char creverse( char f )
{
- static char *table = NULL;
+ static TLS char *table = NULL;
+
+ if( f == 0 )
+ {
+ free( table );
+ table = NULL;
+ return( 0 );
+ }
+
if( table == NULL )
{
+ int i;
table = AllocateCharVec(0x80);
+ for( i=0; i<0x80; i++ ) table[i] = i;
+ table['A'] = 'T';
+ table['C'] = 'G';
+ table['G'] = 'C';
+ table['T'] = 'A';
+ table['U'] = 'A';
+ table['M'] = 'K';
+ table['R'] = 'Y';
+ table['W'] = 'W';
+ table['S'] = 'S';
+ table['Y'] = 'R';
+ table['K'] = 'M';
+ table['V'] = 'B';
+ table['H'] = 'D';
+ table['D'] = 'H';
+ table['B'] = 'V';
+ table['N'] = 'N';
table['a'] = 't';
table['c'] = 'g';
table['g'] = 'c';
table['d'] = 'h';
table['b'] = 'v';
table['n'] = 'n';
- table['-'] = '-';
- table['.'] = '.';
- table['*'] = '*';
+// table['-'] = '-';
+// table['.'] = '.';
+// table['*'] = '*';
}
return( table[(int)f] );
}
-static int addlocalhom_r( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, int skip )
+static int addlocalhom_r( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, int skip, char korh )
{
int pos1, pos2, start1, start2, end1, end2;
char *pt1, *pt2;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
#if 1
sumscore += score;
start1 = pos1; start2 = pos2;
st = 1;
}
- score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]];
+ score += (double)n_dis[(int)amino_n[(unsigned char)*pt1]][(int)amino_n[(unsigned char)*pt2]];
// fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
}
if( *pt1++ != '-' ) pos1++;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
#if 1
sumscore += score;
}
return( nlocalhom );
}
-void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, char korh )
{
int pos1, pos2, start1, start2, end1, end2;
char *pt1, *pt2;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
#if 1
if( divpairscore )
start1 = pos1; start2 = pos2;
st = 1;
}
- score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
+ score += (double)n_dis[(int)amino_n[(unsigned char)*pt1]][(int)amino_n[(unsigned char)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
// fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
}
if( *pt1++ != '-' ) pos1++;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
#if 1
}
}
}
-void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, char korh )
{
int pos1, pos2, start1, start2, end1, end2;
char *pt1, *pt2;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
#if 1
if( divpairscore )
start1 = pos1; start2 = pos2;
st = 1;
}
- iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
+ iscore += n_dis[(int)amino_n[(unsigned char)*pt1]][(int)amino_n[(unsigned char)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
// fprintf( stderr, "%c-%c, iscore(0) = %d\n", *pt1, *pt2, iscore );
}
if( *pt1++ != '-' ) pos1++;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
#if 1
if( divpairscore )
}
}
-void putlocalhom_str( char *al1, char *al2, double *equiv, double scale, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+void putlocalhom_str( char *al1, char *al2, double *equiv, double scale, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, char korh )
{
int posinaln, pos1, pos2, start1, start2, end1, end2;
char *pt1, *pt2;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
tmppt->overlapaa = 1;
// tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
}
}
-void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+
+
+void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, char korh )
{
int pos1, pos2, start1, start2, end1, end2;
char *pt1, *pt2;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
+ tmppt->nokori += 1;
+ localhompt->last = tmppt;
#if 1
if( divpairscore )
start1 = pos1; start2 = pos2;
st = 1;
}
- iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
+ iscore += n_dis[(int)amino_n[(unsigned char)*pt1]][(int)amino_n[(unsigned char)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
// fprintf( stderr, "%c-%c, iscore(0) = %d\n", *pt1, *pt2, iscore );
}
if( *pt1++ != '-' ) pos1++;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
+ tmppt->nokori += 1;
+ localhompt->last = tmppt;
#if 1
if( divpairscore )
}
}
}
-void putlocalhom( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+
+#if 0
+void putlocalhom( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, char korh )
{
int pos1, pos2, start1, start2, end1, end2;
char *pt1, *pt2;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
#if 1
if( divpairscore )
start1 = pos1; start2 = pos2;
st = 1;
}
- score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
+ score += (double)n_dis[(int)amino_n[(unsigned char)*pt1]][(int)amino_n[(unsigned char)*pt2]]; // - offset ¤Ï¤¤¤é¤Ê¤¤¤«¤â
// fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
}
if( *pt1++ != '-' ) pos1++;
tmppt->start2 = start2;
tmppt->end1 = end1 ;
tmppt->end2 = end2 ;
+ tmppt->korh = korh ;
#if 1
if( divpairscore )
}
}
}
+#endif
char *cutal( char *al, int al_display_start, int start, int end )
{
else strncpy( str1, str2, len );
}
-void seqUpper( int nseq, char **seq ) /* not used */
+void seqUpper( int nseq, char **seq )
{
int i, j, len;
for( i=0; i<nseq; i++ )
return( 0 );
}
-float input_new( FILE *fp, int d )
+double input_new( FILE *fp, int d )
{
char mojiretsu[10];
int i, c;
ungetc( c, fp );
}
+#if 0
static int onlyGraph( char *str )
{
char tmp;
while( (tmp=*str++) )
{
if( 0x20 < tmp && tmp < 0x7f ) *res++ = tmp;
- if( tmp == '>' )
+ if( tmp == '>' || tmp == '(' )
{
fprintf( stderr, "========================================================\n" );
fprintf( stderr, "========================================================\n" );
fprintf( stderr, "=== \n" );
fprintf( stderr, "=== ERROR!! \n" );
- fprintf( stderr, "=== In the '--anysymbol' and '--preservecase' modes, \n" );
- fprintf( stderr, "=== '>' in sequence is unacceptable.\n" );
+// fprintf( stderr, "=== In the '--anysymbol' and '--preservecase' modes, \n" );
+ fprintf( stderr, "=== '>' and '(' are acceptable only in title lines.\n" );
fprintf( stderr, "=== \n" );
fprintf( stderr, "========================================================\n" );
fprintf( stderr, "========================================================\n" );
*res = 0;
return( res - bk );
}
+#endif
+
+static int charfilter( unsigned char *str )
+{
+ unsigned char tmp;
+ unsigned char *res = str;
+ unsigned char *bk = str;
+
+ while( (tmp=*str++) )
+ {
+// if( tmp == '=' || tmp == '*' || tmp == '<' || tmp == '>' || tmp == '(' || tmp == ')' )
+ if( tmp == '=' || tmp == '<' || tmp == '>' )
+ {
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "Characters '= < >' are not accepted in the --text mode, \nalthough most printable characters are ok.\n" );
+ fprintf( stderr, "\n" );
+ exit( 1 );
+ }
+// if( 0x20 < tmp && tmp < 0x7f )
+// if( 0x0 <=tmp && tmp < 0x100 &&
+ if( tmp != 0x0a && tmp != 0x20 && tmp != 0x0d )
+// if( tmp != '\n' && tmp != ' ' && tmp != '\t' ) // unprintable characters mo ok.
