/***************************************************************************** # 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 "guiSearchForOpenReadingFrames.h" #include "contig.h" #include "abs.h" #include "please_wait.h" #include "guiMultiContigNavigator.h" #include "bIsStartCodon.h" #include "bIsStopCodon.h" #include "complementSequence.h" guiSearchForOpenReadingFrames :: guiSearchForOpenReadingFrames( Widget widParentShell, Contig* pContig, ContigWin* pContigWin ) : pContig_( pContig ) { PleaseWait* pPleaseWait = new PleaseWait( widParentShell ); pContig_->setPaddedPositionsArray(); RWCString soColumnHeadings1 = " Length Reading Start End"; RWCString soColumnHeadings2 = " Frame Pos Pos"; pGuiMultiContigNav_ = new guiMultiContigNavigator( "Open Reading Frames", soColumnHeadings1, soColumnHeadings2, 100, "", // soTitleOfSpecialPurposeButton NULL, // cbSpecialPurposeButton NULL, // pClientDataForCbSpecialPurposeButton widParentShell, NULL, // pGotoList pContigWin ); int nUnpaddedLength; char* szConsensus = pContig_->szGetUnpaddedConsensus( nUnpaddedLength ); int nReadingFrame; for( nReadingFrame = 1; nReadingFrame <= 3; ++nReadingFrame ) { bool bInORF = false; for( int nBasePos = nReadingFrame - 1; ( nBasePos + 2 ) < nUnpaddedLength; nBasePos += 3 ) { int nUnpaddedStartPos; if ( !bInORF ) { if ( bIsStartCodon( szConsensus[ nBasePos ], szConsensus[ nBasePos + 1 ], szConsensus[ nBasePos + 2 ] ) ) { bInORF = true; nUnpaddedStartPos = nBasePos + 1; // nBasePos is zero-based and nUnpaddedStartPos is 1 based } } else { if ( bIsStopCodon( szConsensus[ nBasePos ], szConsensus[ nBasePos + 1 ], szConsensus[ nBasePos + 2 ] ) ) { bInORF = false; // set up for finding next one in this // reading frame // nBasePos + 2 is the last base of the stop codon // nBasePos + 3 is this last base in 1-based coordinates addThisORFToList( nReadingFrame, nUnpaddedStartPos, nBasePos + 3 ); } } } } complementSequence( szConsensus, nUnpaddedLength ); for( nReadingFrame = 1; nReadingFrame <= 3; ++nReadingFrame ) { bool bInORF = false; for( int nBasePos = nReadingFrame - 1; ( nBasePos + 2 ) < nUnpaddedLength; nBasePos += 3 ) { int nUnpaddedStartPos; if ( !bInORF ) { if ( bIsStartCodon( szConsensus[ nBasePos ], szConsensus[ nBasePos + 1 ], szConsensus[ nBasePos + 2 ] ) ) { bInORF = true; nUnpaddedStartPos = nBasePos + 1; // nBasePos is zero-based and nUnpaddedStartPos is 1 based } } else { if ( bIsStopCodon( szConsensus[ nBasePos ], szConsensus[ nBasePos + 1 ], szConsensus[ nBasePos + 2 ] ) ) { bInORF = false; // set up for finding next one in this // reading frame // now do all the conversion int nRealReadingFrame = - nReadingFrame; int nRealUnpaddedStartPos = ( nUnpaddedLength + 1 ) - nUnpaddedStartPos; int nRealUnpaddedStopPos = ( nUnpaddedLength + 1 ) - ( nBasePos + 3 ); addThisORFToList( nRealReadingFrame, nRealUnpaddedStartPos, nRealUnpaddedStopPos ); } } } } pGuiMultiContigNav_->pGotoList_->sortByLength(); pGuiMultiContigNav_->displayList( false ); // don't re-sort delete pPleaseWait; } void guiSearchForOpenReadingFrames :: addThisORFToList( const int nReadingFrame, const int nUnpaddedStartOfORF, const int nUnpaddedEndOfORF ) { // note: nUnpaddedStartOfORF will be less than nUnpaddedEndOfORF // for top strand ORFs and greater for bottom strand ORFs int nConsPosStart = pContig_->nPaddedIndexFast( nUnpaddedStartOfORF ); int nConsPosEnd = pContig_->nPaddedIndexFast( nUnpaddedEndOfORF ); char szDescription[200]; sprintf( szDescription, "%5d bp %2d %6d to %6d", ABS( nUnpaddedStartOfORF - nUnpaddedEndOfORF ) + 1, // length nReadingFrame, nUnpaddedStartOfORF, nUnpaddedEndOfORF ); gotoItem* pGotoItem = new gotoItem( pContig_, NULL, nConsPosStart, nConsPosEnd, nUnpaddedStartOfORF, nUnpaddedEndOfORF, szDescription, false // don't let gotoItem ctor // mess with description ); pGuiMultiContigNav_->appendToList( pGotoItem ); }