void CShellStep<T>::Serialize( stepArchive &ar) { try{ if (!isSerialized()){ setSerialized(); char out[128] = "(53%) "; strcat(out, this->name); #if NOTIFICATION if (CRepresentationStep::m_pStep->m_bWriteFile) CRepresentationStep::m_pStep->m_pScribView->Notify( out); #else //NOTIFICATION #endif//NOTIFICATION #ifdef SHOWPROGRESS if (CRepresentationStep::m_pStep->m_bWriteFile) CRepresentationStep::m_pStep->m_pScribView->progressBarUpdate( 53); #endif//SHOWPROGRESS writePre(ar); ar << "'', " ; writeNtuple(ar, m_pCFS_faces, m_pCFS_faces->GetSize()); writePost(ar); #ifdef WRITEEULER CBaseStep* pBaseStep=NULL; backPtr( pBaseStep); if (NULL!=pBaseStep){ CManifold_solid_brepStep* pManifold_solid_brepStep=(CManifold_solid_brepStep*) pBaseStep; pManifold_solid_brepStep->eulerCnt.m_numOpenShells++; } #endif//WRITEEULER int is = m_pCFS_faces->GetSize(); for ( int i = 0; i< is; i++){ CFaceStep* pS = (CFaceStep*)m_pCFS_faces->GetAt(i); if (NULL != pS){ pS->m_pBack = this; pS->Serialize(ar); } } } } catch(...){ ar << "\n/*Errors detected in CShellStep::Serialize #\n"; // ar << getNum(); ar << ", but continuing*/\n" ; } #if NOTIFICATION if (CRepresentationStep::m_pStep->m_bWriteFile) CRepresentationStep::m_pStep->m_pScribView->Notify("(65%) CShellStep::Serialize"); #else //NOTIFICATION #endif//NOTIFICATION #ifdef SHOWPROGRESS if (CRepresentationStep::m_pStep->m_bWriteFile) CRepresentationStep::m_pStep->m_pScribView->progressBarUpdate( 65); #endif//SHOWPROGRESS }
void CProduct_definitionStep::Serialize(stepArchive &ar) { #if 0 try{ if (!isSerialized()){ setSerialized(); writePre(ar); ar << "'',#"; ar << m_pPRODUCT_DEFINITION0->getNum(); ar << ",#"; ar << m_pPRODUCT_DEFINITION1->getNum(); ar << ","; if (NULL != m_pPRODUCT_DEFINITION2){ ar << "#"; ar << m_pPRODUCT_DEFINITION2->getNum(); } else { ar << "$"; } writePost(ar); m_pPRODUCT_DEFINITION0->Serialize( ar); m_pPRODUCT_DEFINITION1->Serialize( ar); if (NULL != m_pPRODUCT_DEFINITION2){ m_pPRODUCT_DEFINITION2->Serialize( ar); } } } catch(...){ ar << "\n/*Errors detected in ::Serialize #\n"; // ar << getNum(); ar << ", but continuing*/\n" ; } #endif }
void CDirectionStep::Serialize(stepArchive &ar) { if (!isSerialized()){ setSerialized(); try{ //ack move it inside writePre( ar); ar << "'" << m_szLabelName << "',"; ASSERT( m_bGood); if(!m_bGood){ // ar << "( 1.0, 1.0, 1.0)";// wh 03/12/02 ar << "( "; ar << restol; ar << ", "; ar << restol; ar << ", "; ar << restol; ar << ")"; ar << "\n/* Danger, zero length vector changed to dummy value!*/\n"; } else { writeDouble(ar, m_direction_ratios, sizeof(m_direction_ratios )/sizeof(m_direction_ratios[0])); } writePost( ar); } catch(...){ ar << "\n/*Errors detected in CPlacementStep::Serialize #\n"; // ar << getNum(); ar << ", but continuing*/\n" ; } } }
