--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+
+static char *whereispairalign;
+static char *laraparams;
+static char foldalignopt[1000];
+
+static void t2u( char *seq )
+{
+ while( *seq )
+ {
+ if ( *seq == 'A' ) *seq = 'a';
+ else if( *seq == 'a' ) *seq = 'a';
+ else if( *seq == 'T' ) *seq = 'u';
+ else if( *seq == 't' ) *seq = 'u';
+ else if( *seq == 'U' ) *seq = 'u';
+ else if( *seq == 'u' ) *seq = 'u';
+ else if( *seq == 'G' ) *seq = 'g';
+ else if( *seq == 'g' ) *seq = 'g';
+ else if( *seq == 'C' ) *seq = 'c';
+ else if( *seq == 'c' ) *seq = 'c';
+ else *seq = 'n';
+ seq++;
+ }
+}
+
+static float recallpairfoldalign( char **mseq1, char **mseq2, int m1, int m2, int *of1pt, int *of2pt, int alloclen )
+{
+ static FILE *fp = NULL;
+ float value;
+ char *aln1;
+ char *aln2;
+ int of1tmp, of2tmp;
+
+ if( fp == NULL )
+ {
+ fp = fopen( "_foldalignout", "r" );
+ if( fp == NULL )
+ {
+ fprintf( stderr, "Cannot open _foldalignout\n" );
+ exit( 1 );
+ }
+ }
+
+ aln1 = calloc( alloclen, sizeof( char ) );
+ aln2 = calloc( alloclen, sizeof( char ) );
+
+ readpairfoldalign( fp, *mseq1, *mseq2, aln1, aln2, m1, m2, &of1tmp, &of2tmp, alloclen );
+
+ if( strstr( foldalignopt, "-global") )
+ {
+ fprintf( stderr, "Calling G__align11\n" );
+ value = G__align11( mseq1, mseq2, alloclen );
+ *of1pt = 0;
+ *of2pt = 0;
+ }
+ else
+ {
+ fprintf( stderr, "Calling L__align11\n" );
+ value = L__align11( mseq1, mseq2, alloclen, of1pt, of2pt );
+ }
+
+// value = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame
+
+ if( aln1[0] == 0 )
+ {
+ fprintf( stderr, "FOLDALIGN returned no alignment between %d and %d. Sequence alignment is used instead.\n", m1+1, m2+1 );
+ }
+ else
+ {
+ strcpy( *mseq1, aln1 );
+ strcpy( *mseq2, aln2 );
+ *of1pt = of1tmp;
+ *of2pt = of2tmp;
+ }
+
+// value = naivepairscore11( *mseq1, *mseq2, penalty ); // v6.511 ha kore wo tsukau, global nomi dakara.
+
+// fclose( fp ); // saigo dake yatta houga yoi.
+
+// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+
+
+ free( aln1 );
+ free( aln2 );
+
+ return( value );
+}
+
+static void callfoldalign( int nseq, char **mseq )
+{
+ FILE *fp;
+ int i;
+ int res;
+ static char com[10000];
+
+ for( i=0; i<nseq; i++ )
+ t2u( mseq[i] );
+
+ fp = fopen( "_foldalignin", "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _foldalignin\n" );
+ exit( 1 );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ fprintf( fp, ">%d\n", i+1 );
+ fprintf( fp, "%s\n", mseq[i] );
+ }
+ fclose( fp );
+
+ sprintf( com, "env PATH=%s foldalign210 %s _foldalignin > _foldalignout ", whereispairalign, foldalignopt );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in foldalign\n" );
+ exit( 1 );
+ }
+
+}
+
+static void calllara( int nseq, char **mseq, char *laraarg )
+{
+ FILE *fp;
+ int i;
+ int res;
+ static char com[10000];
+
+ for( i=0; i<nseq; i++ )
+
+ fp = fopen( "_larain", "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _larain\n" );
+ exit( 1 );
+ }
+ for( i=0; i<nseq; i++ )
+ {
+ fprintf( fp, ">%d\n", i+1 );
+ fprintf( fp, "%s\n", mseq[i] );
+ }
+ fclose( fp );
+
+
+// fprintf( stderr, "calling LaRA\n" );
+ sprintf( com, "env PATH=%s:/bin:/usr/bin mafft_lara -i _larain -w _laraout -o _lara.params %s", whereispairalign, laraarg );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in lara\n" );
+ exit( 1 );
+ }
+}
+
+static float recalllara( char **mseq1, char **mseq2, int alloclen )
+{
