--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+
+
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ inputfile = 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;
+ RNAppenalty = NOTSPECIFIED;
+ RNApthr = 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 'o':
+ RNAppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'f':
+ ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'g':
+ ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'O':
+ ppenalty_OP = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'E':
+ ppenalty_EX = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --argc;
+ goto nextoption;
+ case 'h':
+ poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+ --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;
+ TMorJTT = JTT;
+ fprintf( stderr, "jtt %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'm':
+ pamN = atoi( *++argv );
+ scoremtx = 0;
+ TMorJTT = TM;
+ fprintf( stderr, "TM %d\n", pamN );
+ --argc;
+ goto nextoption;
+ case 'l':
+ ppslocal = (int)( atof( *++argv ) * 1000 + 0.5 );
+ pslocal = (int)( 600.0 / 1000.0 * ppslocal + 0.5);
+// fprintf( stderr, "ppslocal = %d\n", ppslocal );
+// fprintf( stderr, "pslocal = %d\n", pslocal );
+ --argc;
+ goto nextoption;
+#if 1
+ case 'a':
+ fmodel = 1;
+ break;
+#endif
+ case 'r':
+ fmodel = -1;
+ break;
+ case 'D':
+ dorp = 'd';
+ break;
+ case 'P':
+ dorp = 'p';
+ break;
+#if 0
+ case 'e':
+ fftscore = 0;
+ break;
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+ case 'R':
+ fftRepeatStop = 1;
+ break;
+#endif
+ case 'Q':
+ calledByXced = 1;
+ break;
+ case 's':
+ treemethod = 's';
+ break;
+ case 'x':
+ disp = 1;
+ break;
+ case 'p':
+ treemethod = 'p';
+ break;
+#if 0
+ case 'a':
+ alg = 'a';
+ break;
+#endif
+ case 'S':
+ alg = 'S';
+ break;
+ case 'L':
+ alg = 'L';
+ break;
+ case 'M':
+ alg = 'M';
+ break;
+ case 'R':
+ alg = 'R';
+ break;
+ case 'N':
+ alg = 'N';
+ break;
+ case 'A':
+ alg = 'A';
+ break;
+ case 'V':
+ alg = 'V';
+ break;
+ case 'C':
+ alg = 'C';
+ break;
+ case 'F':
+ use_fft = 1;
+ break;
+ case 'v':
+ tbrweight = 3;
+ break;
+ case 'd':
+ divpairscore = 1;
+ 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 );
+ }
+}
+
+int countamino( char *s, int end )
+{
+ int val = 0;
+ while( end-- )
+ if( *s++ != '-' ) val++;
+ return( val );
+}
+
+
+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;
+ static char **name, **seq, **useq;
+ static char **mseq1, **mseq2;
+ static char **aseq;
+ static char **bseq;
+ static double *eff;
+ int i;
+ FILE *infp;
+ char c;
+ int alloclen;
+ RNApair **pair1;
+ RNApair **pair2;
+ float **map;
+
+ arguments( argc, argv );
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ getnumlen( infp );
+ rewind( infp );
+
+ if( njob > M )
+ {
+ fprintf( stderr, "The number of sequences must be < %d\n", M );
+ fprintf( stderr, "Please try the splittbfast program for such large data.\n" );
+ exit( 1 );
+ }
+
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+
+ seq = AllocateCharMtx( njob, nlenmax*5+1 );
+ useq = 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;
+
+ pair1 = calloc( nlenmax*5+1, sizeof( RNApair *) );
+ pair2 = calloc( nlenmax*5+1, sizeof( RNApair *) );
+ map = AllocateFloatMtx( nlenmax+1, nlenmax );
+
+ eff = AllocateDoubleVec( njob );
+
+ readData_pointer( infp, name, nlen, seq );
+ fclose( infp );
+
+ for( i=0; i<njob; i++ ) strcpy( useq[i], seq[i] );
+
+ 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] );
+
+
+ fprintf( stderr, "folding group1\n" );
+// rnalocal( seq, useq, eff, eff, njob, njob, alloclen, pair1 );
+ rnaalifoldcall( seq, njob, pair1 );
+ exit( 1 );
+
+#if 0
+ fprintf( stderr, "folding group1\n" );
+ rnalocal( seq+1, useq+1, eff+1, eff+1, 1, 1, alloclen, pair2 );
+ fprintf( stderr, "aligning 1 and 2, phase 1\n" );
+ Lalignmm_hmout( seq, seq+1, eff, eff+1, 1, 1, alloclen, NULL, NULL, NULL, NULL, map );
+
+
+#if 0
+ lgth1 = strlen( seq[0] );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "\n" );
+ if( pair1[i].pos == -1 ) continue;
+ fprintf( stderr, "i=%d (%c):%d", i, seq[0][i], pair1[i].pos );
+ if( map12[pair1[i].pos].pos == -1 ) continue;
+ fprintf( stderr, "%c -> %c ", seq[0][pair1[i].pos], seq[1][map12[pair1[i].pos].pos] );
+ if( pair2[map12[pair1[i].pos].pos].pos == -1 ) continue;
+ fprintf( stderr, "%d:%d (%c)", map12[pair1[i].pos].pos, pair2[map12[pair1[i].pos].pos].pos, seq[1][pair2[map12[pair1[i].pos].pos].pos] );
+ }
+#endif
+
+
+ exit( 1 );
+
+
+ pairalign( name, nlen, bseq, aseq, mseq1, mseq2, eff, alloclen );
+ fprintf( trap_g, "done.\n" );
+#if DEBUG
+ fprintf( stderr, "closing trap_g\n" );
+#endif
+ fclose( trap_g );
+
+// writePre( njob, name, nlen, aseq, !contin );
+#if 0
+ writeData( stdout, njob, name, nlen, aseq );
+#endif
+#if IODEBUG
+ fprintf( stderr, "OSHIMAI\n" );
+#endif
+ SHOWVERSION;
+ return( 0 );
+#endif
+}
git://source.jalview.org / jabaws.git / blobdiff