/***************************************************************************** # Copyright (C) 1994-2008 by David Gordon. # All rights reserved. # # This software is part of a beta-test version of the Consed/Autofinish # package. It should not be redistributed or # used for any commercial purpose, including commercially funded # sequencing, without written permission from the author and the # University of Washington. # # This software is provided ``AS IS'' and any express or implied # warranties, including, but not limited to, the implied warranties of # merchantability and fitness for a particular purpose, are disclaimed. # In no event shall the authors or the University of Washington be # liable for any direct, indirect, incidental, special, exemplary, or # consequential damages (including, but not limited to, procurement of # substitute goods or services; loss of use, data, or profits; or # business interruption) however caused and on any theory of liability, # whether in contract, strict liability, or tort (including negligence # or otherwise) arising in any way out of the use of this software, even # if advised of the possibility of such damage. # # Building Consed from source is error prone and not simple which is # why I provide executables. Due to time limitations I cannot # provide any assistance in building Consed. Even if you do not # modify the source, you may introduce errors due to using a # different version of the compiler, a different version of motif, # different versions of other libraries than I used, etc. For this # reason, if you discover Consed bugs, I can only offer help with # those bugs if you first reproduce those bugs with an executable # provided by me--not an executable you have built. # # Modifying Consed is also difficult. Although Consed is modular, # some modules are used by many other modules. Thus making a change # in one place can have unforeseen effects on many other features. # It may takes months for you to notice these other side-effects # which may not seen connected at all. It is not feasable for me to # provide help with modifying Consed sources because of the # potentially huge amount of time involved. # #*****************************************************************************/ #include "lookForFalsePrimerMatchesOfOnePrimerInOneContig.h" #include "lookForPerfect4MerFalsePrimerMatchesOfOnePrimerInOneContig.h" #include "lookForImperfect3Prime4MerFalsePrimerMatchesOfOnePrimerInOneContig.h" #include "consedParameters.h" void lookForFalsePrimerMatchesOfOnePrimerInOneContig( primerType* pPrimer, Contig* pContigOfTarget, const bool bLookEverywhereInContig, const int nUnpaddedConsPosOfTargetStart, const int nUnpaddedConsPosOfTargetEnd, const bool bForwardNotReversePrimer ) { lookForPerfect4MerFalsePrimerMatchesOfOnePrimerInOneContig( pPrimer, pContigOfTarget, false, // complement contig bLookEverywhereInContig, nUnpaddedConsPosOfTargetStart, nUnpaddedConsPosOfTargetEnd, bForwardNotReversePrimer ); if ( !pPrimer->bAcceptable_ ) return; lookForPerfect4MerFalsePrimerMatchesOfOnePrimerInOneContig( pPrimer, pContigOfTarget, true, // complement contig bLookEverywhereInContig, nUnpaddedConsPosOfTargetStart, nUnpaddedConsPosOfTargetEnd, bForwardNotReversePrimer ); if ( !pPrimer->bAcceptable_ ) return; lookForImperfect3Prime4MerFalsePrimerMatchesOfOnePrimerInOneContig( pPrimer, pContigOfTarget, false, // complement contig bLookEverywhereInContig, nUnpaddedConsPosOfTargetStart, nUnpaddedConsPosOfTargetEnd, bForwardNotReversePrimer ); // if ( !pPrimer->bAcceptable_ ) { // // this is a primer that was eliminated based on a 6-base perfect match // // and a score too high. For debugging, print information about it to // // the xterm // char szDescription[500]; // int n5PrimeFalseMatch = 0; // int n3PrimeFalseMatch = 0; // RWCString soFalseMatchContigName; // // handle case in which there is no false match at all // // so pContigOfStickiestFalseMatch is NULL // if ( pPrimer->pContigOfStickiestFalseMatch_ ) { // if ( pPrimer->bContigOfStickiestFalseMatchIsComplemented_ ) { // n5PrimeFalseMatch = // pPrimer->pContigOfStickiestFalseMatch_->nComplementUnpaddedIndex( pPrimer->nUnpaddedOfStickiestFalseMatch_ ); // n3PrimeFalseMatch = n5PrimeFalseMatch - consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimer_ + 1; // } // else { // n5PrimeFalseMatch = // pPrimer->nUnpaddedOfStickiestFalseMatch_; // n3PrimeFalseMatch = // n5PrimeFalseMatch + // consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimer_ // - 1; // } // soFalseMatchContigName = pPrimer->pContigOfStickiestFalseMatch_->soGetName(); // } // sprintf( szDescription, "%-11s %3d %7d %7d %2d %2d %-11s %7d %7d %-1s %2d %2d %2d %2d ", // (char*) pPrimer->pContig_->soGetName().data(), // pPrimer->nDistanceFromCursor_, // pPrimer->nUnpaddedStart_, // pPrimer->nUnpaddedEnd_, // pPrimer->nUnpaddedLength_, // pPrimer->nScoreOfStickiestFalseMatch_, // (char*) soFalseMatchContigName.data(), // n5PrimeFalseMatch, // n3PrimeFalseMatch, // ( pPrimer->bContigOfStickiestFalseMatchIsComplemented_ ? // "C" : "U" ), // (int) pPrimer->dMeltingTemperature_, // pPrimer->nSelfMatchScore_, // pPrimer->nSequenceInFileStickiestScore_, // (int) pPrimer->ucMinQuality_ ); // printf( "%s\n", szDescription ); // for( int n = 0; n < pPrimer->nUnpaddedLength_; ++n ) // putchar( *(pPrimer->szPrimer_ + n) ); // putchar( '\n' ); // if ( pPrimer->pContigOfStickiestFalseMatch_ ) { // if ( pPrimer->bContigOfStickiestFalseMatchIsComplemented_ ) { // for( int nUnpadded = n5PrimeFalseMatch; // nUnpadded >= n3PrimeFalseMatch; // --nUnpadded ) { // int nConsPos =pPrimer->pContigOfStickiestFalseMatch_->nPaddedIndexFast( nUnpadded ); // char c = pPrimer->pContigOfStickiestFalseMatch_->ntGetCons( nConsPos ).cGetBase(); // putchar( cComplementBase( c ) ); // } // putchar( '\n' ); // } // else { // for( int nUnpadded = n5PrimeFalseMatch; // nUnpadded <= n3PrimeFalseMatch; // ++nUnpadded ) { // int nConsPos = pPrimer->pContigOfStickiestFalseMatch_->nPaddedIndexFast( nUnpadded ); // char c = pPrimer->pContigOfStickiestFalseMatch_->ntGetCons( nConsPos ).cGetBase(); // putchar( c ); // } // putchar( '\n' ); // } // } // } if ( !pPrimer->bAcceptable_ ) return; lookForImperfect3Prime4MerFalsePrimerMatchesOfOnePrimerInOneContig( pPrimer, pContigOfTarget, true, // complement contig bLookEverywhereInContig, nUnpaddedConsPosOfTargetStart, nUnpaddedConsPosOfTargetEnd, bForwardNotReversePrimer ); // if ( !pPrimer->bAcceptable_ ) { // // this is a primer that was eliminated based on a 6-base perfect match // // and a score too high. For debugging, print information about it to // // the xterm // char szDescription[500]; // int n5PrimeFalseMatch = 0; // int n3PrimeFalseMatch = 0; // RWCString soFalseMatchContigName; // // handle case in which there is no false match at all // // so pContigOfStickiestFalseMatch is NULL // if ( pPrimer->pContigOfStickiestFalseMatch_ ) { // if ( pPrimer->bContigOfStickiestFalseMatchIsComplemented_ ) { // n5PrimeFalseMatch = // pPrimer->pContigOfStickiestFalseMatch_->nComplementUnpaddedIndex( pPrimer->nUnpaddedOfStickiestFalseMatch_ ); // n3PrimeFalseMatch = n5PrimeFalseMatch - consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimer_ + 1; // } // else { // n5PrimeFalseMatch = // pPrimer->nUnpaddedOfStickiestFalseMatch_; // n3PrimeFalseMatch = // n5PrimeFalseMatch + // consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimer_ // - 1; // } // soFalseMatchContigName = pPrimer->pContigOfStickiestFalseMatch_->soGetName(); // } // sprintf( szDescription, "%-11s %3d %7d %7d %2d %2d %-11s %7d %7d %-1s %2d %2d %2d %2d ", // (char*) pPrimer->pContig_->soGetName().data(), // pPrimer->nDistanceFromCursor_, // pPrimer->nUnpaddedStart_, // pPrimer->nUnpaddedEnd_, // pPrimer->nUnpaddedLength_, // pPrimer->nScoreOfStickiestFalseMatch_, // (char*) soFalseMatchContigName.data(), // n5PrimeFalseMatch, // n3PrimeFalseMatch, // ( pPrimer->bContigOfStickiestFalseMatchIsComplemented_ ? // "C" : "U" ), // (int) pPrimer->dMeltingTemperature_, // pPrimer->nSelfMatchScore_, // pPrimer->nSequenceInFileStickiestScore_, // (int) pPrimer->ucMinQuality_ ); // printf( "%s\n", szDescription ); // for( int n = 0; n < pPrimer->nUnpaddedLength_; ++n ) // putchar( *(pPrimer->szPrimer_ + n) ); // putchar( '\n' ); // if ( pPrimer->pContigOfStickiestFalseMatch_ ) { // if ( pPrimer->bContigOfStickiestFalseMatchIsComplemented_ ) { // for( int nUnpadded = n5PrimeFalseMatch; // nUnpadded >= n3PrimeFalseMatch; // --nUnpadded ) { // int nConsPos =pPrimer->pContigOfStickiestFalseMatch_->nPaddedIndexFast( nUnpadded ); // char c = pPrimer->pContigOfStickiestFalseMatch_->ntGetCons( nConsPos ).cGetBase(); // putchar( cComplementBase( c ) ); // } // putchar( '\n' ); // } // else { // for( int nUnpadded = n5PrimeFalseMatch; // nUnpadded <= n3PrimeFalseMatch; // ++nUnpadded ) { // int nConsPos = pPrimer->pContigOfStickiestFalseMatch_->nPaddedIndexFast( nUnpadded ); // char c = pPrimer->pContigOfStickiestFalseMatch_->ntGetCons( nConsPos ).cGetBase(); // putchar( c ); // } // putchar( '\n' ); // } // } // } }