From 191ae1be0679d5cf4eda950b3b1bf26fb7dd503d Mon Sep 17 00:00:00 2001 From: westcott Date: Tue, 26 Oct 2010 12:06:29 +0000 Subject: [PATCH] fixes while testing --- aligncommand.cpp | 1 + binsequencecommand.cpp | 1 + bootstrapsharedcommand.cpp | 1 + chimerabellerophoncommand.cpp | 1 + chopseqscommand.cpp | 1 + classifyotucommand.cpp | 1 + classifyseqscommand.cpp | 1 + clearcutcommand.cpp | 1 + clustercommand.cpp | 1 + clusterfragmentscommand.cpp | 1 + clustersplitcommand.cpp | 1 + collectcommand.cpp | 1 + collectsharedcommand.cpp | 1 + consensuscommand.cpp | 1 + deconvolutecommand.cpp | 1 + degapseqscommand.cpp | 1 + deuniqueseqscommand.cpp | 1 + distancecommand.cpp | 1 + filterseqscommand.cpp | 1 + getgroupcommand.cpp | 1 + getlineagecommand.cpp | 1 + getlistcountcommand.cpp | 1 + getoturepcommand.cpp | 1 + getrabundcommand.cpp | 1 + getrelabundcommand.cpp | 1 + getsabundcommand.cpp | 1 + getseqscommand.cpp | 1 + getsharedotucommand.cpp | 1 + hclustercommand.cpp | 1 + heatmapcommand.cpp | 1 + heatmapsimcommand.cpp | 1 + libshuffcommand.cpp | 1 + listseqscommand.cpp | 1 + makegroupcommand.cpp | 1 + matrixoutputcommand.cpp | 1 + mergefilecommand.cpp | 1 + metastatscommand.cpp | 1 + mgclustercommand.cpp | 1 + normalizesharedcommand.cpp | 1 + otuhierarchycommand.cpp | 1 + pairwiseseqscommand.cpp | 1 + parsefastaqcommand.cpp | 1 + parselistscommand.cpp | 1 + parsesffcommand.cpp | 1 + parsimonycommand.cpp | 1 + pcacommand.cpp | 1 + phylodiversitycommand.cpp | 1 + phylotypecommand.cpp | 1 + pipelinepdscommand.cpp | 16 +++++++++------- preclustercommand.cpp | 1 + rarefactcommand.cpp | 1 + rarefactsharedcommand.cpp | 1 + readotucommand.cpp | 1 + removelineagecommand.cpp | 1 + removeseqscommand.cpp | 1 + reversecommand.cpp | 1 + screenseqscommand.cpp | 1 + secondarystructurecommand.cpp | 1 + sensspeccommand.cpp | 1 + seqerrorcommand.cpp | 1 + seqsummarycommand.cpp | 1 + sffinfocommand.cpp | 1 + sharedcommand.cpp | 3 ++- sharedlistvector.cpp | 6 ++++-- splitabundcommand.cpp | 1 + splitgroupscommand.cpp | 1 + summarycommand.cpp | 1 + summarysharedcommand.cpp | 1 + treegroupscommand.cpp | 2 ++ trimseqscommand.cpp | 1 + unifracunweightedcommand.cpp | 2 ++ unifracweightedcommand.cpp | 1 + venncommand.cpp | 1 + 73 files changed, 87 insertions(+), 10 deletions(-) diff --git a/aligncommand.cpp b/aligncommand.cpp index 8a229e3..624aab4 100644 --- a/aligncommand.cpp +++ b/aligncommand.cpp @@ -64,6 +64,7 @@ vector AlignCommand::getRequiredFiles(){ //********************************************************************************************************************** AlignCommand::AlignCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp index a1c965b..bf14d6b 100644 --- a/binsequencecommand.cpp +++ b/binsequencecommand.cpp @@ -48,6 +48,7 @@ vector BinSeqCommand::getRequiredFiles(){ //********************************************************************************************************************** BinSeqCommand::BinSeqCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp index 2b7232d..b7d6c45 100644 --- a/bootstrapsharedcommand.cpp +++ b/bootstrapsharedcommand.cpp @@ -34,6 +34,7 @@ vector BootSharedCommand::getValidParameters(){ //********************************************************************************************************************** BootSharedCommand::BootSharedCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["tree"] = tempOutNames; diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp index d3c8ea5..3409615 100644 --- a/chimerabellerophoncommand.cpp +++ b/chimerabellerophoncommand.cpp @@ -48,6 +48,7 @@ vector ChimeraBellerophonCommand::getRequiredFiles(){ //********************************************************************************************************************** ChimeraBellerophonCommand::ChimeraBellerophonCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["chimera"] = tempOutNames; diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp index 1133ff4..31fe64f 100644 --- a/chopseqscommand.cpp +++ b/chopseqscommand.cpp @@ -25,6 +25,7 @@ vector ChopSeqsCommand::getValidParameters(){ //********************************************************************************************************************** ChopSeqsCommand::ChopSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp index cedc1f2..3469c82 100644 --- a/classifyotucommand.cpp +++ b/classifyotucommand.cpp @@ -25,6 +25,7 @@ vector ClassifyOtuCommand::getValidParameters(){ //********************************************************************************************************************** ClassifyOtuCommand::ClassifyOtuCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["constaxonomy"] = tempOutNames; diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp index 302c4f7..b8d5b8e 100644 --- a/classifyseqscommand.cpp +++ b/classifyseqscommand.cpp @@ -30,6 +30,7 @@ vector ClassifySeqsCommand::getValidParameters(){ //********************************************************************************************************************** ClassifySeqsCommand::ClassifySeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["taxonomy"] = tempOutNames; diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp index 025987f..a2d0aaa 100644 --- a/clearcutcommand.cpp +++ b/clearcutcommand.cpp @@ -31,6 +31,7 @@ vector ClearcutCommand::getValidParameters(){ //********************************************************************************************************************** ClearcutCommand::ClearcutCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["tree"] = tempOutNames; diff --git a/clustercommand.cpp b/clustercommand.cpp index 8a1d120..6043d39 100644 --- a/clustercommand.cpp +++ b/clustercommand.cpp @@ -24,6 +24,7 @@ vector ClusterCommand::getValidParameters(){ //********************************************************************************************************************** ClusterCommand::ClusterCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["list"] = tempOutNames; diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp index b5681db..d24d2ca 100644 --- a/clusterfragmentscommand.cpp +++ b/clusterfragmentscommand.cpp @@ -39,6 +39,7 @@ vector ClusterFragmentsCommand::getValidParameters(){ //********************************************************************************************************************** ClusterFragmentsCommand::ClusterFragmentsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp index 3c957a6..6b5012a 100644 --- a/clustersplitcommand.cpp +++ b/clustersplitcommand.cpp @@ -31,6 +31,7 @@ vector ClusterSplitCommand::getValidParameters(){ //********************************************************************************************************************** ClusterSplitCommand::ClusterSplitCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["list"] = tempOutNames; diff --git a/collectcommand.cpp b/collectcommand.cpp index 3dd2436..9ea55b2 100644 --- a/collectcommand.cpp +++ b/collectcommand.cpp @@ -72,6 +72,7 @@ vector CollectCommand::getRequiredFiles(){ //********************************************************************************************************************** CollectCommand::CollectCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["sobs"] = tempOutNames; diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp index 8719489..d63930d 100644 --- a/collectsharedcommand.cpp +++ b/collectsharedcommand.cpp @@ -71,6 +71,7 @@ vector CollectSharedCommand::getRequiredFiles(){ //********************************************************************************************************************** CollectSharedCommand::CollectSharedCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["sharedchao"] = tempOutNames; diff --git a/consensuscommand.cpp b/consensuscommand.cpp index a746990..0671790 100644 --- a/consensuscommand.cpp +++ b/consensuscommand.cpp @@ -46,6 +46,7 @@ vector ConcensusCommand::getRequiredFiles(){ //********************************************************************************************************************** ConcensusCommand::ConcensusCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["tree"] = tempOutNames; diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp index 3129ea0..dd05afd 100644 --- a/deconvolutecommand.cpp +++ b/deconvolutecommand.cpp @@ -24,6 +24,7 @@ vector DeconvoluteCommand::getValidParameters(){ //********************************************************************************************************************** DeconvoluteCommand::DeconvoluteCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp index f1190c8..2514ae1 100644 --- a/degapseqscommand.cpp +++ b/degapseqscommand.cpp @@ -25,6 +25,7 @@ vector DegapSeqsCommand::getValidParameters(){ //********************************************************************************************************************** DegapSeqsCommand::DegapSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp index a4395a7..f6b32e6 100644 --- a/deuniqueseqscommand.cpp +++ b/deuniqueseqscommand.cpp @@ -25,6 +25,7 @@ vector DeUniqueSeqsCommand::getValidParameters(){ //********************************************************************************************************************** DeUniqueSeqsCommand::DeUniqueSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/distancecommand.cpp b/distancecommand.cpp index f09aa99..07d7f0f 100644 --- a/distancecommand.cpp +++ b/distancecommand.cpp @@ -29,6 +29,7 @@ vector DistanceCommand::getValidParameters(){ //********************************************************************************************************************** DistanceCommand::DistanceCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["phylip"] = tempOutNames; diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp index 1d9ee27..c4a3a95 100644 --- a/filterseqscommand.cpp +++ b/filterseqscommand.cpp @@ -25,6 +25,7 @@ vector FilterSeqsCommand::getValidParameters(){ //********************************************************************************************************************** FilterSeqsCommand::FilterSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp index 40bfb26..2847db1 100644 --- a/getgroupcommand.cpp +++ b/getgroupcommand.cpp @@ -24,6 +24,7 @@ vector GetgroupCommand::getValidParameters(){ //********************************************************************************************************************** GetgroupCommand::GetgroupCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["bootgroup"] = tempOutNames; diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp index 91811fa..eaa8d40 100644 --- a/getlineagecommand.cpp +++ b/getlineagecommand.cpp @@ -27,6 +27,7 @@ vector GetLineageCommand::getValidParameters(){ //********************************************************************************************************************** GetLineageCommand::GetLineageCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp index 31b1748..1ecef65 100644 --- a/getlistcountcommand.cpp +++ b/getlistcountcommand.cpp @@ -24,6 +24,7 @@ vector GetListCountCommand::getValidParameters(){ //********************************************************************************************************************** GetListCountCommand::GetListCountCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["otu"] = tempOutNames; diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp index 1e09dba..0edaf3d 100644 --- a/getoturepcommand.cpp +++ b/getoturepcommand.cpp @@ -38,6 +38,7 @@ inline bool compareGroup(repStruct left, repStruct right){ //********************************************************************************************************************** GetOTURepCommand::GetOTURepCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp index a38aeb3..60f4ece 100644 --- a/getrabundcommand.cpp +++ b/getrabundcommand.cpp @@ -24,6 +24,7 @@ vector GetRAbundCommand::getValidParameters(){ //********************************************************************************************************************** GetRAbundCommand::GetRAbundCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["rabund"] = tempOutNames; diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp index 5b9327b..8c28c47 100644 --- a/getrelabundcommand.cpp +++ b/getrelabundcommand.cpp @@ -24,6 +24,7 @@ vector GetRelAbundCommand::getValidParameters(){ //********************************************************************************************************************** GetRelAbundCommand::GetRelAbundCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["relabund"] = tempOutNames; diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp index 8ad8b4b..3637d29 100644 --- a/getsabundcommand.cpp +++ b/getsabundcommand.cpp @@ -24,6 +24,7 @@ vector GetSAbundCommand::getValidParameters(){ //********************************************************************************************************************** GetSAbundCommand::GetSAbundCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["sabund"] = tempOutNames; diff --git a/getseqscommand.cpp b/getseqscommand.cpp index 34788b8..b48ba28 100644 --- a/getseqscommand.cpp +++ b/getseqscommand.cpp @@ -26,6 +26,7 @@ vector GetSeqsCommand::getValidParameters(){ //********************************************************************************************************************** GetSeqsCommand::GetSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp index f8c245f..699581f 100644 --- a/getsharedotucommand.cpp +++ b/getsharedotucommand.cpp @@ -25,6 +25,7 @@ vector GetSharedOTUCommand::getValidParameters(){ //********************************************************************************************************************** GetSharedOTUCommand::GetSharedOTUCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/hclustercommand.cpp b/hclustercommand.cpp index e236d86..5c08320 100644 --- a/hclustercommand.cpp +++ b/hclustercommand.cpp @@ -24,6 +24,7 @@ vector HClusterCommand::getValidParameters(){ //********************************************************************************************************************** HClusterCommand::HClusterCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["list"] = tempOutNames; diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp index dc4fec2..8920108 100644 --- a/heatmapcommand.cpp +++ b/heatmapcommand.cpp @@ -24,6 +24,7 @@ vector HeatMapCommand::getValidParameters(){ //********************************************************************************************************************** HeatMapCommand::HeatMapCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["svg"] = tempOutNames; diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp index 1eb3cee..7ab178c 100644 --- a/heatmapsimcommand.cpp +++ b/heatmapsimcommand.cpp @@ -34,6 +34,7 @@ vector HeatMapSimCommand::getValidParameters(){ //********************************************************************************************************************** HeatMapSimCommand::HeatMapSimCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["svg"] = tempOutNames; diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp