| 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_calc3( char **seq, int s, double **eff, int ex ); |
| 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 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( 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 conjuction( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char name[M][B], char aname[M][B], 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[M][B], int nlen[M], char **aseq, char **bseq, int ***topol, double **len, int alloclen, LocalHom **localhomtable, RNApair ***single ); |
| 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 * ); |
| 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 ); |
| 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 ); |
| extern float Falign_udpari_long( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int alloclen, int *fftlog ); |
| 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, 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 * ); |
| 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 MSalign11( char **seq1, char **seq2, int alloclen ); |
| extern float G__align11( char **seq1, char **seq2, int alloclen ); |
| 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_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( FILE *fp, 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_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( FILE *fp, int nseq, char name[M][B], double **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 WriteHat2plain( FILE *hat2p, int locnjob, 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[][B], 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 ); |
| extern void readlocalhomtable2( FILE*fp, int njob, LocalHom **localhomtable ); |
| 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 ); |
| 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 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 int 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 ); |
| extern void loadtree( int nseq, int ***topol, float **len, char **name, int *nlen ); |
| 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 ); |
| extern void imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, 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[][B] ); |
| 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 ); |
| |
