--- /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