+++ /dev/null
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 1
-
-double corethr;
-int coreext;
-
-void arguments( int argc, char *argv[] )
-{
- int c;
-
- fftkeika = 1;
- constraint = 0;
- nblosum = 62;
- fmodel = 0;
- calledByXced = 0;
- devide = 0;
- use_fft = 0;
- fftscore = 1;
- fftRepeatStop = 0;
- fftNoAnchStop = 0;
- weight = 3;
- utree = 1;
- tbutree = 1;
- refine = 0;
- check = 1;
- cut = 0.0;
- disp = 0;
- outgap = 1;
- alg = 'A';
- mix = 0;
- tbitr = 0;
- scmtd = 5;
- tbweight = 0;
- tbrweight = 3;
- checkC = 0;
- treemethod = 'x';
- contin = 0;
- scoremtx = 0;
- kobetsubunkatsu = 0;
- dorp = NOTSPECIFIED;
- ppenalty = NOTSPECIFIED;
- ppenalty_ex = NOTSPECIFIED;
- poffset = NOTSPECIFIED;
- kimuraR = NOTSPECIFIED;
- pamN = NOTSPECIFIED;
- geta2 = GETA2;
- fftWinSize = NOTSPECIFIED;
- fftThreshold = NOTSPECIFIED;
- corethr = .5;
- coreext = 0;
-
- while( --argc > 0 && (*++argv)[0] == '-' )
- {
- while ( ( c = *++argv[0] ) )
- {
- switch( c )
- {
- case 'f':
- ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
- fprintf( stderr, "ppenalty = %d\n", ppenalty );
- --argc;
- goto nextoption;
- case 'g':
- ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
- fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
- --argc;
- goto nextoption;
- case 'h':
- poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
- fprintf( stderr, "poffset = %d\n", poffset );
- --argc;
- goto nextoption;
- case 'k':
- kimuraR = atoi( *++argv );
- fprintf( stderr, "kimuraR = %d\n", kimuraR );
- --argc;
- goto nextoption;
- case 'b':
- nblosum = atoi( *++argv );
- scoremtx = 1;
- fprintf( stderr, "blosum %d\n", nblosum );
- --argc;
- goto nextoption;
- case 'j':
- pamN = atoi( *++argv );
- scoremtx = 0;
- fprintf( stderr, "jtt %d\n", pamN );
- --argc;
- goto nextoption;
- case 'l':
- fastathreshold = atof( *++argv );
- constraint = 2;
- fprintf( stderr, "weighti = %f\n", fastathreshold );
- --argc;
- goto nextoption;
- case 'i':
- corethr = atof( *++argv );
- fprintf( stderr, "corethr = %f\n", corethr );
- --argc;
- goto nextoption;
- case 'm':
- fmodel = 1;
- break;
- case 'c':
- coreext = 1;
- break;
- case 'r':
- fmodel = -1;
- break;
- case 'D':
- dorp = 'd';
- break;
- case 'P':
- dorp = 'p';
- break;
- case 'e':
- fftscore = 0;
- break;
- case 'O':
- fftNoAnchStop = 1;
- break;
- case 'R':
- fftRepeatStop = 1;
- break;
- case 'Q':
- calledByXced = 1;
- break;
- case 's':
- treemethod = 's';
- break;
- case 'x':
- treemethod = 'x';
- break;
- case 'p':
- treemethod = 'p';
- break;
- case 'a':
- alg = 'a';
- break;
- case 'A':
- alg = 'A';
- break;
- case 'S':
- alg = 'S';
- break;
- case 'C':
- alg = 'C';
- break;
- case 'F':
- use_fft = 1;
- break;
- case 'v':
- tbrweight = 3;
- break;
- case 'd':
- disp = 1;
- break;
- case 'o':
- outgap = 0;
- break;
-/* Modified 01/08/27, default: user tree */
- case 'J':
- tbutree = 0;
- break;
-/* modification end. */
- case 'z':
- fftThreshold = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'w':
- fftWinSize = atoi( *++argv );
- --argc;
- goto nextoption;
- case 'Z':
- checkC = 1;
- break;
- default:
- fprintf( stderr, "illegal option %c\n", c );
- argc = 0;
- break;
- }
- }
- nextoption:
- ;
- }
- if( argc == 1 )
- {
- cut = atof( (*argv) );
- argc--;
- }
- if( argc != 0 )
- {