+ static FILE *fp = NULL;
+ static char *ungap1;
+ static char *ungap2;
+ static char *ori1;
+ static char *ori2;
+ int res;
+ static char com[10000];
+ float value;
+
+
+ if( fp == NULL )
+ {
+ fp = fopen( "_laraout", "r" );
+ if( fp == NULL )
+ {
+ fprintf( stderr, "Cannot open _laraout\n" );
+ exit( 1 );
+ }
+ ungap1 = AllocateCharVec( alloclen );
+ ungap2 = AllocateCharVec( alloclen );
+ ori1 = AllocateCharVec( alloclen );
+ ori2 = AllocateCharVec( alloclen );
+ }
+
+
+ strcpy( ori1, *mseq1 );
+ strcpy( ori2, *mseq2 );
+
+ fgets( com, 999, fp );
+ myfgets( com, 9999, fp );
+ strcpy( *mseq1, com );
+ myfgets( com, 9999, fp );
+ strcpy( *mseq2, com );
+
+ gappick0( ungap1, *mseq1 );
+ gappick0( ungap2, *mseq2 );
+ t2u( ungap1 );
+ t2u( ungap2 );
+
+ if( strcmp( ungap1, ori1 ) || strcmp( ungap2, ori2 ) )
+ {
+ fprintf( stderr, "SEQUENCE CHANGED!!\n" );
+ fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+ fprintf( stderr, "ungap1 = %s\n", ungap1 );
+ fprintf( stderr, "ori1 = %s\n", ori1 );
+ fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+ fprintf( stderr, "ungap2 = %s\n", ungap2 );
+ fprintf( stderr, "ori2 = %s\n", ori2 );
+ exit( 1 );
+ }
+
+ value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+
+// fclose( fp ); // saigo dake yatta houga yoi.
+
+ return( value );
+}
+
+static float callmxscarna( char **mseq1, char **mseq2, int alloclen )
+{
+ FILE *fp;
+ int res;
+ static char com[10000];
+ float value;
+
+
+ t2u( *mseq1 );
+ t2u( *mseq2 );
+ fp = fopen( "_mxscarnain", "w" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _mxscarnain\n" );
+ exit( 1 );
+ }
+ fprintf( fp, ">1\n" );
+ fprintf( fp, "%s\n", *mseq1 );
+ fprintf( fp, ">2\n" );
+ fprintf( fp, "%s\n", *mseq2 );
+ fclose( fp );
+
+ sprintf( com, "env PATH=%s mxscarna _mxscarnain > _mxscarnaout 2>/dev/null", whereispairalign );
+ res = system( com );
+ if( res )
+ {
+ fprintf( stderr, "Error in mxscarna\n" );
+ exit( 1 );
+ }
+
+ fp = fopen( "_mxscarnaout", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _mxscarnaout\n" );
+ exit( 1 );
+ }
+
+ fgets( com, 999, fp );
+ load1SeqWithoutName_new( fp, *mseq1 );
+ fgets( com, 999, fp );
+ load1SeqWithoutName_new( fp, *mseq2 );
+
+ fclose( fp );
+
+// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
+// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
+
+ value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
+
+ return( value );
+}
+
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+
+ foldalignopt[0] = 0;
+ laraparams = NULL;
+ 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 '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;
+ case 'd':
+ whereispairalign = *++argv;
+ fprintf( stderr, "whereispairalign = %s\n", whereispairalign );
+ --argc;
+ goto nextoption;
+ case 'p':
+ laraparams = *++argv;
+ fprintf( stderr, "laraparams = %s\n", laraparams );
+ --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;
+ case 'e':
+ fftscore = 0;
+ break;
+#if 0
+ case 'O':
+ fftNoAnchStop = 1;
+ break;
+#endif
+ case 'Q':
+ calledByXced = 1;
+ break;
+ case 'x':
+ disp = 1;
+ break;
+#if 0
+ case 'a':
+ alg = 'a';
+ break;
+#endif
+ case 'S':
+ alg = 'S';
+ break;
+ case 'L':
+ alg = 'L';
+ break;
+ case 's':
+ alg = 's';
+ break;
+ case 'B':
+ alg = 'B';
+ break;
+ case 'T':
+ alg = 'T';
+ break;
+ case 'H':
+ alg = 'H';
+ 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 'y':
+ divpairscore = 1;
+ break;
