/***************************************************************************** # 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. # #*****************************************************************************/ tagTypes::pGetTagTypes()->assignValidTagType( "edit", pRes->soTagColorEdit_, tagType::both, false ); tagTypes::pGetTagTypes()->assignValidTagType( "becomeConsensus", pRes->soTagColorBecomeConsensus_, tagType::read, false ); tagTypes::pGetTagTypes()->assignValidTagType( "ignoreMismatches", pRes->soTagColorIgnoreMismatches_, tagType::read, false ); tagTypes::pGetTagTypes()->assignValidTagType( "ignoreMatches", pRes->soTagColorIgnoreMatches_, tagType::read, false ); tagTypes::pGetTagTypes()->assignValidTagType( "significantDiscrepancy", pRes->soTagColorSignificantDiscrepancy_, tagType::read, false ); tagTypes::pGetTagTypes()->assignValidTagType( "compression", pRes->soTagColorCompression_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "dataNeeded", pRes->soTagColorDataNeeded_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( "comment", pRes->soTagColorComment_, tagType::both, true ); tagTypes::pGetTagTypes()->assignValidTagType( "tagsOverlap", pRes->soTagColorTagsOverlap_, tagType::both, false ); tagTypes::pGetTagTypes()->assignValidTagType( "sequencingVector", pRes->soTagColorSequencingVector_, tagType::both, true ); tagTypes::pGetTagTypes()->assignValidTagType( "cloningVector", pRes->soTagColorCloningVector_, tagType::both, true ); tagTypes::pGetTagTypes()->assignValidTagType( "vector", pRes->soTagColorVector_, tagType::both, true ); tagTypes::pGetTagTypes()->assignValidTagType( "oligo", pRes->soTagColorOligo_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( "oligo3PrimeEnd", pRes->soTagColorOligo3PrimeEnd_, tagType::consensus, false ); tagTypes::pGetTagTypes()->assignValidTagType( "chimera", pRes->soTagColorChimera_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "contigName", pRes->soTagColorContigName_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( "polymorphism", pRes->soTagColorPolymorphism_, tagType::both, true ); tagTypes::pGetTagTypes()->assignValidTagType( "homozygoteAA", pRes->soTagColorHomozygoteAA_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "homozygoteCC", pRes->soTagColorHomozygoteCC_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "homozygoteGG", pRes->soTagColorHomozygoteGG_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "homozygoteTT", pRes->soTagColorHomozygoteTT_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "heterozygoteAC", pRes->soTagColorHeterozygoteAC_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "heterozygoteAG", pRes->soTagColorHeterozygoteAG_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "heterozygoteAT", pRes->soTagColorHeterozygoteAT_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "heterozygoteCG", pRes->soTagColorHeterozygoteCG_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "heterozygoteCT", pRes->soTagColorHeterozygoteCT_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "heterozygoteGT", pRes->soTagColorHeterozygoteGT_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "repeat", pRes->soTagColorRepeat_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( "polyPhredRank1", pRes->soTagColorPolyPhredRank1_, tagType::consensus, false ); tagTypes::pGetTagTypes()->assignValidTagType( "polyPhredRank2", pRes->soTagColorPolyPhredRank2_, tagType::consensus, false ); tagTypes::pGetTagTypes()->assignValidTagType( "polyPhredRank3", pRes->soTagColorPolyPhredRank3_, tagType::consensus, false ); tagTypes::pGetTagTypes()->assignValidTagType( "polyPhredRank4", pRes->soTagColorPolyPhredRank4_, tagType::consensus, false ); tagTypes::pGetTagTypes()->assignValidTagType( "polyPhredRank5", pRes->soTagColorPolyPhredRank5_, tagType::consensus, false ); tagTypes::pGetTagTypes()->assignValidTagType( "polyPhredRank6", pRes->soTagColorPolyPhredRank6_, tagType::consensus, false ); tagTypes::pGetTagTypes()->assignValidTagType( "indelSite", pRes->soTagColorIndelSite_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( "heterozygoteIndel", pRes->soTagColorHeterozygoteIndel_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "homozygoteIndel", pRes->soTagColorHomozygoteIndel_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "polymorphismConfirmed", pRes->soTagColorPolymorphismConfirmed_, tagType::both, true ); tagTypes::pGetTagTypes()->assignValidTagType( "matchElsewhereHighQual", pRes->soTagColorMatchElsewhereHighQual_, tagType::both, false ); tagTypes::pGetTagTypes()->assignValidTagType( "matchElsewhereLowQual", pRes->soTagColorMatchElsewhereLowQual_, tagType::both, false ); tagTypes::pGetTagTypes()->assignValidTagType( "G_dropout", pRes->soTagColorG_dropout_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "markedHighQuality", pRes->soTagColorMarkedHighQuality_, tagType::read, false ); tagTypes::pGetTagTypes()->assignValidTagType( "markedLowQuality", pRes->soTagColorMarkedLowQuality_, tagType::read, false ); tagTypes::pGetTagTypes()->assignValidTagType( "autoFinishExp", pRes->soTagColorAutoFinishExp_, tagType::consensus, false ); tagTypes::pGetTagTypes()->assignValidTagType( "doNotFinish", pRes->soTagColorDoNotFinish_, tagType::both, true ); tagTypes::pGetTagTypes()->assignValidTagType( "doNotDoPCR", pRes->soTagColorDoNotDoPCR_, tagType::both, true ); tagTypes::pGetTagTypes()->assignValidTagType( "consedFixedGoldenPath", pRes->soTagColorConsedFixedGoldenPath_, tagType::both, false ); tagTypes::pGetTagTypes()->assignValidTagType( "cloneEnd", pRes->soTagColorCloneEnd_, tagType::both, false ); tagTypes::pGetTagTypes()->assignValidTagType( "editable", pRes->soTagColorEditable_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( "contigEndPair", pRes->soTagColorContigEndPair_, tagType::consensus, false ); tagTypes::pGetTagTypes()->assignValidTagType( "changedGenotype", pRes->soTagColorChangedGenotype_, tagType::read, false ); tagTypes::pGetTagTypes()->assignValidTagType( "startNumberingConsensus", pRes->soTagColorStartNumberingConsensus_, tagType::both, false ); tagTypes::pGetTagTypes()->assignValidTagType( "referenceSequence", pRes->soTagColorReferenceSequence_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( "join", pRes->soTagColorJoin_, tagType::consensus, false ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag1_, pRes->soTagColorCustomTag1_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag2_, pRes->soTagColorCustomTag2_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag3_, pRes->soTagColorCustomTag3_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag4_, pRes->soTagColorCustomTag4_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag5_, pRes->soTagColorCustomTag5_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag6_, pRes->soTagColorCustomTag6_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag7_, pRes->soTagColorCustomTag7_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag8_, pRes->soTagColorCustomTag8_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag9_, pRes->soTagColorCustomTag9_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag10_, pRes->soTagColorCustomTag10_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag11_, pRes->soTagColorCustomTag11_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag12_, pRes->soTagColorCustomTag12_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag13_, pRes->soTagColorCustomTag13_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag14_, pRes->soTagColorCustomTag14_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomTag15_, pRes->soTagColorCustomTag15_, tagType::read, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag1_, pRes->soTagColorCustomConsensusTag1_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag2_, pRes->soTagColorCustomConsensusTag2_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag3_, pRes->soTagColorCustomConsensusTag3_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag4_, pRes->soTagColorCustomConsensusTag4_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag5_, pRes->soTagColorCustomConsensusTag5_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag6_, pRes->soTagColorCustomConsensusTag6_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag7_, pRes->soTagColorCustomConsensusTag7_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag8_, pRes->soTagColorCustomConsensusTag8_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag9_, pRes->soTagColorCustomConsensusTag9_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag10_, pRes->soTagColorCustomConsensusTag10_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag11_, pRes->soTagColorCustomConsensusTag11_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag12_, pRes->soTagColorCustomConsensusTag12_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag13_, pRes->soTagColorCustomConsensusTag13_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag14_, pRes->soTagColorCustomConsensusTag14_, tagType::consensus, true ); tagTypes::pGetTagTypes()->assignValidTagType( pRes->soCustomConsensusTag15_, pRes->soTagColorCustomConsensusTag15_, tagType::consensus, true );