1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
|
extern int intlen( int *num );
extern char seqcheck( char **seq );
extern void scmx_calc( int icyc, char **aseq, double *effarr, float **scmx );
extern void exitall( char arr[] );
extern void display( char **seq, int nseq );
extern void intergroup_score( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value );
extern void intergroup_score_gapnomi( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value );
extern void intergroup_score_new( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value );
extern double score_calc5( char **seq, int s, double **eff, int ex );
extern double score_calc4( char **seq, int s, double **eff, int ex );
extern void upg2( int nseq, double **eff, int ***topol, double **len );
//extern void veryfastsupg_float_realloc_nobk_halfmtx( int njob, float **mtx, int ***topol, float **len );
//extern void veryfastsupg_float_realloc_nobk( int njob, float **mtx, int ***topol, float **len );
extern void veryfastsupg_int_realloc_nobk( int njob, int **mtx, int ***topol, double **len );
extern void veryfastsupg( int nseq, double **oeff, int ***topol, double **len );
extern void veryfastsupg_double( int nseq, double **oeff, int ***topol, double **len );
extern void veryfastsupg_double_loadtree( int nseq, double **oeff, int ***topol, double **len );
extern void veryfastsupg_double_loadtop( int nseq, double **oeff, int ***topol, double **len );
extern void veryfastsupg_int( int nseq, int **oeff, int ***topol, double **len );
extern void fastsupg( int nseq, double **oeff, int ***topol, double **len );
extern void supg( int nseq, double **oeff, int ***topol, double **len );
extern void spg( int nseq, double **oeff, int ***topol, double **len );
extern double ipower( double x, int n );
extern void countnode( int nseq, int ***topol, double **node );
extern void countnode_int( int nseq, int ***topol, int **node );
extern void counteff_simple( int nseq, int ***topol, double **len, double *node );
extern void counteff_simple_float( int nseq, int ***topol, float **len, double *node );
extern void counteff( int nseq, int ***topol, double **len, double **node );
extern float score_calc1( char *seq1, char *seq2 );
extern float score_calcp( char *seq1, char *seq2, int len );
extern float substitution_nid( char *seq1, char *seq2 );
extern float substitution_score( char *seq1, char *seq2 );
extern float substitution_hosei( char *seq1, char *seq2 );
extern float substitution( char *seq1, char *seq2 );
extern void treeconstruction( char **seq, int nseq, int ***topol, double **len, double **eff );
extern float bscore_calc( char **seq, int s, double **eff );
extern void AllocateTmpSeqs( char ***mseq2pt, char **mseq1pt, int locnlenmax );
extern void FreeTmpSeqs( char **mseq2, char *mseq1 );
extern void gappick_samestring( char *aseq );
extern void gappick0( char *aseq, char *seq );
extern void gappick( int nseq, int s, char **aseq, char **mseq2,
double **eff, double *effarr );
extern void commongappick_record( int nseq, char **seq, int *map );
extern void commongappick( int nseq, char **seq );
extern double score_calc0( char **seq, int s, double **eff, int ex );
extern void strins( char *str1, char *str2 );
extern int isaligned( int nseq, char **seq );
extern double score_calc_for_score( int nseq, char **seq );
extern void floatncpy( float *vec1, float *vec2, int len );
extern float score_calc_a( char **seq, int s, double **eff );
extern float score_calc_s( char **seq, int s, double **eff );
extern double score_calc_for_score_s( int s, char **seq );
extern double SSPscore( int s, char **seq );
extern double DSPscore( int s, char **seq );
extern int searchAnchors( int nseq, char **seq, Segment *seg );
extern char *progName( char *str );
extern void dontcalcimportance( int nseq, double *eff, char **seq, LocalHom **localhom );
extern void calcimportance( int nseq, double *eff, char **seq, LocalHom **localhom );
extern void weightimportance2( int nseq, double *eff, LocalHom **localhom );
extern void weightimportance4( int clus1, int clus2, double *eff1, double *eff2, LocalHom ***localhom );
extern void extendlocalhom( int nseq, LocalHom **localhom );