+ {
+ *res++ = tmp;
+// reporterr( "tmp=%d (%c)\n", tmp, tmp );
+ }
+ }
+ *res = 0;
+ return( res - bk );
+}
+
static int onlyAlpha_lower( char *str )
{
b = '\n';
while( ( c = getc( fpp ) ) != EOF &&
- !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
+ !( ( c == '>' || c == EOF ) && b == '\n' ) )
{
*cbuf++ = (char)c; /* Ť¹¤®¤Æ¤â¤·¤é¤Ê¤¤ */
if( cbuf - val == size )
}
ungetc( c, fpp );
*cbuf = 0;
- onlyGraph( val );
+// onlyGraph( val );
+ charfilter( (unsigned char *) val );
// kake2hiku( val );
return( val );
}
b = '\n';
while( ( c = getc( fpp ) ) != EOF &&
- !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
+ !( ( c == '>' || c == EOF ) && b == '\n' ) )
{
*cbuf++ = (char)c; /* Ť¹¤®¤Æ¤â¤·¤é¤Ê¤¤ */
if( cbuf - val == size )
}
ungetc( c, fpp );
*cbuf = 0;
- if( dorp == 'd' )
- onlyAlpha_lower( val );
+
+ if( nblosum == -2 )
+ {
+ charfilter( (unsigned char *) val );
+ }
else
- onlyAlpha_upper( val );
- kake2hiku( val );
+ {
+ if( dorp == 'd' )
+ onlyAlpha_lower( val );
+ else
+ onlyAlpha_upper( val );
+ kake2hiku( val );
+ }
return( val );
}
b = '\n';
while( ( c = getc( fpp ) ) != EOF && /* by T. Nishiyama */
- !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
+ !( ( c == '>' || c == EOF ) && b == '\n' ) )
{
*cbuf++ = (char)c; /* Ť¹¤®¤Æ¤â¤·¤é¤Ê¤¤ */
b = c;
}
+int copydatafromgui( char **namegui, char **seqgui, char **name, int *nlen, char **seq )
+{
+ int i;
+
+
+ for( i=0; i<njob; i++ )
+ {
+ name[i][0] = '=';
+ strncpy( name[i]+1, namegui[i], B-2 );
+ name[i][B-1] = 0;
+
+ strcpy( seq[i], seqgui[i] );
+ nlen[i] = strlen( seq[i] );
+ }
+ if( dorp == 'd' )
+ seqLower( njob, seq );
+ else if( dorp == 'p' )
+ seqUpper( njob, seq );
+ else
+ {
+ reporterr( "DNA or Protein?\n" );
+ return( 1 );
+ }
+#if 0
+ free( tmpseq );
+#endif
+ if( outnumber )
+ {
+ char *namebuf;
+ char *cptr;
+ namebuf = calloc( B+100, sizeof( char ) );
+ for( i=0; i<njob; i++ )
+ {
+ namebuf[0] = '=';
+ cptr = strstr( name[i], "_numo_e_" );
+ if( cptr )
+ sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, cptr+8 );
+ else
+ sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, name[i]+1 );
+ strncpy( name[i], namebuf, B );
+ name[i][B-1] = 0;
+ }
+ free( namebuf );
+ }
+ return( 0 );
+}
+
void readData_pointer( FILE *fp, char **name, int *nlen, char **seq )
{
int i;
seqlen = strlen( tmpseq );
if( dorp == 'd' && upperCase != -1 ) seqLower( 1, &tmpseq );
- for( j=0; j<5; j++ )
+ if( outtable[i] == 2 )
{
- if( regtable[i][j*2] == -1 && regtable[i][j*2+1] == -1 ) continue;
-
- startpos = regtable[i][j*2];
- endpos = regtable[i][j*2+1];
-
- if( startpos > endpos )
- {
- endpos = regtable[i][j*2];
- startpos = regtable[i][j*2+1];
- }
-
- if( startpos < 0 ) startpos = 0;
- if( endpos < 0 ) endpos = 0;
- if( endpos >= seqlen ) endpos = seqlen-1;
- if( startpos >= seqlen ) startpos = seqlen-1;
-
+ startpos = 0;
+ endpos = seqlen-1;
outlen = endpos - startpos + 1;
- if( revtable[i][j] == 'f' )
- {
- fprintf( stderr, "startpos = %d\n", startpos );
- fprintf( stderr, "endpos = %d\n", endpos );
- fprintf( stderr, "outlen = %d\n", outlen );
- fprintf( stdout, "%.*s\n", outlen, tmpseq+startpos );
- }
- else
+ fprintf( stdout, "%.*s\n", outlen, tmpseq+startpos );
+ }
+ else
+ {
+ for( j=0; j<5; j++ )
{
- fs = AllocateCharVec( outlen+1 );
- rs = AllocateCharVec( outlen+1 );
-
- fs[outlen] = 0;
- strncpy( fs, tmpseq+startpos, outlen );
- sreverse( rs, fs );
- fprintf( stdout, "%s\n", rs );
- free( fs );
- free( rs );
+ if( regtable[i][j*2] == -1 && regtable[i][j*2+1] == -1 ) continue;
+
+ startpos = regtable[i][j*2];
+ endpos = regtable[i][j*2+1];
+
+ if( startpos > endpos )
+ {
+ endpos = regtable[i][j*2];
+ startpos = regtable[i][j*2+1];
+ }
+
+ if( startpos < 0 ) startpos = 0;
+ if( endpos < 0 ) endpos = 0;
+ if( endpos >= seqlen ) endpos = seqlen-1;
+ if( startpos >= seqlen ) startpos = seqlen-1;
+
+ outlen = endpos - startpos + 1;
+ if( revtable[i][j] == 'f' )
+ {
+ fprintf( stderr, "startpos = %d\n", startpos );
+ fprintf( stderr, "endpos = %d\n", endpos );
+ fprintf( stderr, "outlen = %d\n", outlen );
+ fprintf( stdout, "%.*s\n", outlen, tmpseq+startpos );
+ }
+ else
+ {
+ fs = AllocateCharVec( outlen+1 );
+ rs = AllocateCharVec( outlen+1 );
+
+ fs[outlen] = 0;
+ strncpy( fs, tmpseq+startpos, outlen );
+ sreverse( rs, fs );
+ fprintf( stdout, "%s\n", rs );
+ free( fs );
+ free( rs );
+ }
}
}
}
}
}
+int countATGCandN( char *s, int *countN, int *total )
+{
+ int nATGC;
+ int nChar;
+ int nN;
+ char c;
+ nN = nATGC = nChar = 0;
+
+ if( *s == 0 )
+ {
+ *total = 0;
+ return( 0 );
+ }
+
+ do
+ {
+ c = tolower( *s );
+ if( isalpha( c ) )
+ {
+ nChar++;
+ if( c == 'a' || c == 't' || c == 'g' || c == 'c' || c == 'u' || c == 'n' )
+ nATGC++;
+ if( c == 'n' )
+ nN++;
+ }
+ }
+ while( *++s );
+
+// reporterr( "nN = %d", nN );
+
+ *total = nChar;
+ *countN = nN;
+ return( nATGC );
+}
+
int countATGC( char *s, int *total )
{
int nATGC;
if( *s == 0 )
{
- total = 0;
+ *total = 0;
return( 0 );
}
return( val );
}
+int countnormalletters( char *seq, char *ref )
+{
+ int val = 0;
+ while( *seq )
+ if( strchr( ref, *seq++ ) ) val++;
+ return( val );
+}
+
void getnumlen_casepreserve( FILE *fp, int *nlenminpt )
{
int total;
}
}
+void getnumlen_nogap_countn( FILE *fp, int *nlenminpt, double *nfreq )
+{
+ int total;
+ int nsite = 0;
+ int atgcnum, nnum, nN;
+ int i, tmp;
+ char *tmpseq, *tmpname;
+ double atgcfreq;
+ tmpname = AllocateCharVec( N );
+ njob = countKUorWA( fp );
+ searchKUorWA( fp );
+ nlenmax = 0;
+ *nlenminpt = 99999999;
+ atgcnum = 0;
+ total = 0;
+ nnum = 0;
+ for( i=0; i<njob; i++ )
+ {
+ myfgets( tmpname, N-1, fp );
+ tmpseq = load1SeqWithoutName_realloc( fp );
+ tmp = countnogaplen( tmpseq );
+ if( tmp > nlenmax ) nlenmax = tmp;
+ if( tmp < *nlenminpt ) *nlenminpt = tmp;
+ atgcnum += countATGCandN( tmpseq, &nN, &nsite );
+ total += nsite;
+ nnum += nN;
+ free( tmpseq );
+ }
+ free( tmpname );
+ atgcfreq = (double)atgcnum / total;
+ *nfreq = (double)nnum / atgcnum;
+// fprintf( stderr, "##### nnum = %d\n", nnum );
+// fprintf( stderr, "##### atgcfreq = %f, *nfreq = %f\n", atgcfreq, *nfreq );
+ if( dorp == NOTSPECIFIED )
+ {
+ if( atgcfreq > 0.75 )
+ {
+ dorp = 'd';
+ upperCase = -1;
+ }
+ else
+ {
+ dorp = 'p';
+ upperCase = 0;
+ }
+ }
+}
void getnumlen_nogap( FILE *fp, int *nlenminpt )
{
int total;
}
free( tmpname );
atgcfreq = (double)atgcnum / total;
- fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+// fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
if( dorp == NOTSPECIFIED )
{
if( atgcfreq > 0.75 )
}
free( tmpname );
atgcfreq = (double)atgcnum / total;
- fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+// fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
if( dorp == NOTSPECIFIED )
{
if( atgcfreq > 0.75 )
}
}
+static void escapehtml( char *res, char *ori, int maxlen )
+{
+ char *res0 = res;
+ while( *ori )
+ {
+ if( *ori == '<' )
+ {
+ strcpy( res, "<" );
+ res += 3;
+ }
+ else if( *ori == '>' )
+ {
+ strcpy( res, ">" );
+ res += 3;
+ }
+ else if( *ori == '&' )
+ {
+ strcpy( res, "&" );
+ res += 4;
+ }
+ else if( *ori == '"' )
+ {
+ strcpy( res, """ );
+ res += 5;
+ }
+ else if( *ori == ' ' )
+ {
+ strcpy( res, " " );
+ res += 5;
+ }
+ else
+ {
+ *res = *ori;
