--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 1
+#define TSUYOSAFACTOR 100
+
+
+static char *pairfile;
+static int nhomologs;
+
+void strip( char *s )
+{
+ char *pt = s;
+ while( *++pt )
+ if( *pt == '\n' ) *pt = 0;
+}
+
+int searchused( char *q, char **keys, int n )
+{
+ int i;
+ for( i=0; i<n; i++ )
+ {
+// fprintf( stderr, "%s ? %s\n", q, names[i] );
+ if( !strcmp( q, keys[i] ) ) return( i );
+ }
+ return( -1 );
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ nhomologs = 2;
+ inputfile = NULL;
+ pairfile = NULL;
+ fftkeika = 0;
+ pslocal = -1000.0;
+ 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 = 1;
+ kobetsubunkatsu = 0;
+ divpairscore = 0;
+ dorp = NOTSPECIFIED;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_OP = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ ppenalty_EX = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ fftWinSize = NOTSPECIFIED;
+ fftThreshold = NOTSPECIFIED;
+
+ while( --argc > 0 && (*++argv)[0] == '-' )
+ {
+ while ( ( c = *++argv[0] ) )
+ {
+ switch( c )
+ {
+ case 'i':
+ inputfile = *++argv;
+ fprintf( stderr, "inputfile = %s\n", inputfile );
+ --argc;
+ goto nextoption;
+ case 'p':
+ pairfile = *++argv;
+ fprintf( stderr, "pairfile = %s\n", pairfile );
+ --argc;
+ goto nextoption;
+ case 't':
+ nhomologs = atoi( *++argv );
+ fprintf( stderr, "nhomologs = %d\n", nhomologs );
+ --argc;
+ goto nextoption;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ 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 );
+ }
+}
+
+int countamino( char *s, int end )
+{
+ int val = 0;
+ while( end-- )
+ if( *s++ != '-' ) val++;
+ return( val );
+}
+
+static void pairalign( char name[M][B], int nlen[M], char **seq, double *effarr, int alloclen )
+{
+ FILE *tmpfp;
+ static char dumm1[B], dumm0[B];
+ int i, j;
+ char *res;
+ FILE *hat3p;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ static char **pseq;
+ LocalHom **localhomtable, *tmpptr;
+ float pscore = 0.0; // by D.Mathog, aguess
+ char *aseq = NULL; // by D.Mathog
+ char **usedseqs = NULL; // by D.Mathog
+ char **usednames = NULL; // by D.Mathog
+ int nused;
+ double tsuyosa;
+
+ tsuyosa = (double)nhomologs * (nhomologs-1) / njob * TSUYOSAFACTOR;
+ fprintf( stderr, "tsuyosa = %f\n", tsuyosa );
+ localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+ for( i=0; i<njob; i++)
+ {
+ localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+ for( j=0; j<njob; j++)
+ {
+ localhomtable[i][j].start1 = -1;
+ localhomtable[i][j].end1 = -1;
+ localhomtable[i][j].start2 = -1;
+ localhomtable[i][j].end2 = -1;
+ localhomtable[i][j].opt = -1.0;
+ localhomtable[i][j].next = NULL;
+ }
+ }
+
+ if( effarr1 == NULL )
+ {
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ pseq = AllocateCharMtx( 2, nlenmax*9+1 );
+ aseq = AllocateCharVec( nlenmax*9+1 );
+ usedseqs = AllocateCharMtx( njob, nlenmax*9+1 );
+ usednames = AllocateCharMtx( njob, B );
+#if 0
+#else
+#endif
+ }
+
+#if 0
+ fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
+#endif
+
+#if 0
+ for( i=0; i<njob; i++ )
+ fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+
+// writePre( njob, name, nlen, aseq, 0 );
+