extern void extendlocalhom2( int nseq, LocalHom **localhom, double **mtx );
extern int makelocal( char *s1, char *s2, int thr );
extern void mdfymtx( char **pair, int s1, double **partialmtx, double **mtx );
extern float score_calc( char **seq, int s );
extern void cpmx_calc( char **seq, float **cpmx, double *eff, int lgth, int clus );
extern void cpmx_calc_new( char **seq, float **cpmx, double *eff, int lgth, int clus );
extern void MScpmx_calc_new( char **seq, float **cpmx, double *eff, int lgth, int clus );
extern void mseqcat( char **seq1, char **seq2, double **eff, double *effarr1, double *effarr2, char name1[M][B], char name2[M][B], int clus1, int clus2 );
extern void strnbcat( char *s1, char *s2, int m );
extern int conjuctionforgaln( int s0, int s1, char **seq, char **aseq, double *peff, double *eff, char **name, char **aname, char *d );
extern int fastconjuction( int *memlist, char **seq, char **aseq, double *peff, double *eff, char name[M][B], char aname[M][B], char *d );
extern int fastconjuction_noname_kozo( int *memlist, char **seq, char **aseq, double *peff, double *eff, double *peff_kozo, double *eff_kozo, char *d );
extern int fastconjuction_noname( int *memlist, char **seq, char **aseq, double *peff, double *eff, char *d );
extern int fastconjuction_noweight( int *memlist, char **seq, char **aseq, double *peff, char *d );
extern int conjuctionfortbfast( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char *d );
extern int conjuctionfortbfast_kozo( double *tmptmp, char **pair, int s, char **seq, char **aseq, double *peff, double *eff, double *peff_kozo, double *eff_kozo, char *d );
extern int conjuction( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char **name, char **aname, char *d );
extern void floatdelete( float **cpmx, int d, int len );
extern void chardelete( char *seq, int d );
extern int RootBranchNode( int nseq, int ***topol, int step, int branch );
extern void BranchLeafNode( int nseq, int ***topol, int *node, int step, int branch );
extern void RootLeafNode( int nseq, int ***topol, int *node );
extern void nodeFromABranch( int nseq, int *result, int **pairwisenode, int ***topol, double **len, int step, int num );
extern void OneClusterAndTheOther( int locnjob, char **pair, int *s1, int *s2, int ***topol, int step, int branch );
extern void makeEffMtx( int nseq, double **mtx, double *vec );
extern void node_eff( int nseq, double *eff, int *node );
extern int shrinklocalhom( char **pair, int s1, int s2, LocalHom **localhom, LocalHom ***localhomshrink );
extern int msshrinklocalhom( char **pair, int s1, int s2, LocalHom **localhom, LocalHom ***localhomshrink );
extern int fastshrinklocalhom( int *mem1, int *mem2, LocalHom **localhom, LocalHom ***localhomshrink );
extern int msfastshrinklocalhom( int *mem1, int *mem2, LocalHom **localhom, LocalHom ***localhomshrink );
extern int TreeDependentIteration( int locnjob, char **name, int nlen[M], char **aseq, char **bseq, int ***topol, double **len, int alloclen, LocalHom **localhomtable, RNApair ***single, int nkozo, char *kozoarivec );
extern void checkMinusLength( int nseq, double **len );
extern void negativeMember2( int *mem, int *query, int locnseq );
extern int *negativeMember( int *query, int locnseq );
extern int IntExistsInVec( int query, int *vector );
extern NodeInCub searchParent( int top, int ***topol, int Start, int End );
extern void stopolInit( int n, Node *stopol );
extern void treeCnv( Node *stopol, int locnseq, int ***topol, double **len, double **bw );
extern int isLeaf( Node node );
extern double syntheticLength( Node *ob, Node *oppositeNode );
extern double calcW( Node *ob, Node *op );
extern void calcBranchWeight( double **bw, int locnseq, Node *stopol, int ***topol, double **len );
extern void branchWeightToPairWeight( int locnseq, int ***topol, double **pw, double **bw );
extern void weightFromABranch_rec( double *result, Node *ob, Node *op );
extern void weightFromABranch( int nseq, double *result, Node *stopol, int ***topol, int step, int LorR );
extern void keika( char *str, int current, int all );
extern double maxItch( double *soukan, int size );
extern void calcNaiseki( Fukusosuu *value, Fukusosuu *x, Fukusosuu *y );