+ }
+ res++;
+ ori++;
+
+ if( res - res0 -10 > N ) break;
+ }
+ *res = 0;
+}
+
void getnumlen_nogap_outallreg_web( FILE *fp, FILE *ofp, int *nlenminpt, int *isalignedpt )
{
int total;
int nsite = 0;
int atgcnum;
int alnlen = 0, alnlen_prev;
- int i, tmp;
- char *tmpseq, *tmpname;
+ int i, tmp, lennormalchar;
+ char *tmpseq, *tmpname, *tmpname2;
double atgcfreq;
tmpname = AllocateCharVec( N );
+ tmpname2 = AllocateCharVec( N );
njob = countKUorWA( fp );
searchKUorWA( fp );
nlenmax = 0;
for( i=0; i<njob; i++ )
{
myfgets( tmpname, N-1, fp );
+ tmpname2[0] = tmpname[0];
+ escapehtml( tmpname2+1, tmpname+1, N );
// fprintf( stdout, "%s\n", tmpname );
+// fprintf( stdout, "%s\n", tmpname2 );
+// exit(1);
tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
tmp = countnogaplen( tmpseq );
// fprintf( stdout, "%d\n", tmp );
if( i>0 && alnlen_prev != alnlen ) *isalignedpt = 0;
alnlen_prev = alnlen;
- free( tmpseq );
atgcfreq = (double)atgcnum / total;
// fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
// if( dorp == NOTSPECIFIED ) // you kentou
}
}
+ if( dorp == 'd' ) lennormalchar = countnormalletters( tmpseq, "atgcuATGCU" );
+ else lennormalchar = countnormalletters( tmpseq, "ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv" );
+ free( tmpseq );
-
-
- fprintf( ofp, " <label for='s%d'><input type='checkbox' id='s%d' name='s%d' checked>%s</label>\n", i, i, i, tmpname );
+ fprintf( ofp, " <label for='s%d'><span id='ss%d'><input type='checkbox' id='s%d' name='s%d' checked></span> <input type='text' class='ll' id='ll%d' style='display:none' size='6' value='%d' readonly='readonly'>%s</label>\n", i, i, i, i, i, lennormalchar, tmpname2 );
fprintf( ofp, "<span id='t%d-0' style='display:none'>", i );
fprintf( ofp, " <a href='javascript:void(0)' onclick='ddcycle(this.form,\"t%d\")'>+reg</a>", i );
- fprintf( ofp, " Begin:<input type='text' name='b%d-0' size='8' value='1'> End:<input type='text' name='e%d-0' size='8' value='%d'>", i, i, tmp );
+ fprintf( ofp, " Begin:<input type='text' name='b%d-0' size='8' value='1' class='ie'> End:<input type='text' name='e%d-0' size='8' value='%d' class='ie'>", i, i, tmp );
if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-0'><input type='checkbox' name='r%d-0' id='r%d-0'>Reverse</label>", i, i, i );
- fprintf( ofp, " Sequence Length:<input type='text' name='l%d' size='8' value='%d' readonly='readonly'>", i, tmp );
+// fprintf( ofp, " Sequence Length:<input type='text' name='l%d' size='8' value='%d' readonly='readonly'>", i, tmp );
fprintf( ofp, "\n</span>" );
fprintf( ofp, "<span id='t%d-1' style='display:none'>", i );
- fprintf( ofp, " Begin:<input type='text' name='b%d-1' size='8' value=''> End:<input type='text' name='e%d-1' size='8' value=''>", i, i );
+ fprintf( ofp, " Begin:<input type='text' name='b%d-1' size='8' value='' class='ie'> End:<input type='text' name='e%d-1' size='8' value='' class='ie'>", i, i );
if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-1'><input type='checkbox' name='r%d-1' id='r%d-1'>Reverse</label>", i, i, i );
fprintf( ofp, "\n</span>" );
fprintf( ofp, "<span id='t%d-2' style='display:none'>", i );
- fprintf( ofp, " Begin:<input type='text' name='b%d-2' size='8' value=''> End:<input type='text' name='e%d-2' size='8' value=''>", i, i );
+ fprintf( ofp, " Begin:<input type='text' name='b%d-2' size='8' value='' class='ie'> End:<input type='text' name='e%d-2' size='8' value='' class='ie'>", i, i );
if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-2'><input type='checkbox' name='r%d-2' id='r%d-2'>Reverse</label>", i, i, i );
fprintf( ofp, "\n</span>" );
fprintf( ofp, "<span id='t%d-3' style='display:none'>", i );
- fprintf( ofp, " Begin:<input type='text' name='b%d-3' size='8' value=''> End:<input type='text' name='e%d-3' size='8' value=''>", i, i );
+ fprintf( ofp, " Begin:<input type='text' name='b%d-3' size='8' value='' class='ie'> End:<input type='text' name='e%d-3' size='8' value='' class='ie'>", i, i );
if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-3'><input type='checkbox' name='r%d-3' id='r%d-3'>Reverse</label>", i, i, i );
fprintf( ofp, "\n</span>" );
fprintf( ofp, "<span id='t%d-4' style='display:none'>", i );
- fprintf( ofp, " Begin:<input type='text' name='b%d-4' size='8' value=''> End:<input type='text' name='e%d-4' size='8' value=''>", i, i );
+ fprintf( ofp, " Begin:<input type='text' name='b%d-4' size='8' value='' class='ie'> End:<input type='text' name='e%d-4' size='8' value='' class='ie'>", i, i );
if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-4'><input type='checkbox' name='r%d-4' id='r%d-4'>Reverse</label>", i, i, i );
fprintf( ofp, "\n</span>" );
}
free( tmpname );
+ free( tmpname2 );
atgcfreq = (double)atgcnum / total;
fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
// if( dorp == NOTSPECIFIED ) // you kentou
upperCase = 0;
}
}
+ fprintf( ofp, "\n" );
if( *isalignedpt )
{
- fprintf( ofp, "\n" );
fprintf( ofp, "<span id='tall-0' style='display:none'>" );
fprintf( ofp, "Cut the alignment\n" );
fprintf( ofp, " <a href='javascript:void(0)' onclick='ddcycle(this.form,\"tall\")'>+reg</a>" );
free( tmpseq );
}
+
atgcfreq = (double)atgcnum / total;
// fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
if( dorp == NOTSPECIFIED )
fprintf( fp, "%.*s\n", C, aseq+j );
}
+void readhat2_doublehalf_part_pointer( FILE *fp, int nseq, int nadd, char **name, double **mtx )
+{
+ int i, j, nseq0, norg;
+ char b[B];
+ fgets( b, B, fp );
+ fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 )
+ {
+ fprintf( stderr, "%d != %d\n", nseq, nseq0 );
+ ErrorExit( "hat2 is wrong." );
+ }
+ fgets( b, B, fp );
+ for( i=0; i<nseq; i++ )
+ {
+#if 0
+ getaline_fp_eof( b, B, fp );
+#else
+ myfgets( b, B-2, fp );
+#endif
+#if 0
+ j = MIN( strlen( b+6 ), 10 );
+ if( strncmp( name[i], b+6 , j ) )
+ {
+ fprintf( stderr, "Error in hat2\n" );
+ fprintf( stderr, "%s != %s\n", b, name[i] );
+ exit( 1 );
+ }
+#endif
+ }
+ norg = nseq-nadd;
+ for( i=0; i<norg; i++ ) for( j=0; j<nadd; j++ )
+ {
+ mtx[i][j] = ( input_new( fp, D ) );
+ }
+}
-void readhat2_floathalf_pointer( FILE *fp, int nseq, char **name, float **mtx )
+void readhat2_doublehalf_pointer( FILE *fp, int nseq, char **name, double **mtx )
{
int i, j, nseq0;
char b[B];
fgets( b, B, fp );
- fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+ fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 )
+ {
+ fprintf( stderr, "%d != %d\n", nseq, nseq0 );
+ ErrorExit( "hat2 is wrong." );
+ }
fgets( b, B, fp );
for( i=0; i<nseq; i++ )
{
mtx[i][j-i] = ( input_new( fp, D ) );
}
}
-void readhat2_floathalf( FILE *fp, int nseq, char name[M][B], float **mtx )
+void readhat2_doublehalf( FILE *fp, int nseq, char name[M][B], double **mtx )
{
int i, j, nseq0;
char b[B];
mtx[i][j-i] = ( input_new( fp, D ) );
}
}
-void readhat2_float( FILE *fp, int nseq, char name[M][B], float **mtx )
+void readhat2_double( FILE *fp, int nseq, char name[M][B], double **mtx )
{
int i, j, nseq0;
char b[B];
}
}
-void WriteFloatHat2_pointer_halfmtx( FILE *hat2p, int locnjob, char **name, float **mtx )
+void WriteFloatHat2_pointer_halfmtx( FILE *hat2p, int locnjob, char **name, double **mtx )
{
int i, j, ijsa;
double max = 0.0;
{
for( j=i+1; j<njob; j++ )
