--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ 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 = 'C';
+ mix = 0;
+ tbitr = 0;
+ scmtd = 5;
+ tbweight = 0;
+ tbrweight = 3;
+ checkC = 0;
+ treemethod = 'x';
+ contin = 0;
+ ppenalty = NOTSPECIFIED;
+ ppenalty_ex = NOTSPECIFIED;
+ poffset = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ geta2 = GETA2;
+ scoremtx = NOTSPECIFIED;
+
+ 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 'D':
+ scoremtx = -1;
+ break;
+ case 'P':
+ scoremtx = 0;
+ break;
+ case 'i':
+ contin = 1;
+ 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':
+ 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 );
+ }
+ readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
+}
+
+
+void treebase( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double **mtx, int ***topol, double **len, double **eff, int alloclen )
+{
+ int i, j, l;
+ int clus1, clus2;
+ int s1, s2, r1, r2;
+ float pscore;
+ static char *indication1, *indication2;
+ static char **name1, **name2;
+ static double **partialmtx = NULL;
+ static int ***partialtopol = NULL;
+ static double **partiallen = NULL;
+ static double **partialeff = NULL;
+ static double *effarr = NULL;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+#if 0
+ char pair[njob][njob];
+#else
+ static char **pair;
+#endif
+ if( partialtopol == NULL )
+ {
+ partialmtx = AllocateDoubleMtx( njob, njob );
+ partialtopol = AllocateIntCub( njob, 2, njob );
+ partialeff = AllocateDoubleMtx( njob, njob );
+ partiallen = AllocateDoubleMtx( njob, 2 );
+ effarr = AllocateDoubleVec( njob );
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( njob*3+100 );
+ indication2 = AllocateCharVec( njob*3+100 );
+ name1 = AllocateCharMtx( njob, B+1 );
+ name2 = AllocateCharMtx( njob, B+1 );
+#if 0
+#else
+ pair = AllocateCharMtx( njob, njob );
+#endif
+ }
+
+ if( checkC )
+ for( i=0; i<njob; i++ ) fprintf( stderr, "eff in tb-%d %f\n", i, eff[i][i] );
+
+ for( i=0; i<njob; i++ ) effarr[i] = eff[i][i];
+ for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
+
+ if( checkC )
+ for( i=0; i<njob; i++ ) fprintf( stderr, "effarr for aseq-%d %f\n", i, effarr[i] );
+
+ writePre( njob, name, nlen, aseq, 0 );
+
+ for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
+ for( i=0; i<njob; i++ ) pair[i][i] = 1;
+ for( l=0; l<njob-1; l++ )
+ {
+ s1 = topol[l][0][0];
+ for( i=0; (r1=topol[l][0][i])>-1; i++ )
+ if( pair[s1][r1] != 1 ) exit( 1 );
+ s2 = topol[l][1][0];
+ for( i=0; (r2=topol[l][1][i])>-1; i++ )
+ if( pair[s2][r2] != 1 ) exit( 1 );
+
+ clus1 = conjuction( pair, s1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
+ clus2 = conjuction( pair, s2, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
+ fprintf( trap_g, "\nSTEP-%d\n", l );
+ fprintf( trap_g, "group1 = %s\n", indication1 );
+ fprintf( trap_g, "group2 = %s\n", indication2 );
+
+ fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
+ fprintf( stderr, "\n" );
+
+ if( checkC )
+ for( i=0; i<clus1; i++ ) fprintf( stderr, "STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
+/*
+ fprintf( stderr, "before align all\n" );
+ display( aseq, njob );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 1 %s \n", indication1 );
+ display( mseq1, clus1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "before align 2 %s \n", indication2 );
+ display( mseq2, clus2 );
+ fprintf( stderr, "\n" );
+*/
+
+ pscore = Fgetlag( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
+
+ for( i=0; (r2=topol[l][1][i])>-1; i++ )
+ {
+ pair[s1][r2] = 1;
+ pair[s2][r2] = 0;
+ }
+
+ writePre( njob, name, nlen, aseq, 0 );
+
+ if( disp ) display( aseq, njob );
+ fprintf( stderr, "\n" );
+
+ }
+}
+
+static void WriteOptions( FILE *fp )
+{
+ 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" );
+ }
+ if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+ else if( scoremtx == 1 ) fprintf( fp, "Dayhoff( machigai ga aru )\n" );
+ else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
+ else if( scoremtx == -1 ) fprintf( fp, "DNA\n" );
+
+ if( scoremtx == 0 || scoremtx == -1 )
+ fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+ else
+ fprintf( fp, "Gap Penalty = %+5.2f\n", (double)ppenalty/1000 );
+
+ if( alg == 'a' )
+ fprintf( fp, "Algorithm A\n" );
+ else if( alg == 'A' )
+ fprintf( fp, "Apgorithm 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( scoremtx == -1 )
+ 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 **mseq1, **mseq2;
+ static char **aseq;
+ static char **bseq;
+ static double **pscore;
+ static double **eff;
+ static double **node0, **node1;
+ int i, j;
+ static int ***topol;
+ static double **len;
+ FILE *prep;
+ char c;
+ int alloclen;
+
+ arguments( argc, argv );
+ getnumlen( stdin );
+ rewind( stdin );
+
+ name = AllocateCharMtx( njob, B+1 );
+ seq = AllocateCharMtx( njob, nlenmax*5+1 );
+ aseq = AllocateCharMtx( njob, nlenmax*5+1 );
+ bseq = AllocateCharMtx( njob, nlenmax*5+1 );
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ alloclen = nlenmax*5;
+
+ topol = AllocateIntCub( njob, 2, njob );
+ len = AllocateDoubleMtx( njob, 2 );
+ pscore = AllocateDoubleMtx( njob, njob );
+ eff = AllocateDoubleMtx( njob, njob );
+ node0 = AllocateDoubleMtx( njob, njob );
+ node1 = AllocateDoubleMtx( njob, njob );
+
+#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;
+ utree = 0; counteff( njob, topol, len, eff ); utree = 1;
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) eff[i][i] = 1.0;
+ }
+
+
+ for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+ treebase( name, nlen, bseq, aseq, mseq1, mseq2, pscore, topol, len, eff, alloclen );
+
+ fprintf( trap_g, "done\n" );
+ fclose( trap_g );
+
+ writePre( njob, name, nlen, aseq, !contin );
+ writeData_pointer( stdout, njob, name, nlen, aseq );
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+}
git://source.jalview.org / jabaws.git / blobdiff