- fprintf( stderr, "options: Check source file !\n" );
- exit( 1 );
- }
- if( tbitr == 1 && outgap == 0 )
- {
- fprintf( stderr, "conflicting options : o, m or u\n" );
- exit( 1 );
- }
- if( alg == 'C' && outgap == 0 )
- {
- fprintf( stderr, "conflicting options : C, o\n" );
- exit( 1 );
- }
-}
-
-
-
-static void WriteOptions( FILE *fp )
-{
-
- if( dorp == 'd' ) fprintf( fp, "DNA\n" );
- else
- {
- if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
- else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
- else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
- }
- fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
- if( use_fft ) fprintf( fp, "FFT on\n" );
-
- fprintf( fp, "tree-base method\n" );
- if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
- else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
- if( tbitr || tbweight )
- {
- fprintf( fp, "iterate at each step\n" );
- if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
- if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
- if( tbweight ) fprintf( fp, " weighted\n" );
- fprintf( fp, "\n" );
- }
-
- fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
-
- if( alg == 'a' )
- fprintf( fp, "Algorithm A\n" );
- else if( alg == 'A' )
- fprintf( fp, "Algorithm A+\n" );
- else if( alg == 'S' )
- fprintf( fp, "Apgorithm S\n" );
- else if( alg == 'C' )
- fprintf( fp, "Apgorithm A+/C\n" );
- else
- fprintf( fp, "Unknown algorithm\n" );
-
- if( treemethod == 'x' )
- fprintf( fp, "Tree = UPGMA (3).\n" );
- else if( treemethod == 's' )
- fprintf( fp, "Tree = UPGMA (2).\n" );
- else if( treemethod == 'p' )
- fprintf( fp, "Tree = UPGMA (1).\n" );
- else
- fprintf( fp, "Unknown tree.\n" );
-
- if( use_fft )
- {
- fprintf( fp, "FFT on\n" );
- if( dorp == 'd' )
- fprintf( fp, "Basis : 4 nucleotides\n" );
- else
- {
- if( fftscore )
- fprintf( fp, "Basis : Polarity and Volume\n" );
- else
- fprintf( fp, "Basis : 20 amino acids\n" );
- }
- fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
- fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
- }
- else
- fprintf( fp, "FFT off\n" );
- fflush( fp );
-}
-
-
-int main( int argc, char *argv[] )
-{
- static int nlen[M];
- static char **name, **seq;
- static char **oseq;
- static double **pscore;
- static double *eff;
- static double **node0, **node1;
- static double *gapc;
- static double *avgap;
- double tmpavgap;
- int i, j, m, goffset;
- static int ***topol;
- static double **len;
- FILE *prep;
- char c;
- int corestart, coreend;
- int alloclen;
- int winsize;
- char *pt, *ot;
- double gapmin;
-
- arguments( argc, argv );
-
- getnumlen( stdin );
- rewind( stdin );
-
- if( njob < 2 )
- {
- fprintf( stderr, "At least 2 sequences should be input!\n"
- "Only %d sequence found.\n", njob );
- exit( 1 );
- }
-
- seq = AllocateCharMtx( njob, nlenmax*9+1 );
- name = AllocateCharMtx( njob, B+1 );
- oseq = AllocateCharMtx( njob, nlenmax*9+1 );
- alloclen = nlenmax*9;
-
- topol = AllocateIntCub( njob, 2, njob );
- len = AllocateDoubleMtx( njob, 2 );
- pscore = AllocateDoubleMtx( njob, njob );
- eff = AllocateDoubleVec( njob );
- node0 = AllocateDoubleMtx( njob, njob );
- node1 = AllocateDoubleMtx( njob, njob );
- gapc = AllocateDoubleVec( alloclen );
- avgap = AllocateDoubleVec( alloclen );
-
-#if 0
- Read( name, nlen, seq );