{
- fprintf( hat2p, "%#6.3f", mtx[i][j-i] );
+ fprintf( hat2p, DFORMAT, mtx[i][j-i] );
ijsa = j-i;
if( ijsa % 12 == 0 || ijsa == locnjob-i-1 ) fprintf( hat2p, "\n" );
}
}
}
-void WriteFloatHat2_pointer( FILE *hat2p, int locnjob, char **name, float **mtx )
+void WriteFloatHat2_pointer( FILE *hat2p, int locnjob, char **name, double **mtx )
{
int i, j;
double max = 0.0;
{
for( j=1; j<locnjob-i; j++ )
{
- fprintf( hat2p, "%#6.3f", mtx[i][j] );
+ fprintf( hat2p, DFORMAT, mtx[i][j] );
if( j % 12 == 0 || j == locnjob-i-1 ) fprintf( hat2p, "\n" );
}
}
}
-void WriteFloatHat2( FILE *hat2p, int locnjob, char name[M][B], float **mtx )
+void WriteFloatHat2( FILE *hat2p, int locnjob, char name[M][B], double **mtx )
{
int i, j;
double max = 0.0;
{
for( j=1; j<locnjob-i; j++ )
{
- fprintf( hat2p, "%#6.3f", mtx[i][j] );
+ fprintf( hat2p, DFORMAT, mtx[i][j] );
if( j % 12 == 0 || j == locnjob-i-1 ) fprintf( hat2p, "\n" );
}
}
{
for( j=i+1; j<locnjob; j++ )
{
- fprintf( hat2p, "%#6.3f", (float)mtx[i][j] / INTMTXSCALE );
+ fprintf( hat2p, DFORMAT, (double)mtx[i][j] / INTMTXSCALE );
if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
}
}
}
+
+void WriteHat2_part_pointer( FILE *hat2p, int locnjob, int nadd, char **name, double **mtx )
+{
+ int i, j;
+ int norg = locnjob-nadd;
+ double max = 0.0;
+// for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+ fprintf( hat2p, "%5d\n", 1 );
+ fprintf( hat2p, "%5d\n", locnjob );
+ fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+ for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+ for( i=0; i<norg; i++ )
+ {
+ for( j=0; j<nadd; j++ )
+ {
+ fprintf( hat2p, DFORMAT, mtx[i][j] );
+ if( (j+1) % 12 == 0 || j == nadd-1 ) fprintf( hat2p, "\n" );
+ }
+ }
+}
+
void WriteHat2_pointer( FILE *hat2p, int locnjob, char **name, double **mtx )
{
int i, j;
{
for( j=i+1; j<locnjob; j++ )
{
- fprintf( hat2p, "%#6.3f", mtx[i][j] );
+ fprintf( hat2p, DFORMAT, mtx[i][j] );
if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
}
}
}
+
void WriteHat2( FILE *hat2p, int locnjob, char name[M][B], double **mtx )
{
int i, j;
{
for( j=i+1; j<locnjob; j++ )
{
- fprintf( hat2p, "%#6.3f", mtx[i][j] );
+ fprintf( hat2p, DFORMAT, mtx[i][j] );
if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
}
}
return count;
}
-int ReadBlastm7( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
+int ReadBlastm7( FILE *fp, double *dis, int qmem, char **name, LocalHom *localhomlist )
{
int count=0;
char b[B];
// fprintf( stderr, "t=%d, score = %f, qstart=%d, qend=%d, tstart=%d, tend=%d, overlapaa=%d\n", junban[count], score, qstart, qend, tstart, tend, overlapaa );
- nlocalhom += addlocalhom_r( qal, tal, localhomlist+junban[count], qstart, tstart, score, overlapaa, nlocalhom );
+ nlocalhom += addlocalhom_r( qal, tal, localhomlist+junban[count], qstart, tstart, score, overlapaa, nlocalhom, 'h' );
while( fgets( b, B-1, fp ) )
if( !strncmp( " </Hsp>:", b, 18 ) ) break;
return count;
}
-int ReadFasta34noalign( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
+int ReadFasta34noalign( FILE *fp, double *dis, int qmem, char **name, LocalHom *localhomlist )
{
int count=0;
char b[B];
return count;
}
-int ReadFasta34m10_nuc( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
+int ReadFasta34m10_nuc( FILE *fp, double *dis, int qmem, char **name, LocalHom *localhomlist )
{
int count=0;
char b[B];
// fprintf( stderr, "tal2 = %s\n", tal2 );
// fprintf( stderr, "putting %d - %d, opt = %d\n", qmem, junban[count-1], opt );
- putlocalhom( qal2, tal2, localhomlist+junban[count-1], qstart, tstart, opt, overlapaa );
+ putlocalhom2( qal2, tal2, localhomlist+junban[count-1], qstart, tstart, opt, overlapaa, 'h' );
}
// fprintf( stderr, "count = %d\n", count );
return count;
}
-int ReadFasta34m10( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist )
+int ReadFasta34m10( FILE *fp, double *dis, int qmem, char **name, LocalHom *localhomlist )
{
int count=0;
char b[B];
// fprintf( stderr, "tal2 = %s\n", tal2 );
// fprintf( stderr, "putting %d - %d, opt = %d\n", qmem, junban[count-1], opt );
- putlocalhom( qal2, tal2, localhomlist+junban[count-1], qstart, tstart, opt, overlapaa );
+ putlocalhom2( qal2, tal2, localhomlist+junban[count-1], qstart, tstart, opt, overlapaa, 'h' );
}
// fprintf( stderr, "count = %d\n", count );
return count;
fflush( trap_g );
}
+void closeFiles( void )
+{
+ fclose( prep_g );
+ fclose( trap_g );
+}
-void WriteForFasta( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq )
+
+void WriteForFasta( FILE *fp, int locnjob, char **name, int nlen[M], char **aseq )
{
static char b[N];
int i, j;
}
}
-void readlocalhomtable2( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
+void readlocalhomtable2_target( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec, int *targetmap )
+{
+ double opt;
+ static char buff[B];
+ char infor[100];
+ int i, j, overlapaa, start1, end1, start2, end2, it, jt;
+ LocalHom *tmpptr1, *tmpptr2;
+
+// for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
+
+ while ( NULL != fgets( buff, B-1, fp ) )
+ {
+// fprintf( stderr, "\n" );
+ sscanf( buff, "%d %d %d %lf %d %d %d %d %s", &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+ if( *infor == 'k' ) kozoarivec[i] = kozoarivec[j] = 1;
+
+#if 0
+ if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+ it = targetmap[i];
+ if( it == -1 )
+ {
+ reporterr( "hat3 ga okashii. _target_ \n" );
+ exit( 1 );
+ }
+ jt = targetmap[j];
+
+
+
+// if( i < j )
+ {
+ if( localhomtable[it][j].nokori++ > 0 )
+ {
+ tmpptr1 = localhomtable[it][j].last;
+// fprintf( stderr, "reallocating, localhomtable[%d][%d].nokori = %d\n", i, j, localhomtable[i][j].nokori );
+ tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr1 = tmpptr1->next;
+ tmpptr1->extended = -1;
+ tmpptr1->next = NULL;
+ localhomtable[it][j].last = tmpptr1;
+// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", i, j, localhomtable[i][j].nokori );
+ }
+ else
+ {
+ tmpptr1 = localhomtable[it]+j;
+// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", i, j, localhomtable[i][j].nokori );
+ }
+
+ tmpptr1->start1 = start1;
+ tmpptr1->start2 = start2;
+ tmpptr1->end1 = end1;
+ tmpptr1->end2 = end2;
+// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr1->opt = opt;
+ tmpptr1->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr1->overlapaa = overlapaa;
+ tmpptr1->korh = *infor;
+ }
+// else
+ if( jt != -1 )
+ {
+ if( localhomtable[jt][i].nokori++ > 0 )
+ {
+ tmpptr2 = localhomtable[jt][i].last;
+ tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr2 = tmpptr2->next;
+ tmpptr2->extended = -1;
+ tmpptr2->next = NULL;
+ localhomtable[jt][i].last = tmpptr2;
+// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", j, i, localhomtable[j][i].nokori );
+ }
+ else
+ {
+ tmpptr2 = localhomtable[jt]+i;
+// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", j, i, localhomtable[j][i].nokori );
+ }
+
+ tmpptr2->start2 = start1;
+ tmpptr2->start1 = start2;
+ tmpptr2->end2 = end1;
+ tmpptr2->end1 = end2;
+// tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr2->opt = opt;
+ tmpptr2->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr2->overlapaa = overlapaa;
+ tmpptr2->korh = *infor;
+