+/* Modified 01/08/27, default: user tree */
+ case 'J':
+ tbutree = 0;
+ break;
+/* modification end. */
+ case 'o':
+// foldalignopt = *++argv;
+ strcat( foldalignopt, " " );
+ strcat( foldalignopt, *++argv );
+ fprintf( stderr, "foldalignopt = %s\n", foldalignopt );
+ --argc;
+ goto nextoption;
+ 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 pairalign( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *effarr, int alloclen )
+{
+ int i, j, ilim;
+ int clus1, clus2;
+ int off1, off2;
+ float pscore = 0.0; // by D.Mathog
+ static char *indication1, *indication2;
+ FILE *hat2p, *hat3p;
+ static double **distancemtx;
+ static double *effarr1 = NULL;
+ static double *effarr2 = NULL;
+ char *pt;
+ char *hat2file = "hat2";
+ LocalHom **localhomtable, *tmpptr;
+ static char **pair;
+ int intdum;
+ double bunbo;
+
+ 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;
+ localhomtable[i][j].nokori = 0;
+ }
+ }
+
+ if( effarr1 == NULL )
+ {
+ distancemtx = AllocateDoubleMtx( njob, njob );
+ effarr1 = AllocateDoubleVec( njob );
+ effarr2 = AllocateDoubleVec( njob );
+ indication1 = AllocateCharVec( 150 );
+ indication2 = AllocateCharVec( 150 );
+#if 0
+#else
+ pair = AllocateCharMtx( njob, njob );
+#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 );
+
+ 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;
+
+ if( alg == 'H' )
+ {
+ fprintf( stderr, "Calling FOLDALIGN with option '%s'\n", foldalignopt );
+ callfoldalign( njob, seq );
+ fprintf( stderr, "done.\n" );
+ }
+ if( alg == 'B' )
+ {
+ fprintf( stderr, "Calling LARA\n" );
+ calllara( njob, seq, "" );
+ fprintf( stderr, "done.\n" );
+ }
+ if( alg == 'T' )
+ {
+ fprintf( stderr, "Calling SLARA\n" );
+ calllara( njob, seq, "-s" );
+ fprintf( stderr, "done.\n" );
+ }
+
+ ilim = njob - 1;
+ for( i=0; i<ilim; i++ )
+ {
+ fprintf( stderr, "% 5d / %d\r", i, njob );
+ for( j=i+1; j<njob; j++ )
+ {
+
+ if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
+ {
+ distancemtx[i][j] = pscore;
+ continue;
+ }
+
+ strcpy( aseq[i], seq[i] );
+ strcpy( aseq[j], seq[j] );
+ clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
+ clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
+ // fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
+ // fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
+
+#if 0
+ fprintf( stderr, "group1 = %.66s", indication1 );
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "group2 = %.66s", indication2 );
+ fprintf( stderr, "\n" );
+#endif
+ // for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
+
+#if 1
+ if( use_fft )
+ {
+ pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
+ off1 = off2 = 0;
+ }
+ else
+#endif
+ {
+ switch( alg )
+ {
+ case( 'a' ):
+ pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
+ off1 = off2 = 0;
+ break;
+ case( 'A' ):
+ pscore = G__align11( mseq1, mseq2, alloclen, NULL, 0, NULL );
+ off1 = off2 = 0;
+ break;
+#if 0
+ case( 'V' ):
+ pscore = VAalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j );
+ fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore );
+ break;
+ case( 'S' ):
+ fprintf( stderr, "aligning %d-%d\n", i, j );
+ pscore = suboptalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j );
+ fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore );
+ break;
+#endif
+ case( 'N' ):
+ pscore = genL__align11( mseq1, mseq2, alloclen, &off1, &off2 );
+// fprintf( stderr, "pscore = %f\n", pscore );