-#else
- readData_pointer( stdin, name, nlen, seq );
-#endif
-
- constants( njob, seq );
-
-#if 0
- fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
-#endif
-
- initSignalSM();
-
- initFiles();
-
- WriteOptions( trap_g );
-
- c = seqcheck( seq );
- if( c )
- {
- fprintf( stderr, "Illeagal character %c\n", c );
- exit( 1 );
- }
-
- writePre( njob, name, nlen, seq, 0 );
-
- if( tbutree == 0 )
- {
- for( i=1; i<njob; i++ )
- {
- if( nlen[i] != nlen[0] )
- {
- fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
- exit( 1 );
- }
- }
- for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
- {
- /*
- pscore[i][j] = (double)score_calc1( seq[i], seq[j] );
- */
- pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
- }
- }
- else
- {
- fprintf( stderr, "Loading 'hat2' ... " );
- prep = fopen( "hat2", "r" );
- if( prep == NULL ) ErrorExit( "Make hat2." );
- readhat2_pointer( prep, njob, name, pscore );
- fclose( prep );
- fprintf( stderr, "done.\n" );
-
-#if 0
- prep = fopen( "hat2_check", "w" );
- WriteHat2( prep, njob, name, pscore );
- fclose( prep );
-#endif
-
- }
-
- fprintf( stderr, "Constructing dendrogram ... " );
- if( treemethod == 'x' )
- supg( njob, pscore, topol, len );
- else if( treemethod == 's' )
- spg( njob, pscore, topol, len );
- else if( treemethod == 'p' )
- upg2( njob, pscore, topol, len );
- else
- ErrorExit( "Incorrect tree\n" );
- fprintf( stderr, "done.\n" );
-
- countnode( njob, topol, node0 );
- if( tbrweight )
- {
- weight = 3;
-#if 0
- utree = 0; counteff( njob, topol, len, eff ); utree = 1;
-#else
- counteff_simple( njob, topol, len, eff );
-#endif
- }
- else
- {
- for( i=0; i<njob; i++ ) eff[i] = 1.0;
- }
-
-
- for( i=0; i<nlenmax; i++ )
- {
- gapc[i] = 0.0;
- for( j=0; j<njob; j++ )
- {
- if( seq[j][i] == '-' ) gapc[i] += eff[j];
- }
- }
-
- gapmin = 1.0;
- winsize = fftWinSize;
- goffset = winsize/2;
- tmpavgap = 0.0;
- corestart = coreend = -1;
- for( i=0; i<winsize; i++ )
- {
- tmpavgap += gapc[i];
- }
- for( i=winsize; i<nlenmax; i++ )
- {
- m = i - goffset;
- avgap[m] = tmpavgap / winsize;
-// fprintf( stdout, "%d %f %f\n", m, avgap[m], gapc[i] );
- if( avgap[m] < corethr )
- {
- if( corestart == -1 )
- corestart = i - winsize;
-// fprintf( stdout, "ok, gapmin = %f, corestart = %d, coreend = %d\n", gapmin, corestart, coreend );
- if( avgap[m] < gapmin )
- {
- gapmin = avgap[m];
- }
- coreend = i;
- }
- tmpavgap -= gapc[i-winsize];
- tmpavgap += gapc[i];
- }
- if( corestart == -1 || coreend == -1 )
- {
- corestart = 0;
- coreend = nlenmax-1;
- }
-
- for( i=0; i<njob; i++ )
- {
- pt = oseq[i];
- m = winsize;
- while( m-- ) *pt++ = '-';
- for( j=corestart; j<=coreend; j++ )
- *pt++ = seq[i][j];
- m = winsize;
- while( m-- ) *pt++ = '-';
- *pt = 0;
-
- ot = oseq[i]+winsize-1;
- pt = seq[i]+corestart-1;
- if( coreext ) m = winsize;
- else m = 0;
- while( m && --pt > seq[i] )
- if( *pt != '-' )
- {
- *ot-- = *pt;
- m--;
- }
-
- ot = oseq[i]+winsize+coreend-corestart+1;
- pt = seq[i]+coreend;
- if( coreext ) m = winsize;
- else m = 0;
- while( m && *(++pt) )
- {
- if( *pt != '-' )
- {
- *ot++ = *pt;
- m--;
- }
- }
- fprintf( stdout, ">%s\n", name[i] );
- fprintf( stdout, "%s\n", oseq[i] );
- }
-
- exit( 1 );
-
- SHOWVERSION;
- return( 0 );
-}
git://source.jalview.org / jabaws.git / blobdiff