+// fprintf( stderr, "i=%d, j=%d, st1=%d, en1=%d, opt = %f\n", i, j, tmpptr1->start1, tmpptr1->end1, opt );
+ }
+
+ }
+}
+
+void readlocalhomtable2_half( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
+{
+ double opt;
+ static char buff[B];
+ char infor[100];
+ int i, j, overlapaa, start1, end1, start2, end2;
+ LocalHom *tmpptr1;
+
+// for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
+
+ while ( NULL != fgets( buff, B-1, fp ) )
+ {
+// fprintf( stderr, "\n" );
+ sscanf( buff, "%d %d %d %lf %d %d %d %d %s", &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+ if( *infor == 'k' ) kozoarivec[i] = kozoarivec[j] = 1;
+
+#if 0
+ if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+ if( j <= i )
+ {
+ reporterr( "Check hat3. The first sequence must be younger than the second one.\n" );
+ exit( 1 );
+ }
+ {
+ if( localhomtable[i][j-i].nokori++ > 0 )
+ {
+ tmpptr1 = localhomtable[i][j-i].last;
+// fprintf( stderr, "reallocating, localhomtable[%d][%d].nokori = %d\n", i, j, localhomtable[i][j].nokori );
+ tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr1 = tmpptr1->next;
+ tmpptr1->extended = -1;
+ tmpptr1->next = NULL;
+ localhomtable[i][j-i].last = tmpptr1;
+// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", i, j, localhomtable[i][j-i].nokori );
+ }
+ else
+ {
+ tmpptr1 = localhomtable[i]+j-i;
+// fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", i, j, localhomtable[i][j-i].nokori );
+ }
+
+ tmpptr1->start1 = start1;
+ tmpptr1->start2 = start2;
+ tmpptr1->end1 = end1;
+ tmpptr1->end2 = end2;
+// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr1->opt = opt;
+ tmpptr1->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr1->overlapaa = overlapaa;
+ tmpptr1->korh = *infor;
+ }
+
+ }
+}
+
+void readlocalhomtable2( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
{
double opt;
static char buff[B];
}
}
-void readlocalhomtable( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
+
+#if 0
+void readlocalhomtable_target( FILE*fp, int ntarget, int njob, LocalHom **localhomtable, char *kozoarivec, int *targetmap )
{
double opt;
static char buff[B];
char infor[100];
- int i, j, overlapaa, start1, end1, start2, end2;
+ int i, j, overlapaa, start1, end1, start2, end2, it, jt;
int **nlocalhom = NULL;
LocalHom *tmpptr1=NULL, *tmpptr2=NULL; // by D.Mathog, a guess
nlocalhom = AllocateIntMtx( njob, njob );
- for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
+ for( i=0; i<ntarget; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
while ( NULL != fgets( buff, B-1, fp ) )
{
if( start1 == end1 || start2 == end2 ) continue; //mondai ari
#endif
+ printf( "reading %d-%d\n", i, j );
+
+ it = targetmap[i];
+ if( it == -1 )
+ {
+ reporterr( "hat3 ga okashii. _target_ \n" );
+ exit( 1 );
+ }
+ jt = targetmap[j];
// if( i < j )
{
+ if( nlocalhom[it][j]++ > 0 )
+ {
+ printf( "extending %d-%d, ->%d\n", i, j, nlocalhom[it][j] );
+// fprintf( stderr, "reallocating, nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+ tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr1 = tmpptr1->next;
+ tmpptr1->next = NULL;
+ }
+ else
+ {
+ tmpptr1 = localhomtable[it]+j;
+// fprintf( stderr, "nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+ }
+
+ tmpptr1->start1 = start1; // CHUUI!!!!
+ tmpptr1->start2 = start2;
+ tmpptr1->end1 = end1; // CHUUI!!!!
+ tmpptr1->end2 = end2;
+// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr1->opt = opt;
+ tmpptr1->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr1->overlapaa = overlapaa;
+ tmpptr1->korh = *infor;
+
+// fprintf( stderr, "i=%d, j=%d, opt = %f\n", i, j, opt );
+
+
+ }
+// else
+
+ if( jt != -1 )
+ {
+ if( nlocalhom[jt][i]++ > 0 )
+ {
+ printf( "extending %d-%d, ->%d\n", i, j, nlocalhom[jt][i] );
+ tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr2 = tmpptr2->next;
+ tmpptr2->next = NULL;
+ }
+ else
+ tmpptr2 = localhomtable[jt]+i;
+
+ tmpptr2->start2 = start1; // CHUUI!!!!
+ tmpptr2->start1 = start2;
+ tmpptr2->end2 = end1; // CHUUI!!!!
+ tmpptr2->end1 = end2;
+// tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr2->opt = opt;
+ tmpptr2->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr2->overlapaa = overlapaa;
+ tmpptr2->korh = *infor;
+
+// fprintf( stderr, "j=%d, i=%d, opt = %f\n", j, i, opt );
+ }
+
+ }
+ LocalHom *tmpptr;
+ for( tmpptr = localhomtable[1]+11; tmpptr; tmpptr=tmpptr->next )
+ fprintf( stdout, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f, next=%p\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt / 600 * 5.8, tmpptr->next );
+ FreeIntMtx( nlocalhom );
+}
+
+void readlocalhomtable_half( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
+{
+ double opt;
+ static char buff[B];
+ char infor[100];
+ int i, j, overlapaa, start1, end1, start2, end2;
+ int **nlocalhom = NULL;
+ LocalHom *tmpptr1=NULL; // by D.Mathog, a guess
+
+ nlocalhom = AllocateIntMtx( njob, njob );
+ for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
+
+ while ( NULL != fgets( buff, B-1, fp ) )
+ {
+// fprintf( stderr, "\n" );
+ sscanf( buff, "%d %d %d %lf %d %d %d %d %s", &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+ if( *infor == 'k' ) kozoarivec[i] = kozoarivec[j] = 1;
+
+#if 0
+ if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+
+ if( j <= i )
+ {
+ reporterr( "Check hat3. The first sequence must be younger than the second one.\n" );
+ exit( 1 );
+ }
+ {
if( nlocalhom[i][j]++ > 0 )
{
// fprintf( stderr, "reallocating, nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
}
else
{
- tmpptr1 = localhomtable[i]+j;
+ tmpptr1 = localhomtable[i]+j-i;
// fprintf( stderr, "nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
}
- tmpptr1->start1 = start1;
+ tmpptr1->start1 = start1; // CHUUI!!!!
tmpptr1->start2 = start2;
- tmpptr1->end1 = end1;
+ tmpptr1->end1 = end1; // CHUUI!!!!
tmpptr1->end2 = end2;
// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
// tmpptr1->opt = opt;
// fprintf( stderr, "i=%d, j=%d, opt = %f\n", i, j, opt );
}
-// else
+ }
+ FreeIntMtx( nlocalhom );
+}
+#endif
+
+void readlocalhomtable( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
+{
+ double opt;
+ static char buff[B];
+ char infor[100];
+ int i, j, overlapaa, start1, end1, start2, end2;
+ int **nlocalhom = NULL;
+ LocalHom *tmpptr1=NULL, *tmpptr2=NULL; // by D.Mathog, a guess
+
+ nlocalhom = AllocateIntMtx( njob, njob );
+ for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
+
+ while ( NULL != fgets( buff, B-1, fp ) )
+ {
+// fprintf( stderr, "\n" );
+ sscanf( buff, "%d %d %d %lf %d %d %d %d %s", &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+ if( *infor == 'k' ) kozoarivec[i] = kozoarivec[j] = 1;
+
+#if 0
+ if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+
+ if( j <= i )
+ {
+ reporterr( "Check hat3. The first sequence must be younger than the second one.\n" );
+ exit( 1 );
+ }
+ {
+ if( nlocalhom[i][j]++ > 0 )
+ {
+// fprintf( stderr, "reallocating, nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+ tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr1 = tmpptr1->next;
+ tmpptr1->next = NULL;
+ }
+ else
+ {
+ tmpptr1 = localhomtable[i]+j;
+// fprintf( stderr, "nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+ }
+
+ tmpptr1->start1 = start1; // CHUUI!!!!
