgth1+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
450 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
451 initverticalw[i] += fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
452 WMMTX[i][0] = initverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
453 if( maxinh[0] < initverticalw[i] ) maxinh[0] = initverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
454 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
455 maxinw[0] = currentw[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
456 for( j=1; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
457 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
458 currentw[j] += fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
459 WMMTX[0][j] = currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
460 if( maxinw[0] < currentw[j] ) maxinw[0] = currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
461 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
462
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
463 for( j=1; j<lgth2+1; ++j )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
464 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
465 m[j] = currentw[j-1]; mp[j] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
466 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
467
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
468 lastverticalw[0] = currentw[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
469
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
470 lasti = lgth1+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
471
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
472 for( i=1; i<lasti; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
473 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
474 wtmp = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
475 previousw = currentw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
476 currentw = wtmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
477
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
478 previousw[0] = initverticalw[i-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
479
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
480 match_calc( currentw, seq1, seq2, i, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
481
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
482 currentw[0] = initverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
483
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
484 mi = previousw[0]; mpi = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
485
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
486 maxinwpt = maxinw + i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
487 *maxinwpt = currentw[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
488
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
489 fprintf( stderr, "currentw[0] = %f, *maxinwpt = %f\n", currentw[0], maxinw[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
490
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
491 ijppt = ijp[i] + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
492 mjpt = m + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
493 prept = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
494 curpt = currentw + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
495 mpjpt = mp + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
496 lastj = lgth2+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
497
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
498 for( j=1; j<lastj; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
499 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
500 wm = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
501 *ijppt = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
502
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
503 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
504 fprintf( stderr, "%5.0f->", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
505 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
506 g = mi + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
507 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
508 fprintf( stderr, "%5.0f?", g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
509 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
510 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
511 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
512 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
513 *ijppt = -( j - mpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
514 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
515 g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
516 if( g >= mi )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
517 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
518 mi = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
519 mpi = j-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
520 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
521 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
522 mi += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
523 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
524
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
525 g = *mjpt + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
526 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
527 fprintf( stderr, "%5.0f?", g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
528 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
529 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
530 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
531 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
532 *ijppt = +( i - *mpjpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
533 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
534 g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
535 if( g >= *mjpt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
536 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
537 *mjpt = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
538 *mpjpt = i-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
539 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
540 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
541 m[j] += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
542 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
543
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
544 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
545 fprintf( stderr, "%5.0f ", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
546 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
547 *curpt += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
548
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
549 WMMTX[i][j] = *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
550
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
551
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
552 if( j<lgth2 && *maxinwpt < *curpt ) *maxinwpt = *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
553 if( j<lgth2 && maxinh[j] < *curpt ) maxinh[j] = *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
554 // fprintf( stderr, "maxintwpt = %f\n", *maxinwpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
555
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
556 ijppt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
557 mjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
558 prept++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
559 mpjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
560 curpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
561 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
562 lastverticalw[i] = currentw[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
563 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
564
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
565 wmmax = -999.9;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
566 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
567 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
568 g = lastverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
569 if( g > wmmax )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
570 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
571 wmmax = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
572 iin = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
573 jin = lgth2-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
574 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
575 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
576 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
577 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
578 g = currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
579 if( g > wmmax )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
580 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
581 wmmax = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
582 iin = lgth1-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
583 jin = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
584 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
585 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
586
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
587 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
588 fprintf( stderr, "maxinw[%d] = %f\n", i, maxinw[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
589 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
590 fprintf( stderr, "maxinh[%d] = %f\n", j, maxinh[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
591
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
592 fprintf( stderr, "wmmax = %f (%d,%d)\n", wmmax, iin, jin );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
593 if( iin == lgth1 - 1 && jin == lgth2 - 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
594 ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
595 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
596 wmmax += fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
597
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
598 fprintf( stderr, "wmmax = %f\n", wmmax );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
599
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
600 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
601 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
602 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
603 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
604 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
605 fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
606 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
607 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
608 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
609 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
610
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
611 mseq1[0] += lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
612 *mseq1[0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
613 mseq2[0] += lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
614 *mseq2[0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
615
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
616 backdp( WMMTX, wmmax, maxinw, maxinh, lgth1, lgth2, alloclen, w1, w2, initverticalw, m, mp, iin, jin, seq1, seq2, mseq1, mseq2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
617
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
618 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
619 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
620 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
621 fprintf( stderr, ">MSres\n%s\n", mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
622 fprintf( stderr, ">MSres\n%s\n", mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
623 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
624
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
625 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
626 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
627 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
628 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
629 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
630 fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
631 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
632 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
633 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
634 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
635
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
636 mseq1[0] = mseq[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
637 mseq2[0] = mseq[1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
638 mseq1[0] += lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
639 *mseq1[0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
640 mseq2[0] += lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
641 *mseq2[0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
642
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
643 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
644
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
645
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
646 resultlen = strlen( mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
647 if( alloclen < resultlen || resultlen > N )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
648 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
649 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
650 ErrorExit( "LENGTH OVER!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
651 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
652
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
653
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
654 strcpy( seq1[0], mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
655 strcpy( seq2[0], mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
656 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
657 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
658 fprintf( stderr, ">\n%s\n", mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
659 fprintf( stderr, ">\n%s\n", mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
660 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
661
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
662
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
663 return( wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
664 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
nick
parents:
diff changeset
665