extern Fukusosuu *AllocateFukusosuuVec( int l1 );
extern Fukusosuu **AllocateFukusosuuMtx( int l1, int l2 );
extern Fukusosuu ***AllocateFukusosuuCub( int l1, int l2, int l3 );
extern void FreeFukusosuuVec( Fukusosuu *vec );
extern void FreeFukusosuuMtx( Fukusosuu **mtx );
extern int getKouho( int *kouho, int nkouho, double *soukan, int nlen2 );
extern void zurasu2( int lag, int clus1, int clus2, char **seq1, char **seq2, char **aseq1, char **aseq2 );
extern void zurasu( int lag, int clus1, int clus2, char **seq1, char **seq2, char **aseq1, char **aseq2 );
extern int alignableReagion( int clus1, int clus2, char **seq1, char **seq2, double *eff1, double *eff2, Segment *seg );
extern void blockAlign( int *cut1, int *cut2, double **ocrossscore, int *ncut );
extern void blockAlign2( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut );
extern void blockAlign3( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut );
extern float A__align11( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch );
extern float imp_match_out_scH( int i1, int j1 );
extern void imp_match_init_strictH( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
extern float imp_match_out_scQ( int i1, int j1 );
extern float imp_match_out_scR( int i1, int j1 );
extern void imp_match_init_strictQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
extern void imp_match_init_strictR( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
extern void imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom );
extern float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *, char *, char *, char *, int *, int, int *, int headgp, int tailgp );
extern float Lalignmm_hmout( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *, char *, char *, char *, float **map );
extern float Lalign2m2m_hmout( char **seq1, char **seq2, char **seq1r, char **seq2r, char *dir1, char *dir2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *, char *, char *, char *, float **map );
extern float MSalign11( char **seq1, char **seq2, int alloclen );
//extern float rnalocal( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, RNApair **pair );
extern float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *, int, int *, int headgp, int tailgp );
extern float H__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
extern float Q__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
extern float Q__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *gapmap1, int *gapmap2 );
extern float R__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
extern float R__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
extern float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 );
extern float D__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 );
extern float translate_and_Calign( char **mseq1, char **mseq2, double *effarr1, double *effarr2, int clus1, int clus2, int alloclen );
extern double Fgetlag( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int alloclen );
extern float Falign( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int alloclen, int *fftlog, int *, int, int * );
extern float Falign_udpari_long( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int alloclen, int *fftlog );
float Falign_localhom( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int alloclen, LocalHom ***localhom, float *totalimpmatch, int *gapmap1, int *gapmap2, int *chudanpt, int chudanref, int *chudanres );
extern float part_imp_match_out_sc( int i1, int j1 );
extern float part_imp_match_out_scQ( int i1, int j1 );
extern void part_imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, int forscore );
extern void part_imp_match_init_strictQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
extern void part_imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom );
extern float partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *, char *, char *, char *, int *, int, int * );
extern float partQ__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *, char *, char *, char *);
extern float G__align11( char **seq1, char **seq2, int alloclen, int headgp, int tailgp );
extern float G__align11_noalign( int mtx[0x80][0x80], int penal, int penal_ex, char **seq1, char **seq2, int alloclen );