+ tmpptr1->start2 = start2;
+ tmpptr1->end1 = end1; // CHUUI!!!!
+ tmpptr1->end2 = end2;
+// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr1->opt = opt;
+ tmpptr1->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr1->overlapaa = overlapaa;
+ tmpptr1->korh = *infor;
+
+// fprintf( stderr, "i=%d, j=%d, opt = %f\n", i, j, opt );
+ }
+// else
+ {
+ if( nlocalhom[j][i]++ > 0 )
+ {
+ tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr2 = tmpptr2->next;
+ tmpptr2->next = NULL;
+ }
+ else
+ tmpptr2 = localhomtable[j]+i;
+
+ tmpptr2->start2 = start1; // CHUUI!!!!
+ tmpptr2->start1 = start2;
+ tmpptr2->end2 = end1; // CHUUI!!!!
+ tmpptr2->end1 = end2;
+// tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr2->opt = opt;
+ tmpptr2->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr2->overlapaa = overlapaa;
+ tmpptr2->korh = *infor;
+
+// fprintf( stderr, "j=%d, i=%d, opt = %f\n", j, i, opt );
+ }
+
+ }
+ FreeIntMtx( nlocalhom );
+}
+
+
+void readlocalhomtable_two( FILE*fp, int norg, int nadd, LocalHom **localhomtable, LocalHom **localhomtablex, char *kozoarivec ) // for test only
+{
+ double opt;
+ static char buff[B];
+ char infor[100];
+ int i, j, overlapaa, start1, end1, start2, end2;
+ int **nlocalhom = NULL;
+ int **nlocalhomx = NULL;
+ LocalHom *tmpptr1=NULL, *tmpptr2=NULL; // by D.Mathog, a guess
+
+ nlocalhom = AllocateIntMtx( norg, nadd );
+ for( i=0; i<norg; i++ ) for( j=0; j<nadd; j++ ) nlocalhom[i][j] = 0;
+ nlocalhomx = AllocateIntMtx( nadd, norg );
+ for( i=0; i<nadd; i++ ) for( j=0; j<norg; j++ ) nlocalhomx[i][j] = 0;
+
+ while ( NULL != fgets( buff, B-1, fp ) )
+ {
+// fprintf( stderr, "\n" );
+ sscanf( buff, "%d %d %d %lf %d %d %d %d %s", &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+ if( *infor == 'k' )
+ {
+ fprintf( stderr, "Not supported!\n" );
+ exit( 1 );
+ }
+ j -= norg;
+
+#if 0
+ if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+
+// if( i < j )
+ {
+ if( nlocalhom[i][j]++ > 0 )
+ {
+// fprintf( stderr, "reallocating, nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+ tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr1 = tmpptr1->next;
+ tmpptr1->next = NULL;
+ }
+ else
+ {
+ tmpptr1 = localhomtable[i]+j;
+// fprintf( stderr, "nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+ }
+
+ tmpptr1->start1 = start1; // CHUUI!!!!
+ tmpptr1->start2 = start2;
+ tmpptr1->end1 = end1; // CHUUI!!!!
+ tmpptr1->end2 = end2;
+// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr1->opt = opt;
+ tmpptr1->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr1->overlapaa = overlapaa;
+ tmpptr1->korh = *infor;
+
+// fprintf( stderr, "i=%d, j=%d, opt = %f\n", i, j, opt );
+ }
+
+ {
+ if( nlocalhomx[j][i]++ > 0 )
+ {
+ tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr2 = tmpptr2->next;
+ tmpptr2->next = NULL;
+ }
+ else
+ tmpptr2 = localhomtablex[j]+i;
+
+ tmpptr2->start2 = start1+1; // CHUUI!!!!
+ tmpptr2->start1 = start2;
+ tmpptr2->end2 = end1+1; // CHUUI!!!!
+ tmpptr2->end1 = end2;
+// tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr2->opt = opt;
+ tmpptr2->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr2->overlapaa = overlapaa;
+ tmpptr2->korh = *infor;
+
+// fprintf( stderr, "j=%d, i=%d, opt = %f\n", j, i, opt );
+ }
+
+ }
+ FreeIntMtx( nlocalhom );
+ FreeIntMtx( nlocalhomx );
+}
+
+void readlocalhomtable_one( FILE*fp, int norg, int nadd, LocalHom **localhomtable, char *kozoarivec ) // for test only
+{
+ double opt;
+ static char buff[B];
+ char infor[100];
+ int i, j, overlapaa, start1, end1, start2, end2;
+ int **nlocalhom = NULL;
+ LocalHom *tmpptr1=NULL; // by D.Mathog, a guess
+
+ nlocalhom = AllocateIntMtx( norg, nadd );
+ for( i=0; i<norg; i++ ) for( j=0; j<nadd; j++ ) nlocalhom[i][j] = 0;
+
+ while ( NULL != fgets( buff, B-1, fp ) )
+ {
+// fprintf( stderr, "\n" );
+ sscanf( buff, "%d %d %d %lf %d %d %d %d %s", &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+ if( *infor == 'k' )
+ {
+ fprintf( stderr, "Not supported!\n" );
+ exit( 1 );
+ }
+ j -= norg;
+
+#if 0
+ if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+
+// if( i < j )
+ {
+ if( nlocalhom[i][j]++ > 0 )
+ {
+// fprintf( stderr, "reallocating, nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+ tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+ tmpptr1 = tmpptr1->next;
+ tmpptr1->next = NULL;
+ }
+ else
+ {
+ tmpptr1 = localhomtable[i]+j;
+// fprintf( stderr, "nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+ }
+
+ tmpptr1->start1 = start1; // CHUUI!!!!
+ tmpptr1->start2 = start2;
+ tmpptr1->end1 = end1; // CHUUI!!!!
