+++ /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