+ fprintf( stderr, "opening %s\n", pairfile );
+ tmpfp = fopen( pairfile, "r" );
+ if( !tmpfp )
+ {
+ fprintf( stderr, "Cannot open %s\n", pairfile );
+ exit( 1 );
+ }
+ searchKUorWA( tmpfp );
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ nused = 0;
+ while( 1 )
+ {
+ res = fgets( dumm0, B-1, tmpfp );
+ strip( dumm0 );
+ if( res == NULL )
+ {
+ break;
+ }
+ load1SeqWithoutName_new( tmpfp, pseq[0] );
+ gappick0( aseq, pseq[0] );
+ i = searchused( aseq, usedseqs, nused );
+ if( i == -1 )
+ {
+ strcpy( usednames[nused], dumm0+1 );
+ strcpy( usedseqs[nused], aseq );
+ i = nused;
+ nused++;
+ }
+ fprintf( stderr, "i = %d\n", i );
+
+ res = fgets( dumm1, B-1, tmpfp );
+ strip( dumm1 );
+ if( res == NULL )
+ {
+ fprintf( stderr, "ERROR: The number of sequences in %s must be even.\n", pairfile );
+ exit( 1 );
+ }
+ load1SeqWithoutName_new( tmpfp, pseq[1] );
+ gappick0( aseq, pseq[1] );
+ j = searchused( aseq, usedseqs, nused );
+ if( j == -1 )
+ {
+ strcpy( usednames[nused], dumm1+1 );
+ strcpy( usedseqs[nused], aseq );
+ j = nused;
+ nused++;
+ }
+ fprintf( stderr, "j = %d\n", j );
+
+ if( strlen( pseq[0] ) != strlen( pseq[1] ) )
+ {
+ fprintf( stderr, "Not aligned, %s - %s\n", dumm0, dumm1 );
+ exit( 1 );
+ }
+
+
+ fprintf( stderr, "adding %d-%d\n", i, j );
+ putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) );
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
+ }
+ }
+ fclose( tmpfp );
+ fclose( hat3p );
+
+ for( i=0; i<nused; i++ )
+ fprintf( stdout, ">%s\n%s\n", usednames[i], usedseqs[i] );
+
+
+#if 0
+ fprintf( stderr, "##### writing hat3\n" );
+ hat3p = fopen( "hat3", "w" );
+ if( !hat3p ) ErrorExit( "Cannot open hat3." );
+ ilim = njob-1;
+ for( i=0; i<ilim; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+ {
+ if( tmpptr->opt == -1.0 ) continue;
+ fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next );
+ }
+ }
+ }
+ fclose( hat3p );
+#endif
+#if DEBUG
+ fprintf( stderr, "calling FreeLocalHomTable\n" );
+#endif
+ FreeLocalHomTable( localhomtable, njob );
+#if DEBUG
+ fprintf( stderr, "done. FreeLocalHomTable\n" );
+#endif
+}
+
+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[M][B], **seq;
+ static char **bseq;
+ static double *eff;
+ int i;
+ char c;
+ int alloclen;
+ FILE *infp;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ if( !pairfile )
+ {
+ fprintf( stderr, "Usage: %s -p pairfile -i inputfile \n", argv[0] );
+ exit( 1 );
+ }
+
+ getnumlen( infp );
+ rewind( infp );
+
+ 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 );
+ bseq = AllocateCharMtx( njob, nlenmax*9+1 );
+ alloclen = nlenmax*9;
+
+ eff = AllocateDoubleVec( njob );
+
+#if 0
+ Read( name, nlen, seq );
+#else
+ readData( infp, name, nlen, seq );
+#endif
+ fclose( infp );
+
+ 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 );
+
+ for( i=0; i<njob; i++ ) eff[i] = 1.0;
+
+
+ for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+
+ pairalign( name, nlen, bseq, eff, alloclen );
+
+ fprintf( trap_g, "done.\n" );
+#if DEBUG
+ fprintf( stderr, "closing trap_g\n" );
+#endif
+ fclose( trap_g );
+
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+}
git://source.jalview.org / jabaws.git / blobdiff