+ tmpptr1->end2 = end2;
+// tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
+// tmpptr1->opt = opt;
+ tmpptr1->opt = ( opt + 0.00 ) / 5.8 * 600;
+ tmpptr1->overlapaa = overlapaa;
+ tmpptr1->korh = *infor;
+
+// fprintf( stderr, "i=%d, j=%d, opt = %f\n", i, j, opt );
+ }
+
+ }
+ FreeIntMtx( nlocalhom );
+}
+
+void outlocalhom_part( LocalHom **localhom, int norg, int nadd )
+{
+ int i, j;
+ LocalHom *tmpptr;
+ for( i=0; i<norg; i++ ) for( j=0; j<nadd; j++ )
+ {
+ tmpptr = localhom[i]+j;
+ fprintf( stdout, "%d-%d\n", i, j+norg );
+ do
+ {
+ fprintf( stdout, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt / 600 * 5.8 );
+ }
+ while( (tmpptr=tmpptr->next) );
+ }
+}
+
+void outlocalhom_target( LocalHom **localhom, int norg, int nadd )
+{
+ int i, j;
+ LocalHom *tmpptr;
+ for( i=0; i<norg; i++ ) for( j=0; j<nadd; j++ )
+ {
+ tmpptr = localhom[i]+j;
+ fprintf( stdout, "%d-%d\n", i, j );
+ for( ; tmpptr; tmpptr=tmpptr->next )
+ {
+ fprintf( stdout, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f, next=%p\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt / 600 * 5.8, (void *)tmpptr->next );
+ }
+// while( (tmpptr=tmpptr->next) );
+ }
+}
+
+void outlocalhom_half( LocalHom **localhom, int nseq )
+{
+ int i, j;
+ LocalHom *tmpptr;
+ for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+ {
+ tmpptr = localhom[i]+j-i;
+ fprintf( stdout, "%d-%d\n", i, j );
+ do
+ {
+ fprintf( stdout, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f, next=%p\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt / 600 * 5.8, (void *)tmpptr->next );
+ }
+ while( (tmpptr=tmpptr->next) );
+ }
+}
+
+void outlocalhom( LocalHom **localhom, int nseq )
+{
+ int i, j;
+ LocalHom *tmpptr;
+ for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
+ {
+ tmpptr = localhom[i]+j;
+ fprintf( stderr, "%d-%d\n", i, j );
+ do
+ {
+ fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt );
+ }
+ while( (tmpptr=tmpptr->next) );
+ }
+}
+
+void outlocalhompt( LocalHom ***localhom, int n1, int n2 )
+{
+ int i, j;
+ LocalHom *tmpptr;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ tmpptr = localhom[i][j];
+// fprintf( stdout, "%d-%d\n", i, j );
+ do
+ {
+ fprintf( stdout, "%d-%d, reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f\n", i, j, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt );
+ }
+ while( (tmpptr=tmpptr->next) );
+ }
+}
+
+void FreeLocalHomTable_part( LocalHom **localhomtable, int n, int m )
+{
+ int i, j;
+ LocalHom *ppp, *tmpptr;
+ for( i=0; i<n; i++ )
+ {
+ for( j=0; j<m; j++ )
+ {
+ tmpptr=localhomtable[i]+j;
+ ppp = tmpptr->next;
+ for( ; tmpptr; tmpptr=ppp )
+ {
+#if DEBUG
+ fprintf( stderr, "i=%d, j=%d\n", i, j );
+#endif
+ ppp = tmpptr->next;
+ if( tmpptr!=localhomtable[i]+j )
+ {
+#if DEBUG
+ fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+ free( tmpptr );
+ }
+ }
+ }
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+ free( localhomtable[i] );
+ }
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable\n" );
+#endif
+ free( localhomtable );
+#if DEBUG
+ fprintf( stderr, "freed\n" );
+#endif
+}
+
+void FreeLocalHomTable_two( LocalHom **localhomtable, int n, int m )
+{
+ int i, j;
+ LocalHom *ppp, *tmpptr;
+ for( i=0; i<n; i++ )
+ {
+ for( j=0; j<m; j++ )
+ {
+ tmpptr=localhomtable[i]+j;
+ ppp = tmpptr->next;
+ for( ; tmpptr; tmpptr=ppp )
+ {
+#if DEBUG
+ fprintf( stderr, "i=%d, j=%d\n", i, j );
+#endif
+ ppp = tmpptr->next;
+ if( tmpptr!=localhomtable[i]+j )
+ {
+#if DEBUG
+ fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+ free( tmpptr );
+ }
+ }
+ }
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+ free( localhomtable[i] );
+ }
+
+ for( i=n; i<n+m; i++ )
+ {
+ for( j=0; j<n; j++ )
{
- if( nlocalhom[j][i]++ > 0 )
+ tmpptr=localhomtable[i]+j;
+ ppp = tmpptr->next;
+ for( ; tmpptr; tmpptr=ppp )
{
- tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
- tmpptr2 = tmpptr2->next;
- tmpptr2->next = NULL;
+#if DEBUG
+ fprintf( stderr, "i=%d, j=%d\n", i, j );
+#endif
+ ppp = tmpptr->next;
+ if( tmpptr!=localhomtable[i]+j )
+ {
+#if DEBUG
+ fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+ free( tmpptr );
+ }
}
- else
- tmpptr2 = localhomtable[j]+i;
-
- tmpptr2->start2 = start1;
- tmpptr2->start1 = start2;
- tmpptr2->end2 = end1;
- tmpptr2->end1 = end2;
-// tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8 * 600;
-// tmpptr2->opt = opt;
- tmpptr2->opt = ( opt + 0.00 ) / 5.8 * 600;
- tmpptr2->overlapaa = overlapaa;
- tmpptr2->korh = *infor;
}
-
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+ free( localhomtable[i] );
}
- FreeIntMtx( nlocalhom );
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable\n" );
+#endif
+ free( localhomtable );
+#if DEBUG
+ fprintf( stderr, "freed\n" );
+#endif
}
-void outlocalhom( LocalHom **localhom, int nseq )
+void FreeLocalHomTable_one( LocalHom **localhomtable, int n, int m )
{
int i, j;
- LocalHom *tmpptr;
- for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
+ LocalHom *ppp, *tmpptr;
+ for( i=0; i<n; i++ )
{
- tmpptr = localhom[i]+j;
- fprintf( stderr, "%d-%d\n", i, j );
- do
+ for( j=0; j<m; j++ )
{
- fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt );
+ tmpptr=localhomtable[i]+j;
+ ppp = tmpptr->next;
+ for( ; tmpptr; tmpptr=ppp )
+ {
+#if DEBUG
+ fprintf( stderr, "i=%d, j=%d\n", i, j );
+#endif
+ ppp = tmpptr->next;
+ if( tmpptr!=localhomtable[i]+j )
+ {
+#if DEBUG
+ fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+ free( tmpptr );
+ }
+ }
}
- while( (tmpptr=tmpptr->next) );
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+ free( localhomtable[i] );
}
+
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable\n" );
+#endif
+ free( localhomtable );
+#if DEBUG
+ fprintf( stderr, "freed\n" );
+#endif
}
-void outlocalhompt( LocalHom ***localhom, int n1, int n2 )
+void FreeLocalHomTable_half( LocalHom **localhomtable, int n )
{
int i, j;
- LocalHom *tmpptr;
- for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ LocalHom *ppp, *tmpptr;
+ for( i=0; i<n; i++ )
{
- tmpptr = localhom[i][j];
- fprintf( stderr, "%d-%d\n", i, j );
- do
+ for( j=0; j<n-i; j++ )
{
- fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f, wimp=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt, tmpptr->wimportance );
+ tmpptr=localhomtable[i]+j;
+ ppp = tmpptr->next;
+ for( ; tmpptr; tmpptr=ppp )
+ {
+#if DEBUG
+ fprintf( stderr, "i=%d, j=%d\n", i, j );
+#endif
+ ppp = tmpptr->next;
+ if( tmpptr!=localhomtable[i]+j )
+ {
+#if DEBUG
+ fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+ free( tmpptr );
+ }
+ }
}
- while( (tmpptr=tmpptr->next) );
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+ free( localhomtable[i] );
}
+#if DEBUG
+ fprintf( stderr, "freeing localhomtable\n" );
+#endif
+ free( localhomtable );
+#if DEBUG
+ fprintf( stderr, "freed\n" );
+#endif
}
-
void FreeLocalHomTable( LocalHom **localhomtable, int n )
{
int i, j;