index e48cf33..e7fb357 100644 --- a/libshuffcommand.cpp +++ b/libshuffcommand.cpp @@ -33,6 +33,7 @@ vector LibShuffCommand::getValidParameters(){ //********************************************************************************************************************** LibShuffCommand::LibShuffCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["coverage"] = tempOutNames; diff --git a/listseqscommand.cpp b/listseqscommand.cpp index c8c8297..b4b4674 100644 --- a/listseqscommand.cpp +++ b/listseqscommand.cpp @@ -26,6 +26,7 @@ vector ListSeqsCommand::getValidParameters(){ //********************************************************************************************************************** ListSeqsCommand::ListSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["accnos"] = tempOutNames; diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp index 611f00f..c427db5 100644 --- a/makegroupcommand.cpp +++ b/makegroupcommand.cpp @@ -25,6 +25,7 @@ vector MakeGroupCommand::getValidParameters(){ //********************************************************************************************************************** MakeGroupCommand::MakeGroupCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["group"] = tempOutNames; diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp index 020ccff..2ea9377 100644 --- a/matrixoutputcommand.cpp +++ b/matrixoutputcommand.cpp @@ -34,6 +34,7 @@ vector MatrixOutputCommand::getValidParameters(){ //********************************************************************************************************************** MatrixOutputCommand::MatrixOutputCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["phylip"] = tempOutNames; diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp index d431dd3..c7e5b65 100644 --- a/mergefilecommand.cpp +++ b/mergefilecommand.cpp @@ -24,6 +24,7 @@ vector MergeFileCommand::getValidParameters(){ //********************************************************************************************************************** MergeFileCommand::MergeFileCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["merge"] = tempOutNames; diff --git a/metastatscommand.cpp b/metastatscommand.cpp index f0496b2..866bc94 100644 --- a/metastatscommand.cpp +++ b/metastatscommand.cpp @@ -26,6 +26,7 @@ vector MetaStatsCommand::getValidParameters(){ //********************************************************************************************************************** MetaStatsCommand::MetaStatsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["metastats"] = tempOutNames; diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp index e5dd1a3..3ed9bf2 100644 --- a/mgclustercommand.cpp +++ b/mgclustercommand.cpp @@ -25,6 +25,7 @@ vector MGClusterCommand::getValidParameters(){ //********************************************************************************************************************** MGClusterCommand::MGClusterCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["list"] = tempOutNames; diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp index 8fc5d30..93bc7f2 100644 --- a/normalizesharedcommand.cpp +++ b/normalizesharedcommand.cpp @@ -24,6 +24,7 @@ vector NormalizeSharedCommand::getValidParameters(){ //********************************************************************************************************************** NormalizeSharedCommand::NormalizeSharedCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["shared"] = tempOutNames; diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp index 022ff3a..14138de 100644 --- a/otuhierarchycommand.cpp +++ b/otuhierarchycommand.cpp @@ -24,6 +24,7 @@ vector OtuHierarchyCommand::getValidParameters(){ //********************************************************************************************************************** OtuHierarchyCommand::OtuHierarchyCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["otuheirarchy"] = tempOutNames; diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp index 733c470..aed03cd 100644 --- a/pairwiseseqscommand.cpp +++ b/pairwiseseqscommand.cpp @@ -61,6 +61,7 @@ vector PairwiseSeqsCommand::getRequiredFiles(){ //********************************************************************************************************************** PairwiseSeqsCommand::PairwiseSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["phylip"] = tempOutNames; diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp index 31de119..1e66431 100644 --- a/parsefastaqcommand.cpp +++ b/parsefastaqcommand.cpp @@ -25,6 +25,7 @@ vector ParseFastaQCommand::getValidParameters(){ //********************************************************************************************************************** ParseFastaQCommand::ParseFastaQCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/parselistscommand.cpp b/parselistscommand.cpp index 84d9104..9cf5a73 100644 --- a/parselistscommand.cpp +++ b/parselistscommand.cpp @@ -25,6 +25,7 @@ vector ParseListCommand::getValidParameters(){ //********************************************************************************************************************** ParseListCommand::ParseListCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["list"] = tempOutNames; diff --git a/parsesffcommand.cpp b/parsesffcommand.cpp index c636ec9..e2f9d61 100644 --- a/parsesffcommand.cpp +++ b/parsesffcommand.cpp @@ -25,6 +25,7 @@ vector ParseSFFCommand::getValidParameters(){ //********************************************************************************************************************** ParseSFFCommand::ParseSFFCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["flow"] = tempOutNames; diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index b879395..3d6818b 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -24,6 +24,7 @@ vector ParsimonyCommand::getValidParameters(){ //********************************************************************************************************************** ParsimonyCommand::ParsimonyCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["parsimony"] = tempOutNames; diff --git a/pcacommand.cpp b/pcacommand.cpp index 4a4e55e..ee0a546 100644 --- a/pcacommand.cpp +++ b/pcacommand.cpp @@ -25,6 +25,7 @@ vector PCACommand::getValidParameters(){ //********************************************************************************************************************** PCACommand::PCACommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["pcoa"] = tempOutNames; diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp index 1c90eca..efa14cd 100644 --- a/phylodiversitycommand.cpp +++ b/phylodiversitycommand.cpp @@ -24,6 +24,7 @@ vector PhyloDiversityCommand::getValidParameters(){ //********************************************************************************************************************** PhyloDiversityCommand::PhyloDiversityCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["phylodiv"] = tempOutNames; diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp index c4751b5..2018170 100644 --- a/phylotypecommand.cpp +++ b/phylotypecommand.cpp @@ -28,6 +28,7 @@ vector PhylotypeCommand::getValidParameters(){ //********************************************************************************************************************** PhylotypeCommand::PhylotypeCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["list"] = tempOutNames; diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp index d928122..ae2663d 100644 --- a/pipelinepdscommand.cpp +++ b/pipelinepdscommand.cpp @@ -355,12 +355,12 @@ bool PipelineCommand::parseCommand(string nextCommand, string& name, string& opt bool PipelineCommand::checkForValidAndRequiredParameters(string name, string options, map >& mothurMadeFiles){ try { - + if (name == "system") { return false; } //get shell of the command so we can check to make sure its valid without running it Command* command = cFactory->getCommand(name); - + //check to make sure all parameters are valid for command vector validParameters = command->getValidParameters(); @@ -372,6 +372,7 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt map >::iterator itMade; for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, validParameters, it->second) != true) { return true; } // not valid if (it->second == "mothurmade") { itMade = mothurMadeFiles.find(it->first); @@ -385,7 +386,7 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt } } } - + //is the command missing any required vector requiredParameters = command->getRequiredParameters(); @@ -404,7 +405,7 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt if (!hasOr) { m->mothurOut(name + " requires the " + requiredParameters[i] + " parameter, please correct."); m->mothurOutEndLine(); } } } - + // if all are needed and not all are found if ((!hasOr) && (numFound != requiredParameters.size())) { return true; } //if one is needed and none are found @@ -415,7 +416,7 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt for (itMade = thisCommandsFile.begin(); itMade != thisCommandsFile.end(); itMade++) { mothurMadeFiles[itMade->first] = itMade->second; //adds any new types } - + return false; } catch(exception& e) { @@ -440,8 +441,8 @@ int PipelineCommand::runUsersPipeline(){ CommandOptionParser parser(nextCommand); string commandName = parser.getCommandString(); string options = parser.getOptionString(); - - if (options != "") { + + if ((options != "") && (commandName != "system")) { bool error = fillInMothurMade(options, mothurMadeFiles); if (error) { in.close(); return 0; } } @@ -532,6 +533,7 @@ int PipelineCommand::runUsersPipeline(){ //********************************************************************************************************************** bool PipelineCommand::fillInMothurMade(string& options, map >& mothurMadeFiles){ try { + OptionParser parser(options); map parameters = parser.getParameters(); map::iterator it; diff --git a/preclustercommand.cpp