void CPlaneStep::Serialize( stepArchive &ar) { try { if (!isSerialized()) { setSerialized(); writePre( ar); ar << "'',#"; ar << m_pPosition->getNum(); writePost( ar); ASSERT( this == m_pPosition->m_pBack ); m_pPosition->Serialize(ar); } } catch(...) { ar << "\n/*Errors detected in "; ar << m_szTheClass; ar << "::Serialize #\n"; // ar << getNum(); ar << ", but continuing*/\n" ; } }
void CLineStep::Serialize(stepArchive &ar) { try{ if (!isSerialized()){ setSerialized(); writePre(ar); ar << "'',#"; ar << m_pPos->getNum(); ar << ",#"; ar << m_pDir->getNum(); writePost(ar); m_pPos->Serialize( ar); m_pDir->Serialize( ar); } } catch(...){ setSerialized(); ar << "\n/*Error caught in CCurveStep::Serialize!*/\n"; } }
void CCurveStep::Serialize(stepArchive &ar) { try{ if (!isSerialized()){ setSerialized(); writePre(ar); ar << "'',#"; // ar << m_rPos.getNum(); ar << ",#"; // ar << m_rDir.getNum(); writePost(ar); // m_rPos.Serialize( ar); // m_rDir.Serialize( ar); } } catch(...){ setSerialized(); ar << "\n/*Error caught in CCurveStep::Serialize!*/\n"; } }
int main( int argc, char *argv[] ) { char **argv2; static int *nlen; static char **name, **seq; static char **seq1, **seq2; static char **mseq1, **mseq2; static char **aseq; static char **bseq; static double **pscore; static double *eff; int i, j, len1, len2; static int ***topol; static double **len; FILE *gp1, *gp2; char c; int nlenmax1, nlenmax2, nseq1, nseq2; int alloclen; argv2 = arguments( argc, argv ); fprintf( stderr, "####### in galn\n" ); initFiles(); fprintf( stderr, "file1 = %s\n", argv2[0] ); fprintf( stderr, "file2 = %s\n", argv2[1] ); gp1 = fopen( argv2[0], "r" ); if( !gp1 ) ErrorExit( "cannot open file1" ); gp2 = fopen( argv2[1], "r" ); if( !gp2 ) ErrorExit( "cannot open file2" ); #if 0 PreRead( gp1, &nseq1, &nlenmax1 ); PreRead( gp2, &nseq2, &nlenmax2 ); #else getnumlen( gp1 ); nseq1 = njob; nlenmax1 = nlenmax; getnumlen( gp2 ); nseq2 = njob; nlenmax2 = nlenmax; #endif njob = nseq1 + nseq2; nlenmax = MAX( nlenmax1, nlenmax2 ); rewind( gp1 ); rewind( gp2 ); name = AllocateCharMtx( njob, B ); nlen = AllocateIntVec( njob ); seq1 = AllocateCharMtx( nseq1, nlenmax*3 ); seq2 = AllocateCharMtx( nseq2, nlenmax*3 ); seq = AllocateCharMtx( njob, 1 ); aseq = AllocateCharMtx( njob, nlenmax*3 ); bseq = AllocateCharMtx( njob, nlenmax*3 ); mseq1 = AllocateCharMtx( njob, 1 ); mseq2 = AllocateCharMtx( njob, 1 ); alloclen = nlenmax * 3; topol = AllocateIntCub( njob, 2, njob ); len = AllocateDoubleMtx( njob, 2 ); pscore = AllocateDoubleMtx( njob, njob ); eff = AllocateDoubleVec( njob ); #if 0 njob=nseq2; FRead( gp2, name+nseq1, nlen+nseq1, seq2 ); njob=nseq1; FRead( gp1, name, nlen, seq1 ); #else njob=nseq2; readDataforgaln( gp2, name+nseq1, nlen+nseq1, seq2 ); njob=nseq1; readDataforgaln( gp1, name, nlen, seq1 ); #endif njob = nseq1 + nseq2; #if 0 // CHUUI commongappick( nseq1, seq1 ); commongappick( nseq2, seq2 ); #endif for( i=0; i<nseq1; i++ ) seq[i] = seq1[i]; for( i=nseq1; i<njob; i++ ) seq[i] = seq2[i-nseq1]; /* Write( stdout, njob, name, nlen, seq ); */ constants( njob, seq ); WriteOptions( trap_g ); c = seqcheck( seq ); if( c ) { fprintf( stderr, "Illeagal character %c\n", c ); exit( 1 ); } for( i=1; i<nseq1; i++ ) { if( nlen[i] != nlen[0] ) ErrorExit( "group1 is not aligned." ); } for( i=nseq1+1; i<njob; i++ ) { if( nlen[i] != nlen[nseq1] ) ErrorExit( "group2 is not aligned." ); } if( tbutree == 0 ) { for( i=0; i<nseq1; i++ ) { for( j=i+1; j<nseq1; j++ ) { pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] ); // fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] ); } for( j=nseq1; j<njob; j++ ) { pscore[i][j] = 3.0; // fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] ); } } for( i=nseq1; i<njob-1; i++ ) { for( j=i+1; j<njob; j++ ) { pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] ); // fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] ); } } // fprintf( stderr, "\n" ); } else { fprintf( stderr, "Not supported\n" ); exit( 1 ); #if 0 prep = fopen( "hat2", "r" ); if( prep == NULL ) ErrorExit( "Make hat2." ); readhat2( prep, njob, name, pscore ); fclose( prep ); #endif } fprintf( stderr, "Constructing dendrogram ... " ); if( treemethod == 'x' ) veryfastsupg( njob, pscore, topol, len ); else ErrorExit( "Incorrect tree\n" ); fprintf( stderr, "done.\n" ); if( tbrweight ) { weight = 3; counteff_simple( njob, topol, len, eff ); // for( i=0; i<njob; i++ ) fprintf( stderr, "eff[%d] = %f\n", i, eff[i] ); } else { for( i=0; i<njob; i++ ) eff[i] = 1.0; } len1 = strlen( seq[0] ); len2 = strlen( seq[nseq1] ); if( len1 > 30000 || len2 > 30000 ) { fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 ); alg = 'M'; } GroupAlign( nseq1, nseq2, name, nlen, seq, aseq, mseq1, mseq2, topol, len, eff, alloclen ); #if 0 writePre( njob, name, nlen, aseq, 1 ); #else writeDataforgaln( stdout, njob, name, nlen, aseq ); #endif SHOWVERSION; return( 0 ); }
int main( int argc, char *argv[] ) { static int nlen[M]; static char **name, **seq; static char **oseq; static double **pscore; static double *eff; static double **node0, **node1; static double *gapc; static double *avgap; double tmpavgap; int i, j, m, goffset; static int ***topol; static double **len; FILE *prep; char c; int corestart, coreend; int alloclen; int winsize; char *pt, *ot; double gapmin; arguments( argc, argv ); getnumlen( stdin ); rewind( stdin ); if( njob < 2 ) { fprintf( stderr, "At least 2 sequences should be input!\n" "Only %d sequence found.\n", njob ); exit( 1 ); } seq = AllocateCharMtx( njob, nlenmax*9+1 ); name = AllocateCharMtx( njob, B+1 ); oseq = AllocateCharMtx( njob, nlenmax*9+1 ); alloclen = nlenmax*9; topol = AllocateIntCub( njob, 2, njob ); len = AllocateDoubleMtx( njob, 2 ); pscore = AllocateDoubleMtx( njob, njob ); eff = AllocateDoubleVec( njob ); node0 = AllocateDoubleMtx( njob, njob ); node1 = AllocateDoubleMtx( njob, njob ); gapc = AllocateDoubleVec( alloclen ); avgap = AllocateDoubleVec( alloclen ); #if 0 Read( name, nlen, seq ); #else readData_pointer( stdin, name, nlen, seq ); #endif constants( njob, seq ); #if 0 fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset ); #endif initSignalSM(); initFiles(); WriteOptions( trap_g ); c = seqcheck( seq ); if( c ) { fprintf( stderr, "Illeagal character %c\n", c ); exit( 1 ); } writePre( njob, name, nlen, seq, 0 ); if( tbutree == 0 ) { for( i=1; i<njob; i++ ) { if( nlen[i] != nlen[0] ) { fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" ); exit( 1 ); } } for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ ) { /* pscore[i][j] = (double)score_calc1( seq[i], seq[j] ); */ pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] ); } } else { fprintf( stderr, "Loading 'hat2' ... " ); prep = fopen( "hat2", "r" ); if( prep == NULL ) ErrorExit( "Make hat2." ); readhat2_pointer( prep, njob, name, pscore ); fclose( prep ); fprintf( stderr, "done.\n" ); #if 0 prep = fopen( "hat2_check", "w" ); WriteHat2( prep, njob, name, pscore ); fclose( prep ); #endif } fprintf( stderr, "Constructing dendrogram ... " ); if( treemethod == 'x' ) supg( njob, pscore, topol, len ); else if( treemethod == 's' ) spg( njob, pscore, topol, len ); else if( treemethod == 'p' ) upg2( njob, pscore, topol, len ); else ErrorExit( "Incorrect tree\n" ); fprintf( stderr, "done.\n" ); countnode( njob, topol, node0 ); if( tbrweight ) { weight = 3; #if 0 utree = 0; counteff( njob, topol, len, eff ); utree = 1; #else counteff_simple( njob, topol, len, eff ); #endif } else { for( i=0; i<njob; i++ ) eff[i] = 1.0; } for( i=0; i<nlenmax; i++ ) { gapc[i] = 0.0; for( j=0; j<njob; j++ ) { if( seq[j][i] == '-' ) gapc[i] += eff[j]; } } gapmin = 1.0; winsize = fftWinSize; goffset = winsize/2; tmpavgap = 0.0; corestart = coreend = -1; for( i=0; i<winsize; i++ ) { tmpavgap += gapc[i]; } for( i=winsize; i<nlenmax; i++ ) { m = i - goffset; avgap[m] = tmpavgap / winsize; // fprintf( stdout, "%d %f %f\n", m, avgap[m], gapc[i] ); if( avgap[m] < corethr ) { if( corestart == -1 ) corestart = i - winsize; // fprintf( stdout, "ok, gapmin = %f, corestart = %d, coreend = %d\n", gapmin, corestart, coreend ); if( avgap[m] < gapmin ) { gapmin = avgap[m]; } coreend = i; } tmpavgap -= gapc[i-winsize]; tmpavgap += gapc[i]; } if( corestart == -1 || coreend == -1 ) { corestart = 0; coreend = nlenmax-1; } for( i=0; i<njob; i++ ) { pt = oseq[i]; m = winsize; while( m-- ) *pt++ = '-'; for( j=corestart; j<=coreend; j++ ) *pt++ = seq[i][j]; m = winsize; while( m-- ) *pt++ = '-'; *pt = 0; ot = oseq[i]+winsize-1; pt = seq[i]+corestart-1; if( coreext ) m = winsize; else m = 0; while( m && --pt > seq[i] ) if( *pt != '-' ) { *ot-- = *pt; m--; } ot = oseq[i]+winsize+coreend-corestart+1; pt = seq[i]+coreend; if( coreext ) m = winsize; else m = 0; while( m && *(++pt) ) { if( *pt != '-' ) { *ot++ = *pt; m--; } } fprintf( stdout, ">%s\n", name[i] ); fprintf( stdout, "%s\n", oseq[i] ); } exit( 1 ); SHOWVERSION; return( 0 ); }