extern float L__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt );
extern float genL__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt );
extern float genG__align11( char **seq1, char **seq2, int alloclen );
extern float VAalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt );
extern float suboptalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt )
;
extern int fft(int n, Fukusosuu *x, int dum);
extern void topolcpy( int s1[], int s2[], int *mpt1, int *mpt2 );
extern void topolcat( int s1[], int s2[], int *mpt1, int *mpt2 );
extern void topolsort( int m, int s[] );
extern void topolswap( int s1[], int s2[], int *mpt1, int *mpt2 );
extern void reduc( double **mtx, int nseq, int im, int jm );
extern void nj( int nseq, double **omtx, int ***topol, double **dis );
extern void JTTmtx( double **rsr, double *freq, char locamino[26], char locgrp[26], int isTM );
extern void BLOSUMmtx( int n, double **matrix, double *freq, char *amino, char *amino_grp );
extern void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
extern void putlocalhom_str( char *al1, char *al2, double *equiv, double scale, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
extern void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
extern void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
extern void putlocalhom( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
extern char *cutal( char *al, int al_display_start, int start, int end );
extern void ErrorExit( char *message );
extern void strncpy_caseC( char *str1, char *str2, int len );
extern void seqUpper( int nseq, char **seq );
extern void seqLower( int nseq, char **seq );
extern int getaline_fp_eof( char *s, int l, FILE *fp );
extern int getaline_fp_eof_new(char s[], int l, FILE *fp);
extern int myfgets(char s[], int l, FILE *fp);
extern float input_new( FILE *fp, int d );
extern void PreRead( FILE *fp, int *locnjob, int *locnlenmax );
extern int allSpace( char *str );
extern void Read( char name[M][B], int nlen[M], char **seq );
extern void FRead( FILE *fp, char name[][B], int nlen[], char **seq );
extern void kake2hiku( char *str );
extern void readDataforgaln( FILE *fp, char **name, int *nlen, char **seq );
extern void readData( FILE *fp, char name[][B], int nlen[], char **seq );
extern void readData_pointer_casepreserve( FILE *fp, char **name, int *nlen, char **seq );
extern void readData_pointer( FILE *fp, char **name, int *nlen, char **seq );
extern void readData_pointer2( FILE *fp, int nseq, char **name, int *nlen, char **seq );
extern void readData_varlen( FILE *fp, char **name, int *nlen, char **seq );
extern int countATGC( char *s, int *total );
extern void getnumlen( FILE *fp );
extern void getnumlen_casepreserve( FILE *fp, int *nlenmin );
extern void getnumlen_nogap( FILE *fp, int *nlenmin );
extern void WriteGapFill( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq );
extern void writeDataforgaln( FILE *fp, int locnjob, char **name, int *nlen, char **aseq );
extern void writeData( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq );
extern void writeData_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq );
extern void readhat2_floathalf( FILE *fp, int nseq, char name[M][B], float **mtx );
extern void readhat2_floathalf_pointer( FILE *fp, int nseq, char **name, float **mtx );
extern void readhat2_float( FILE *fp, int nseq, char name[M][B], float **mtx );
extern void readhat2_int( FILE *fp, int nseq, char name[M][B], int **mtx );
extern void readhat2_pointer( FILE *fp, int nseq, char **name, double **mtx );
extern void readhat2( FILE *fp, int nseq, char name[M][B], double **mtx );
extern void WriteFloatHat2_pointer_halfmtx( FILE *hat2p, int locnjob, char **name, float **mtx );
extern void WriteFloatHat2( FILE *hat2p, int locnjob, char name[M][B], float **mtx );
extern void WriteHat2_int( FILE *hat2p, int locnjob, char name[M][B], int **mtx );
extern void WriteHat2( FILE *hat2p, int locnjob, char name[M][B], double **mtx );
extern void WriteHat2_pointer( FILE *hat2p, int locnjob, char **name, double **mtx );
extern int ReadFasta_sub( FILE *fp, double *dis, int nseq, char name[M][B] );
