--- /dev/null
+#include "mltaln.h"
+
+#define DEBUG 0
+
+
+static char *comment;
+static char *orderfile;
+static int format;
+static int namelen;
+
+static void fillspace( char *seq, int lenmax )
+{
+ int len = strlen( seq );
+ seq += len;
+ lenmax -= len;
+ while( lenmax-- ) *seq++ = ' ';
+ *seq = 0;
+}
+
+void setmark_clustal( int nlen, int nseq, char **seq, char *mark )
+{
+ int i, j, k;
+
+ char *strong[] = {
+ "STA",
+ "NEQK",
+ "NHQK",
+ "NDEQ",
+ "QHRK",
+ "MILV",
+ "MILF",
+ "HY",
+ "FYW",
+ };
+ int nstrong = 9;
+ char *weaker[] = {
+ "CSA",
+ "ATV",
+ "SAG",
+ "STNK",
+ "STPA",
+ "SGND",
+ "SNDEQK",
+ "NDEQHK",
+ "NEQHRK",
+ "FVLIM",
+ "HFY",
+ };
+ int nweaker = 11;
+
+ for( i=0; i<nlen; i++ )
+ {
+ mark[i] = ' ';
+ for( j=0; j<nseq; j++ )
+ if( '-' == seq[j][i] ) break;
+ if( j != nseq )
+ {
+ continue;
+ }
+ for( j=0; j<nseq; j++ )
+ if( toupper( seq[0][i] ) != toupper( seq[j][i] ) ) break;
+ if( j == nseq )
+ {
+ mark[i] = '*';
+ continue;
+ }
+ for( k=0; k<nstrong; k++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ if( !strchr( strong[k], toupper( seq[j][i] ) ) ) break;
+ }
+ if( j == nseq ) break;
+ }
+ if( k < nstrong )
+ {
+ mark[i] = ':';
+ continue;
+ }
+ for( k=0; k<nweaker; k++ )
+ {
+ for( j=0; j<nseq; j++ )
+ {
+ if( !strchr( weaker[k], toupper( seq[j][i] ) ) ) break;
+ }
+ if( j == nseq ) break;
+ }
+ if( k < nweaker )
+ {
+ mark[i] = '.';
+ continue;
+ }
+ }
+ mark[nlen] = 0;
+}
+
+void setmark( int nlen, int nseq, char **seq, char *mark )
+{
+ int i, j;
+
+ for( i=0; i<nlen; i++ )
+ {
+ mark[i] = ' ';
+ for( j=0; j<nseq; j++ )
+ if( '-' == seq[j][i] ) break;
+ if( j != nseq )
+ {
+ continue;
+ }
+ for( j=0; j<nseq; j++ )
+ if( seq[0][i] != seq[j][i] ) break;
+ if( j == nseq )
+ {
+ mark[i] = '*';
+ continue;
+ }
+ for( j=0; j<nseq; j++ )
+ if( amino_grp[(int)seq[0][i]] != amino_grp[(int)seq[j][i]] ) break;
+ if( j == nseq )
+ {
+ mark[i] = '.';
+ continue;
+ }
+ }
+ mark[nlen] = 0;
+}
+
+void arguments( int argc, char *argv[] )
+{
+ int c;
+ namelen = 15;
+ scoremtx = 1;
+ nblosum = 62;
+ dorp = NOTSPECIFIED;
+ kimuraR = NOTSPECIFIED;
+ pamN = NOTSPECIFIED;
+ inputfile = NULL;
+ comment = NULL;
+ orderfile = NULL;
+ format = 'c';
+
+ 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 'c':
+ comment = *++argv;
+ fprintf( stderr, "comment = %s\n", comment );
+ --argc;
+ goto nextoption;
+ case 'r':
+ orderfile = *++argv;
+ fprintf( stderr, "orderfile = %s\n", orderfile );
+ --argc;
+ goto nextoption;
+ case 'n':
+ namelen = atoi( *++argv );
+ fprintf( stderr, "namelen = %d\n", namelen );
+ --argc;
+ goto nextoption;
+ case 'f':
+ format = 'f';
+ break;
+ case 'y':
+ format = 'y';
+ break;
+ default:
+ fprintf( stderr, "illegal option %c\n", c );
+ argc = 0;
+ break;
+ }
+ }
+ nextoption:
+ ;
+ }
+ if( argc != 0 )
+ {
+ fprintf( stderr, "options: Check source file !\n" );
+ exit( 1 );
+ }
+}
+
+
+int main( int argc, char *argv[] )
+{
+ static int *nlen;
+ static char **name, **seq, *mark;
+ static int *order;
+ int i;
+ FILE *infp;
+ FILE *orderfp;
+ char gett[B];
+ int nlenmin;
+
+ arguments( argc, argv );
+
+
+ if( inputfile )
+ {
+ infp = fopen( inputfile, "r" );
+ if( !infp )
+ {
+ fprintf( stderr, "Cannot open %s\n", inputfile );
+ exit( 1 );
+ }
+ }
+ else
+ infp = stdin;
+
+ getnumlen_casepreserve( infp, &nlenmin );
+ rewind( infp );
+
+ seq = AllocateCharMtx( njob, nlenmax*2+1 );
+ mark = AllocateCharVec( nlenmax*2+1 );
+ order = AllocateIntVec( njob );
+ name = AllocateCharMtx( njob, B+1 );
+ nlen = AllocateIntVec( njob );
+
+
+ if( orderfile )
+ {
+ orderfp = fopen( orderfile, "r" );
+ if( !orderfile )
+ {
+ fprintf( stderr, "Cannot open %s\n", orderfile );
+ exit( 1 );
+ }
+ for( i=0; i<njob; i++ )
+ {
+ fgets( gett, B-1, orderfp );
+ order[i] = atoi( gett );
+ }
+ fclose( orderfp );
+ }
+ else
+ {
+ for( i=0; i<njob; i++ ) order[i] = i;
+ }
+
+ readData_pointer_casepreserve( infp, name, nlen, seq );
+ fclose( infp );
+
+ if( format == 'c' || format == 'y' ) for( i=0; i<njob; i++ ) fillspace( seq[i], nlenmax );
+ constants( njob, seq );
+
+// initSignalSM();
+
+// initFiles();
+
+
+
+// setmark( nlenmax, njob, seq, mark );
+ setmark_clustal( nlenmax, njob, seq, mark );
+
+ if( format == 'f' )
+ writeData_reorder_pointer( stdout, njob, name, nlen, seq, order );
+ else if( format == 'c' )
+ clustalout_pointer( stdout, njob, nlenmax, seq, name, mark, comment, order, namelen );
+ else if( format == 'y' )
+ phylipout_pointer( stdout, njob, nlenmax, seq, name, order );
+ else
+ fprintf( stderr, "Unknown format\n" );
+
+// SHOWVERSION;
+ return( 0 );
+}
git://source.jalview.org / jabaws.git / blobdiff