+ break;
+ case( 'L' ):
+ pscore = L__align11( mseq1, mseq2, alloclen, &off1, &off2 );
+// fprintf( stderr, "pscore (1) = %f\n", pscore );
+// pscore = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame
+// fprintf( stderr, "pscore (2) = %f\n\n", pscore );
+ break;
+ case( 'H' ):
+ pscore = recallpairfoldalign( mseq1, mseq2, i, j, &off1, &off2, alloclen );
+ break;
+ case( 'B' ):
+ case( 'T' ):
+ pscore = recalllara( mseq1, mseq2, alloclen );
+ off1 = off2 = 0;
+// fprintf( stderr, "lara, pscore = %f\n", pscore );
+ break;
+ case( 's' ):
+ pscore = callmxscarna( mseq1, mseq2, alloclen );
+ off1 = off2 = 0;
+// fprintf( stderr, "scarna, pscore = %f\n", pscore );
+ break;
+ case( 'M' ):
+// pscore = MSalign11( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL );
+ pscore = MSalign11( mseq1, mseq2, alloclen );
+// fprintf( stderr, "pscore = %f\n", pscore );
+ break;
+ ErrorExit( "ERROR IN SOURCE FILE" );
+ }
+ }
+ distancemtx[i][j] = pscore;
+#if SCOREOUT
+ fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
+#endif
+// fprintf( stderr, "pslocal = %d\n", pslocal );
+// offset = makelocal( *mseq1, *mseq2, pslocal );
+#if 0
+ fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
+ fprintf( stderr, ">%d\n%s\n>%d\n%s\n>\n", i, mseq1[0], j, mseq2[0] );
+#endif
+
+// putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, countamino( *mseq1, off1 ), countamino( *mseq2, off2 ), pscore, strlen( mseq1[0] ) );
+// fprintf( stderr, "pscore = %f\n", pscore );
+ if( alg == 'H' )
+// if( alg == 'H' || alg == 's' || alg == 'B' ) // next version
+ putlocalhom_ext( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
+ else if( alg != 'S' && alg != 'V' )
+ putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
+ }
+ }
+ for( i=0; i<njob; i++ )
+ {
+ pscore = 0.0;
+ for( pt=seq[i]; *pt; pt++ )
+ pscore += amino_dis[(int)*pt][(int)*pt];
+ distancemtx[i][i] = pscore;
+
+ }
+
+ ilim = njob-1;
+ for( i=0; i<ilim; i++ )
+ {
+ for( j=i+1; j<njob; j++ )
+ {
+ bunbo = MIN( distancemtx[i][i], distancemtx[j][j] );
+ if( bunbo == 0.0 )
+ distancemtx[i][j] = 2.0;
+ else
+ distancemtx[i][j] = ( 1.0 - distancemtx[i][j] / bunbo ) * 2.0;
+ }
+ }
+
+ hat2p = fopen( hat2file, "w" );
+ if( !hat2p ) ErrorExit( "Cannot open hat2." );
+ WriteHat2( hat2p, njob, name, distancemtx );
+ fclose( hat2p );
+
+ 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 %7.5f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
+ }
+ }
+ }
+ fclose( hat3p );
+#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( 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 **mseq1, **mseq2;
+ static char **aseq;
+ static char **bseq;
+ static double *eff;
+ int i;
+ FILE *infp;
+ char c;
+ int alloclen;
+
+ 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 < 2 )
+ {
+ fprintf( stderr, "At least 2 sequences should be input!\n"
+ "Only %d sequence found.\n", njob );
+ exit( 1 );
+ }
+ 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 );
+ }
+
+ seq = AllocateCharMtx( njob, nlenmax*9+1 );
+ aseq = AllocateCharMtx( njob, nlenmax*9+1 );
+ bseq = AllocateCharMtx( njob, nlenmax*9+1 );
+ mseq1 = AllocateCharMtx( njob, 0 );
+ mseq2 = AllocateCharMtx( njob, 0 );
+ 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, "Illegal 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, 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 );
+}
git://source.jalview.org / jabaws.git / blobdiff