903 	char **mseq1, **mseq2;  in treebasethread()  local
928 	mseq2 = AllocateCharMtx( njob, 0 );  in treebasethread()
967 			free( mseq2 );  in treebasethread()
1055 		clus2 = fastconjuction_noname( topol[l][1], localcopy, mseq2, effarr2, effarr, indication2, 0.0 );  in treebasethread()
1058 		clus2 = fastconjuction_noweight( topol[l][1], localcopy, mseq2, effarr2,  indication2 );  in treebasethread()
1074         if( strlen( mseq2[j] ) != len2 )   in treebasethread()
1095         if( strlen( mseq2[j] ) != len2 )   in treebasethread()
1148 …pscore = Falign_udpari_long( NULL, NULL, dynamicmtx, mseq1, mseq2, effarr1, effarr2, NULL, NULL, c…  in treebasethread()
1152 …pscore = Falign( NULL, NULL, dynamicmtx, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2,…  in treebasethread()
1162 					pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );  in treebasethread()
1167 …pscore = MSalignmm( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NUL…  in treebasethread()
1173 						pscore = G__align11( dynamicmtx, mseq1, mseq2, *alloclen, outgap, outgap );  in treebasethread()
1178 …pscore = D__align_ls( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &…  in treebasethread()
1185 						pscore = G__align11( dynamicmtx, mseq1, mseq2, *alloclen, outgap, outgap );  in treebasethread()
1190 …pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dum…  in treebasethread()
1219 			makeskiptable( clus2, skiptable2, mseq2 ); // allocate suru.  in treebasethread()
1244 …newdistmtx[immin][immax-immin] = ( 1.0 - naivepairscorefast( mseq1[i], mseq2[m], skiptable1[i], sk…  in treebasethread()
1246 …newdistmtx[immin][immax-immin] = ( 1.0 - naivepairscore11( mseq1[i], mseq2[m], penalty_dist ) / bu…  in treebasethread()
1299 …nt *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq1, char **mseq2, int ***topol, Tre…  in treebase()  argument
1404 		clus2 = fastconjuction_noname( topol[l][1], aseq, mseq2, effarr2, effarr, indication2, 0.0 );  in treebase()
1407 		clus2 = fastconjuction_noweight( topol[l][1], aseq, mseq2, effarr2,  indication2 );  in treebase()
1431 			findcommongaps( clus2, mseq2, gapmap );  in treebase()
1432 			commongappick( clus2, mseq2 );  in treebase()
1433 			len2nocommongap = strlen( mseq2[0] );  in treebase()
1454         if( strlen( mseq2[j] ) != len2 )   in treebase()
1476         if( strlen( mseq2[j] ) != len2 )   in treebase()
1539 …pscore = Falign_udpari_long( NULL, NULL, dynamicmtx, mseq1, mseq2, effarr1, effarr2, NULL, NULL, c…  in treebase()
1543 …pscore = Falign( NULL, NULL, dynamicmtx, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2,…  in treebase()
1554 					pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );  in treebase()
1559 …pscore = MSalignmm( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NUL…  in treebase()
1565 						pscore = G__align11( dynamicmtx, mseq1, mseq2, *alloclen, outgap, outgap );  in treebase()
1570 …pscore = D__align_ls( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &…  in treebase()
1577 						pscore = G__align11( dynamicmtx, mseq1, mseq2, *alloclen, outgap, outgap );  in treebase()
1582 …pscore = A__align( dynamicmtx, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dum…  in treebase()
1615 			for( i=0; i<clus2; i++ ) reporterr(       ">STEP1 mseq2[%d] = \n%s\n", i, mseq2[i] );  in treebase()
1634 			for( i=0; i<clus2; i++ ) reporterr(       ">STEP3 mseq2[%d] = \n%s\n", i, mseq2[i] );  in treebase()
1647 				reporterr( "mseq2[%d] bef change = %s\n", i, mseq2[i] );  in treebase()
1648 				eq2dash( mseq2[i] );  in treebase()
1649 				reporterr( "mseq2[%d] aft change = %s\n", i, mseq2[i] );  in treebase()
1652 			for( i=0; i<clus2; i++ ) eq2dash( mseq2[i] );  in treebase()
1657 			eq2dashmatometehayaku( mseq2, clus2 );  in treebase()
1676 			makeskiptable( clus2, skiptable2, mseq2 ); // allocate suru.  in treebase()
1704 …newdistmtx[immin][immax-immin] = ( 1.0 - naivepairscorefast( mseq1[i], mseq2[m], skiptable1[i], sk…  in treebase()
1706 …newdistmtx[immin][immax-immin] = ( 1.0 - naivepairscore11( mseq1[i], mseq2[m], penalty_dist ) / bu…  in treebase()
1836 	char **mseq1 = NULL, **mseq2 = NULL;  in disttbfast()  local
1981 	mseq2 = AllocateCharMtx( njob, 0 );  in disttbfast()
2739 …if( treebase( nlen, bseq, nadd, mergeoralign, mseq1, mseq2, topol, dep, eff, mtx, selfscore, &allo…  in disttbfast()
2745 …if( treebase( nlen, bseq, nadd, mergeoralign, mseq1, mseq2, topol, dep, eff, NULL, NULL, &alloclen…  in disttbfast()
2972 	free( mseq2 );  in disttbfast()
2993 	if( mseq2 ) free( mseq2 ); mseq2 = NULL;  in disttbfast()