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JWS-112 Bumping version of Mafft to version 7.310.
[jabaws.git] / binaries / src / mafft / core / restoreu.c
diff --git a/binaries/src/mafft/core/restoreu.c b/binaries/src/mafft/core/restoreu.c
index 40055da..eb2b665 100644 (file)
--- a/binaries/src/mafft/core/restoreu.c
+++ b/binaries/src/mafft/core/restoreu.c
@@ -3,6 +3,7 @@
 #define DEBUG 0
 
 char *alignmentfile;
+int keeplength;
 
 static void fillorichar( int nseq, int *oripos, char **a, char **s )
 {
@@ -10,6 +11,7 @@ static void fillorichar( int nseq, int *oripos, char **a, char **s )
        char *pta, *pts;
        for( i=0; i<nseq; i++ )
        {
+
                pta = a[i];
                pts = s[oripos[i]];
                while( *pta )
@@ -18,14 +20,14 @@ static void fillorichar( int nseq, int *oripos, char **a, char **s )
                        if( *pta++ == 0 )
                        {
                                fprintf( stderr, "ERROR!!\n" );
-                               fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
+                               fprintf( stderr, "alignment is inconsistent with the original sequences (1)\n" );
                                exit( 1 );
                        }
                }
                if( *pts != 0 )
                {
                        fprintf( stderr, "ERROR!!\n" );
-                       fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
+                       fprintf( stderr, "alignment is inconsistent with the original sequences (2)\n" );
                        exit( 1 );
                }
        }
@@ -35,6 +37,8 @@ void arguments( int argc, char *argv[] )
 {
     int c;
 
+       keeplength = 0;
+
     while( --argc > 0 && (*++argv)[0] == '-' )
        {
         while ( (c = *++argv[0]) )
@@ -49,6 +53,13 @@ void arguments( int argc, char *argv[] )
                                        alignmentfile = *++argv;
                                        --argc;
                                        goto nextoption;
+                               case 'Z': // add2ndharfarg wo tsukau tame.
+                                       break;
+                               case 'p': // add2ndharfarg wo tsukau tame.
+                                       break;
+                               case 'Y':
+                                       keeplength = 1;
+                                       break;
                 default:
                     fprintf( stderr, "illegal option %c\n", c );
                     argc = 0;
@@ -71,6 +82,7 @@ int main( int argc, char *argv[] )
 {
        FILE *infp;
        FILE *alfp;
+       FILE *dlfp;
        char **name;
        char **aname;
        char **oname;
@@ -78,10 +90,13 @@ int main( int argc, char *argv[] )
        char **aseq;
        int *nlen;
        int *oripos;
-       char *npt, *npt2;
+       char *npt, *npt0, *npt2, *pt, *pt2;
        int i, o, prelen;
        int nlenmin;
        int njobs, njoba;
+//     int **dlist;
+//     int *ndel;
+       char *gett;
 
        arguments( argc, argv );
 
@@ -111,6 +126,16 @@ int main( int argc, char *argv[] )
                fprintf( stderr, "No alignment is given.\n" );
                exit( 1 );
        }
+
+       if( keeplength )
+       {
+               dlfp = fopen( "_deletelist", "r" );
+               if( !dlfp )
+               {
+                       fprintf( stderr, "Cannot open _deletefile\n" );
+                       exit( 1 );
+               }
+       }
        
        dorp = NOTSPECIFIED;
        getnumlen_casepreserve( infp, &nlenmin );
@@ -122,6 +147,7 @@ int main( int argc, char *argv[] )
        nlen = AllocateIntVec( njob );
        oripos = AllocateIntVec( njob );
        readData_pointer_casepreserve( infp, name, nlen, seq );
+       fclose( infp );
 
        dorp = NOTSPECIFIED;
        getnumlen( alfp );
@@ -131,9 +157,42 @@ int main( int argc, char *argv[] )
        aname = AllocateCharMtx( njob, B+1 );
        oname = AllocateCharMtx( njob, B+1 );
        readData_pointer( alfp, aname, nlen, aseq );
+       fclose( alfp );
 
