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