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Viewing changes to core/tbfast.c

  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2014-10-05 09:00:33 UTC
  • mfrom: (1.1.23)
  • Revision ID: package-import@ubuntu.com-20141005090033-jz7hffbtf1xnirrn
Tags: 7.187-1
* New upstream release.
* Conforms to Policy 3.9.6.

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Lines of Context:
core/tbfast.c
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        float *selfscore;
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        float **iscore;
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        char **seq;
 
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        int **skiptable;
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        Jobtable *jobpospt;
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        pthread_mutex_t *mutex;
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} distancematrixthread_arg_t;
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        tbrweight = 3;
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        checkC = 0;
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        treemethod = 'X';
 
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        sueff_global = 0.1;
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        contin = 0;
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        scoremtx = 1;
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        kobetsubunkatsu = 0;
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#endif
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                                case 'X':
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                                        treemethod = 'X';
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                                        break;
 
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                                        sueff_global = atof( *++argv );
 
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                                        fprintf( stderr, "sueff_global = %f\n", sueff_global );
 
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                                        --argc;
 
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                                        goto nextoption;
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                                case 'E':
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                                        treemethod = 'E';
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                                        break;
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        float *selfscore = targ->selfscore;
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        float **iscore = targ->iscore;
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        char **seq = targ->seq;
 
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        int **skiptable = targ->skiptable;
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        Jobtable *jobpospt = targ->jobpospt;
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        float ssi, ssj, bunbo;
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                if( bunbo == 0.0 )
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                        iscore[i][j-i] = 2.0; // 2013/Oct/17
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                else
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                        iscore[i][j-i] = ( 1.0 - naivepairscore11( seq[i], seq[j], penalty_dist ) / bunbo ) * 2.0; // 2013/Oct/17
 
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//                      iscore[i][j-i] = ( 1.0 - naivepairscore11( seq[i], seq[j], penalty_dist ) / bunbo ) * 2.0; // 2013/Oct/17
 
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                        iscore[i][j-i] = ( 1.0 - naivepairscorefast( seq[i], seq[j], skiptable[i], skiptable[j], penalty_dist ) / bunbo ) * 2.0; // 2014/Aug/15 fast
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        }
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}
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        static char **mseq1, **mseq2;
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        static char **bseq;
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        static float **iscore, **iscore_kozo;
 
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        int **skiptable;
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        static double *eff, *eff_kozo, *eff_kozo_mapped = NULL;
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        int i, j, ien, ik, jk;
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        static int ***topol, ***topol_kozo;
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                        fprintf( stderr, "Making a distance matrix .. \n" );
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                        fflush( stderr );
 
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                        skiptable = AllocateIntMtx( njob, 0 );
 
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                        makeskiptable( njob, skiptable, seq ); // allocate suru.
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                        ien = njob-1;
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                        for( i=0; i<njob; i++ ) 
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                        {
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                                selfscore[i] = naivepairscore11( seq[i], seq[i], penalty_dist );
 
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//                              selfscore[i] = naivepairscore11( seq[i], seq[i], penalty_dist );
 
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                                selfscore[i] = naivepairscorefast( seq[i], seq[i], skiptable[i], skiptable[i], penalty_dist );
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//                              fprintf( stderr, "penalty = %d\n", penalty );
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//                              fprintf( stderr, "penalty_dist = %d\n", penalty_dist );
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                        }
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                                        targ[i].selfscore = selfscore;
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                                        targ[i].iscore = iscore;
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                                        targ[i].seq = seq;
 
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                                        targ[i].skiptable = skiptable;
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                                        targ[i].jobpospt = &jobpos;
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                                        targ[i].mutex = &mutex;
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                                                        iscore[i][j-i] = 2.0; // 2013/Oct/17 2bai
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                                                else
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//                                                      iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty_dist ) / MIN( selfscore[i], selfscore[j] );
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                                                        iscore[i][j-i] = ( 1.0 - naivepairscore11( seq[i], seq[j], penalty_dist ) / bunbo ) * 2.0; // 2013/Oct/17 2bai
 
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//                                                      iscore[i][j-i] = ( 1.0 - naivepairscore11( seq[i], seq[j], penalty_dist ) / bunbo ) * 2.0; // 2013/Oct/17 2bai
 
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                                                        iscore[i][j-i] = ( 1.0 - naivepairscorefast( seq[i], seq[j], skiptable[i], skiptable[j], penalty_dist ) / bunbo ) * 2.0; // 2014/Aug/15 fast
 
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//exit( 1 );
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#if 0
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                                                fprintf( stderr, "### ssj = %f\n", ssj );
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                                }
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                        }
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                        fprintf( stderr, "\ndone.\n\n" );
 
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                        FreeIntMtx( skiptable );
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                        fflush( stderr );
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                }
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                else
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                }
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                else if( subalignment ) // merge error no tame
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                {
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                        fixed_supg_float_realloc_nobk_halfmtx_treeout_constrained( njob, iscore, topol, len, name, nlen, dep, nsubalignments, subtable );
 
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                        fixed_supg_float_realloc_nobk_halfmtx_treeout_constrained( njob, iscore, topol, len, name, nlen, dep, nsubalignments, subtable, 1 );
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                }
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                else if( treeout ) // merge error no tame
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                {
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                        fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( njob, iscore, topol, len, name, nlen, dep );
 
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                        fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( njob, iscore, topol, len, name, nlen, dep, 1 );
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                }
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                else
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                {
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                        fixed_musclesupg_float_realloc_nobk_halfmtx( njob, iscore, topol, len, dep, 1 );
 
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                        fixed_musclesupg_float_realloc_nobk_halfmtx( njob, iscore, topol, len, dep, 1, 1 );
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                }
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//              else 
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//                      ErrorExit( "Incorrect tree\n" );
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//                      for( i=0; i<nkozo-1; i++ )
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//                              for( j=i+1; j<nkozo; j++ )
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//                                      fprintf( stderr, "iscore_kozo[%d][%d] =~ %f\n", i, j, iscore_kozo[i][j-i] );
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                        fixed_musclesupg_float_realloc_nobk_halfmtx( nkozo, iscore_kozo, topol_kozo, len_kozo, NULL, 1 );
 
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                        fixed_musclesupg_float_realloc_nobk_halfmtx( nkozo, iscore_kozo, topol_kozo, len_kozo, NULL, 1, 1 );
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                }
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                fprintf( stderr, "\ndone.\n\n" );
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                fflush( stderr );