return( val );
}
-void phylipout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, int *order )
+void phylipout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, int *order, int namelen )
{
int pos, pos2, j;
+ if( namelen == -1 ) namelen = 10;
pos = 0;
fprintf( fp, " %d %d\n", nseq, maxlen );
for( j=0; j<nseq; j++ )
{
if( pos == 0 )
- fprintf( fp, "%-10.10s", extractfirstword( name[order[j]]+1 ) );
+ fprintf( fp, "%-*.*s", namelen, namelen, extractfirstword( name[order[j]]+1 ) );
else
- fprintf( fp, " " );
+ fprintf( fp, "%-*.*s", namelen, namelen, "" );
pos2 = pos;
while( pos2 < pos+41 && pos2 < maxlen )
void clustalout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, char *mark, char *comment, int *order, int namelen )
{
int pos, j;
+ if( namelen == -1 ) namelen = 15;
pos = 0;
if( comment == NULL )
fprintf( fp, "CLUSTAL format alignment by MAFFT (v%s)\n\n", VERSION );
return( val );
}
+static void tab2space( char *s ) // nen no tame
+{
+ while( *s )
+ {
+ if( *s == '\t' ) *s = ' ';
+ s++;
+ }
+}
+
+static int readasubalignment( char *s, int *t, int *preservegaps )
+{
+ int v = 0;
+ char status = 's';
+ char *pt = s;
+ *preservegaps = 0;
+ tab2space( s );
+ while( *pt )
+ {
+ if( *pt == ' ' )
+ {
+ status = 's';
+ }
+ else
+ {
+ if( status == 's' )
+ {
+ if( *pt == '\n' || *pt == '#' ) break;
+ status = 'n';
+ t[v] = atoi( pt );
+ if( t[v] == 0 )
+ {
+ fprintf( stderr, "Format error? Sequences must be specified as 1, 2, 3...\n" );
+ exit( 1 );
+ }
+ if( t[v] < 0 ) *preservegaps = 1;
+ t[v] = abs( t[v] );
+ t[v] -= 1;
+ v++;
+ }
+ }
+ pt++;
+ }
+ t[v] = -1;
+ return( v );
+}
+
+static int countspace( char *s )
+{
+ int v = 0;
+ char status = 's';
+ char *pt = s;
+ tab2space( s );
+ while( *pt )
+ {
+ if( *pt == ' ' )
+ {
+ status = 's';
+ }
+ else
+ {
+ if( status == 's' )
+ {
+ if( *pt == '\n' || *pt == '#' ) break;
+ v++;
+ status = 'n';
+ if( atoi( pt ) == 0 )
+ {
+ fprintf( stderr, "Format error? Sequences should be specified as 1, 2, 3...\n" );
+ exit( 1 );
+ }
+ }
+ }
+ pt++;
+ }
+ return( v );
+}
+
+
+void readsubalignmentstable( int nseq, int **table, int *preservegaps, int *nsubpt, int *maxmempt )
+{
+ FILE *fp;
+ char *line;
+ int linelen = 1000000;
+ int nmem;
+ int lpos;
+ int i, p;
+ int *tab01;
+
+ line = calloc( linelen, sizeof( char ) );
+ fp = fopen( "_subalignmentstable", "r" );
+ if( !fp )
+ {
+ fprintf( stderr, "Cannot open _subalignmentstable\n" );
+ exit( 1 );
+ }
+ if( table == NULL )
+ {
+ *nsubpt = 0;
+ *maxmempt = 0;
+ while( 1 )
+ {
+ fgets( line, linelen-1, fp );
+ if( feof( fp ) ) break;
+ if( line[strlen(line)-1] != '\n' )
+ {
+ fprintf( stderr, "too long line? \n" );
+ exit( 1 );
+ }
+ if( line[0] == '#' ) continue;
+ if( atoi( line ) == 0 ) continue;
+ nmem = countspace( line );
+ if( nmem > *maxmempt ) *maxmempt = nmem;
+ (*nsubpt)++;
+ }
+ }
+ else
+ {
+ tab01 = calloc( nseq, sizeof( int ) );
+ for( i=0; i<nseq; i++ ) tab01[i] = 0;
+ lpos = 0;
+ while( 1 )
+ {
+ fgets( line, linelen-1, fp );
+ if( feof( fp ) ) break;
+ if( line[strlen(line)-1] != '\n' )
+ {
+ fprintf( stderr, "too long line? \n" );
+ exit( 1 );
+ }
+ if( line[0] == '#' ) continue;
+ if( atoi( line ) == 0 ) continue;
+ readasubalignment( line, table[lpos], preservegaps+lpos );
+ for( i=0; (p=table[lpos][i])!=-1; i++ )
+ {
+ if( tab01[p] )
+ {
+ fprintf( stderr, "\nSequence %d appears in different groups.\n", p+1 );
+ fprintf( stderr, "Hierarchical grouping is not supported.\n\n" );
+ exit( 1 );
+ }
+ tab01[p] = 1;
+ if( p > nseq-1 )
+ {
+ fprintf( stderr, "Sequence %d does not exist in the input sequence file.\n", p+1 );
+ exit( 1 );
+ }
+ }
+ lpos++;
+ }
+ free( tab01 );
+ }
+ fclose( fp );
+ free( line );
+}
+
void readmccaskill( FILE *fp, RNApair **pairprob, int length )
{
int *pairnum;
int i;
int left, right;
- float prob;
+ double prob;
int c;
pairnum = (int *)calloc( length, sizeof( int ) );
{
if( c != '>' )
{
- fprintf( stderr, "format error in hat4\n" );
+ fprintf( stderr, "format error in hat4 - 1\n" );
exit( 1 );
}
}
if( feof( fp ) ) break;
c = getc( fp );
ungetc( c, fp );
- if( c == '>' )
+ if( c == '>' || c == EOF )
{
break;
}
fgets( gett, 999, fp );
// fprintf( stderr, "gett = %s\n", gett );
- sscanf( gett, "%d %d %f", &left, &right, &prob );
+ sscanf( gett, "%d %d %lf", &left, &right, &prob );
if( left >= length || right >= length )
{
- fprintf( stderr, "format error in hat4\n" );
+ fprintf( stderr, "format error in hat4 - 2\n" );
exit( 1 );
}
free( maptoseq1 );
free( maptoseq2 );
}
+
+int myatoi( char *in )
+{
+ if( in == NULL )
+ {
+ fprintf( stderr, "Error in myatoi()\n" );
+ exit( 1 );
+ }
+ return( atoi( in ) );
+}
+
+double myatof( char *in )
+{
+ if( in == NULL )
+ {
+ fprintf( stderr, "Error in myatof()\n" );
+ exit( 1 );
+ }
+ return( atof( in ) );
+}
+
+void reporterr( const char *str, ... )
+{
+// static int loglen = 0;
+ va_list args;
+
+ if( gmsg )
+ {
+# if 1 // ato de sakujo
+ static FILE *errtmpfp = NULL;
+ if( errtmpfp == NULL )
+ errtmpfp = fopen( "maffterr", "w" );
+ else
+ errtmpfp = fopen( "maffterr", "a" );
+ va_start( args, str );
+ vfprintf( errtmpfp, str, args );
+ va_end( args );
+ fclose( errtmpfp );
+#endif
+
+#if 0
+ char *tmpptr;
+ tmpptr = (char *)realloc( *gmsg, (loglen+10000) * sizeof( char ) );
+ if( tmpptr == NULL )
+ {
+ fprintf( stderr, "Cannot relloc *gmsg\n" );
+ exit( 1 );
+ }
+ *gmsg = tmpptr;
+ va_start( args, str );
+ loglen += vsprintf( *gmsg + loglen, str, args );
+ va_end( args );
+
+
+ va_start( args, str );
+ loglen += vsprintf( *gmsg + loglen, str, args );
+ va_end( args );
+ *(*gmsg + loglen) = 0;
+ if( loglen > gmsglen - 100 ) loglen = 0; // tekitou
+#endif
+
+ }
+ else
+ {
+ va_start( args, str );
+ vfprintf( stderr, str, args );
+ va_end( args );
+// fflush( stderr ); // iru?
+ }
+ return;
+}
+
+
+#ifndef mingw
+void setstacksize(rlim_t kStackSize )
+{
+// const rlim_t kStackSize = 100 * 1024 * 1024; // min stack size = 10MB
+ struct rlimit rl;
+ int result;
+ rlim_t originalsize;
+
+ result = getrlimit(RLIMIT_STACK, &rl);
+ if (result == 0)
+ {
+ originalsize = rl.rlim_cur;
+ if (rl.rlim_cur < kStackSize)
+ {
+ rl.rlim_cur = kStackSize;
+ reporterr( "stacksize: %d kb->%d kb\n", originalsize/1024, rl.rlim_cur/1024 );
+ result = setrlimit(RLIMIT_STACK, &rl);
+ if (result != 0)
+ {
+ reporterr( "Warning: Failed to extend stack size. It's ok in most cases but there may be problems in --pileup and --chainedtree.\n" );
+ }
+ }
+ else
+ reporterr( "stacksize: %d kb\n", rl.rlim_cur / 1024 );
+ }
+ else
+ reporterr( "Warning: Cannot check stack size.\n" );
+}
+#endif
+
+
+
+
+#if 0
+#include <sys/time.h>
+#include <sys/resource.h>
+
+void use_getrusage(void)
+{
+ struct rusage r;
+ if (getrusage(RUSAGE_SELF, &r) != 0) {
+ /*Failure*/
+ }
+ fprintf(stderr, "\nmaxrss = %ld MB\n", r.ru_maxrss/1000);
+}
+
+#endif
git://source.jalview.org / jabaws.git / blobdiff