extern int ReadSsearch( FILE *fp, double *dis, int nseq, char name[M][B] );
extern int ReadBlastm7( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
extern int ReadBlastm7_scoreonly( FILE *fp, double *dis, int nin );
extern int ReadBlastm7_avscore( FILE *fp, double *dis, int nin );
extern int ReadFasta34noalign( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
extern int ReadFasta34m10_nuc( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
extern int ReadFasta34m10( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
extern int ReadFasta34m10_scoreonly_nuc( FILE *fp, double *dis, int nin );
extern int ReadFasta34m10_scoreonly( FILE *fp, double *dis, int nin );
extern int ReadFasta34( FILE *fp, double *dis, int nseq, char name[M][B], LocalHom *localhomlist );
extern int ReadFasta3( FILE *fp, double *dis, int nseq, char name[M][B] );
extern int ReadFasta( FILE *fp, double *dis, int nseq, char name[M][B] );
extern int ReadOpt( FILE *fp, int opt[M], int nseq, char name[M][B] );
extern int ReadOpt2( FILE *fp, int opt[M], int nseq, char name[M][B] );
extern int writePre( int nseq, char **name, int nlen[M], char **aseq, int force );
extern void readOtherOptions( int *ppidptr, int *fftThresholdptr, int *fftWinSizeptr );
extern void initSignalSM( void );
extern void initFiles( void );
extern void WriteForFasta( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq );
extern void readlocalhomtable( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec );
extern void readlocalhomtable2( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec );
extern void outlocalhom( LocalHom **localhom, int nseq );
extern void outlocalhompt( LocalHom ***localhom, int n1, int n2 );
extern void FreeLocalHomTable( LocalHom **localhomtable, int n ) ;
extern void constants( int nseq, char **seq );
extern void clustalout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, char *mark, char *comment, int *order, int namelen );
extern void phylipout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, int *order );
extern void writeData_reorder( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq, int *order );
extern void writeData_reorder_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq, int *order );
extern void resetlocalhom( int, LocalHom ** );
extern int load1SeqWithoutName_new( FILE *fpp, char *cbuf );
extern char *load1SeqWithoutName_realloc( FILE *fpp );
extern char *load1SeqWithoutName_realloc_casepreserve( FILE *fpp );
extern int disttbfast( char **in, int nlen[M], char name[M][B] );
extern void searchKUorWA( FILE *fp );
extern void gapireru( char *res, char *ori, char *gt );
extern int seqlen( char *seq );
extern void st_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len );
extern void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len );
extern void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len );
extern void st_FinalGapCount_zure( float *fgcp, int clus, char **seq, double *eff, int len );
extern void getdiaminofreq_x( float *freq, int clus, char **seq, double *eff, int len );
extern void new_FinalGapCount_zure( float *fgcp, int clus, char **seq, double *eff, int len, char *s, char *e );
extern void new_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len, char *g );
extern void new_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len, char *g );
extern void new_OpeningGapCount_zure( float *ogcp, int clus, char **seq, double *eff, int len, char *s, char *e );
extern void getGapPattern( float *fgcp, int clus, char **seq, double *eff, int len, char *g );
extern void getgapfreq( float *freq, int clus, char **seq, double *eff, int len );
extern void getgapfreq_zure( float *freq, int clus, char **seq, double *eff, int len );
//extern void getgapfreq_zure_part( float *freq, int clus, char **seq, double *eff, int len, char *s );
extern void getgapfreq_zure_part( float *freq, int clus, char **seq, double *eff, int len, char *s );
extern void getdiaminofreq_part( float *freq, int clus, char **seq, double *eff, int len, char *s, char *e );
extern void getdigapfreq_part( float *freq, int clus, char **seq, double *eff, int len, char *s, char *e );