        for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
 
+//     reporterr( "seq[njob-1] = %s\n", seq[njob-1] );
+
+       if( keeplength )
+       {
+               gett = calloc( 1000, sizeof( char ) );
+//             ndel = (int *)calloc( njob, sizeof( int ) );
+//             for( i=0; i<njob; i++ ) ndel[i] = 0;
+//             dlist = (int **)calloc( njob+1, sizeof( int * ) );
+//             for( i=0; i<njob; i++ ) dlist[i] = NULL;
+//             dlist[njob] = NULL;
+
+               while( 1 )
+               {
+                       fgets( gett, 999, dlfp );
+                       if( feof( dlfp ) ) break;
+                       sscanf( gett, "%d %d", &i, &o );
+//                     reporterr( "%d, %d\n", i, o );
+//                     dlist[i] = realloc( dlist[i], sizeof( int ) * (ndel[i]+2) );
+//                     dlist[i][ndel[i]] = o;
+//                     ndel[i]++;
+
+                       seq[i][o] = '-';
+
+               }
+               fclose( dlfp );
+       }
+
+       for( i=0; i<njob; i++ )
+       {
+               gappick_samestring( seq[i] );
+       }
+
        if( njoba != njobs )
        {
                fprintf( stderr, "ERROR!!\n" );
@@ -161,41 +220,70 @@ int main( int argc, char *argv[] )
                fprintf( stderr, "npt2 = %s\n", npt2 );
 
                o = oripos[i] = atoi( npt2 );
-               npt = strstr( npt2, "_oripos_" );
+               npt = strstr( npt2, "_oe_" );
                if( npt == NULL )
                {
                        fprintf( stderr, "Format error!\n" );
                        exit( 1 );
                }
-               npt += 8;
+               npt += 4;
                strcat( oname[i], npt+1 );
 #endif
-               npt = strstr( aname[i], "_oripos_" );
-               if( npt == NULL )
+               npt0 = strstr( aname[i], "_os_" );
+               if( npt0 == NULL )
                {
                        fprintf( stderr, "Format error!\n" );
                        exit( 1 );
                }
-               npt2 = npt - 2;
-               while( isdigit( *npt2-- ) );
-               npt2 += 2;
-               npt += 8;
+               npt2 = npt0 + 4;
                o = oripos[i] = atoi( npt2 );
-//             fprintf( stderr, "npt2 = :%s:\n", npt2 );
-//             fprintf( stderr, "npt = :%s:\n", npt );
-//             fprintf( stderr, "aname[i] = :%s:\n", aname[i] );
-//             fprintf( stderr, "npt2-aname[i] = :%d:\n", npt2-aname[i] );
 
-               prelen = npt2-aname[i];
+               npt = strstr( aname[i], "_oe_" );
+               if( npt == NULL )
+               {
+                       fprintf( stderr, "Format error!\n" );
+                       exit( 1 );
+               }
+               npt += 4;
+
+               pt2 = npt;
+               pt = npt2 - 4;
+               while( *pt ) *pt++ = *pt2++; // okashii
+
+               prelen = npt0-aname[i];
                strncpy( oname[i], aname[i], prelen ); oname[i][prelen] = 0;
-               strcat( oname[i], npt+1 );
+               strcat( oname[i], npt0 );
+
+#if 0
+               pt = strstr( aname[i], "_numo_e" );
+               if( pt ) pt += 8;
+               else pt = aname[i] + 1;
+
+               if( strstr( pt, "_seed_" ) ) pt += 6;
+
+               fprintf( stderr, "pt = :%s:\n", pt );
+
+#endif
+//             fprintf( stderr, "npt0 = :%s:\n", npt0 );
+//
+//             reporterr( "oname[i] = %s\n", oname[i] );
+//             reporterr( "aname[i] = %s\n", aname[i] );
+//             reporterr( " name[i] = %s\n",  name[i] );
+
+//             fprintf( stderr, "aname[i] = :%s:\n", aname[i] );
+//             fprintf( stderr, "pt = :%s:\n", pt );
+//             fprintf( stderr, "oname[i] = :%s:\n", oname[i] );
+//             fprintf( stderr, "name[o] = :%s:\n", name[o] );
 
-               if( strncmp( npt, name[o], 10 ) )
+               if( strncmp( npt0, name[o]+1, 10 ) )
                {
                        fprintf( stderr, "ERROR!!\n" );
                        fprintf( stderr, "In input file,\n" );
                        fprintf( stderr, "name[%d] = %s\n", o, name[o] );
                        fprintf( stderr, "but in alignment file,\n" );
+                       fprintf( stderr, "oname[%d] = %s\n", i, oname[i] );
+                       fprintf( stderr, "npt0 = %s\n", npt0 );
+                       fprintf( stderr, "prelen = %d\n", prelen );
                        fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
                        exit( 1 );
                }
@@ -223,7 +311,9 @@ int main( int argc, char *argv[] )
        FreeCharMtx( aseq );
        FreeCharMtx( name );
        FreeCharMtx( aname );
+       FreeCharMtx( oname );
        free( nlen );
+       free( oripos );
 
        return( 0 );
 }