extern void getdiaminofreq_st( float *freq, int clus, char **seq, double *eff, int len );
extern void getdigapfreq_st( float *freq, int clus, char **seq, double *eff, int len );
extern void st_getGapPattern( Gappat **gpat, int clus, char **seq, double *eff, int len );
extern void getkyokaigap( char *g, char **s, int pos, int n );
extern double *loadaamtx( void );
extern float naivepairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
extern float naivepairscore11( char *seq1, char *seq2, int penal );
extern float naiveQpairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
extern float naiveRpairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
extern float naiveHpairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
extern void foldrna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, float **impmtx, int *gapmap1, int *gapmap2, RNApair *pair );
extern void foldrna_gappick( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, float **impmtx, int *gapmap1, int *gapmap2, RNApair *pair );
extern void imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
extern void imp_rnaQ( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
extern void part_imp_rnaQ( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
extern void part_imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
extern void imp_rnaQ_gappick( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
extern void foldalignedrna( int clus1, int clus2, char **mseq1, char **mseq2, double *effarr1, double *effarr2, RNApair *rnapairboth );
void readmccaskill( FILE *fp, RNApair **pairprob, int length );
void makegrouprna( RNApair ***group, RNApair ***all, int *memlist );
void makegrouprnait( RNApair ***group, RNApair ***all, char **pair, int s );
extern void fixed_musclesupg_float_realloc_nobk_halfmtx( int nseq, float **eff, int ***topol, float **len, Treedep * );
extern void loadtree( int nseq, int ***topol, float **len, char **name, int *nlen, Treedep * );
extern void loadtop( int nseq, float **eff, int ***topol, float **len );
extern void fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( int nseq, float **eff, int ***topol, float **len, char **name, int *nlen, Treedep * );
extern void fixed_musclesupg_double_treeout( int nseq, double **eff, int ***topol, double **len, char **name );
extern void imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1kozo, double*eff2kozo, LocalHom ***localhom, int forscore );
extern void miyataout_reorder_pointer( FILE *fp, int locnjob, int nlenmax, char **name, int *nlen, char **aseq, int *order );
extern void veryfastsupg_double_outtree( int nseq, double **eff, int ***topol, double **len, char **name );
extern void cpmx_ribosum( char **seq, char **seqr, char *dir, float **cpmx, double *eff, int lgth, int clus );
extern void rnaalifoldcall( char **seq, int nseq, RNApair **pairprob );
extern void readpairfoldalign( FILE *fp, char *seq1, char *seq2, char *aln1, char *aln2, int q1, int q2, int *of1, int *of2, int sumlen );
extern void write1seq( FILE *fp, char *aseq );
extern void assignstrweight( int nseq, double *strweight, Node *stopol, int ***topol, int step, int LorR, char *kozoari, double *seqweight );
extern void cutData( FILE *, int **, char **, int * );
extern void cutAlignment( FILE *, int **, char **, int *, char **, char ** );
extern void catData( FILE * );
extern void getnumlen_nogap_outallreg_web( FILE *fp, FILE *ofp, int *nlenminpt, int *isalignedpt );
extern void getnumlen_nogap_outallreg( FILE *fp, int *nlenminpt );
extern double plainscore( int nseq, char **seq );
extern void eq2dash( char *s );
extern void findnewgaps( int n, char **seq, int *gaplen );
extern void findcommongaps( int, char **, int * );
extern void adjustgapmap( int, int *, char * );
extern void insertnewgaps( int njob, int *alreadyaligned, char **seq, int *ex1, int *ex2, int *gaplen, int *gapmap, int alloclen, char alg );
extern void restorecommongaps( int n, char **seq, int *top0, int *top1, int *gaplen, int alloclen );
extern int samemember( int *mem, int *cand );
extern int includemember( int *mem, int *cand );
extern void profilealignment( int n0, int n1, int n2, char **aln0, char **aln1, char **aln2, int alloclen, char alg );
|