b/preclustercommand.cpp index e6ccc9b..3a3aafc 100644 --- a/preclustercommand.cpp +++ b/preclustercommand.cpp @@ -26,6 +26,7 @@ vector PreClusterCommand::getValidParameters(){ //********************************************************************************************************************** PreClusterCommand::PreClusterCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp index d430ffc..cb37727 100644 --- a/rarefactcommand.cpp +++ b/rarefactcommand.cpp @@ -62,6 +62,7 @@ vector RareFactCommand::getRequiredFiles(){ //********************************************************************************************************************** RareFactCommand::RareFactCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["rarefaction"] = tempOutNames; diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp index 0be8141..8cf1f2f 100644 --- a/rarefactsharedcommand.cpp +++ b/rarefactsharedcommand.cpp @@ -26,6 +26,7 @@ vector RareFactSharedCommand::getValidParameters(){ //********************************************************************************************************************** RareFactSharedCommand::RareFactSharedCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["sharedrarefaction"] = tempOutNames; diff --git a/readotucommand.cpp b/readotucommand.cpp index 24a30cb..8683fc3 100644 --- a/readotucommand.cpp +++ b/readotucommand.cpp @@ -24,6 +24,7 @@ vector ReadOtuCommand::getValidParameters(){ //********************************************************************************************************************** ReadOtuCommand::ReadOtuCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["rabund"] = tempOutNames; diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp index 629416a..1ea9c39 100644 --- a/removelineagecommand.cpp +++ b/removelineagecommand.cpp @@ -26,6 +26,7 @@ vector RemoveLineageCommand::getValidParameters(){ //********************************************************************************************************************** RemoveLineageCommand::RemoveLineageCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp index afba651..c0e04d5 100644 --- a/removeseqscommand.cpp +++ b/removeseqscommand.cpp @@ -26,6 +26,7 @@ vector RemoveSeqsCommand::getValidParameters(){ //********************************************************************************************************************** RemoveSeqsCommand::RemoveSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/reversecommand.cpp b/reversecommand.cpp index d179f0d..7b58162 100644 --- a/reversecommand.cpp +++ b/reversecommand.cpp @@ -25,6 +25,7 @@ vector ReverseSeqsCommand::getValidParameters(){ //********************************************************************************************************************** ReverseSeqsCommand::ReverseSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp index 5845b8f..8a7a108 100644 --- a/screenseqscommand.cpp +++ b/screenseqscommand.cpp @@ -26,6 +26,7 @@ vector ScreenSeqsCommand::getValidParameters(){ //********************************************************************************************************************** ScreenSeqsCommand::ScreenSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp index 36e0f60..26bd354 100644 --- a/secondarystructurecommand.cpp +++ b/secondarystructurecommand.cpp @@ -25,6 +25,7 @@ vector AlignCheckCommand::getValidParameters(){ //********************************************************************************************************************** AlignCheckCommand::AlignCheckCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["aligncheck"] = tempOutNames; diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp index 78dce17..045736d 100644 --- a/sensspeccommand.cpp +++ b/sensspeccommand.cpp @@ -24,6 +24,7 @@ vector SensSpecCommand::getValidParameters(){ //********************************************************************************************************************** SensSpecCommand::SensSpecCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["sensspec"] = tempOutNames; diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp index 1f880f3..0da4d1c 100644 --- a/seqerrorcommand.cpp +++ b/seqerrorcommand.cpp @@ -24,6 +24,7 @@ vector SeqErrorCommand::getValidParameters(){ //********************************************************************************************************************** SeqErrorCommand::SeqErrorCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["error"] = tempOutNames; diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp index 7d074c4..5776b97 100644 --- a/seqsummarycommand.cpp +++ b/seqsummarycommand.cpp @@ -25,6 +25,7 @@ vector SeqSummaryCommand::getValidParameters(){ //********************************************************************************************************************** SeqSummaryCommand::SeqSummaryCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["summary"] = tempOutNames; diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp index 1175446..d0ec9e2 100644 --- a/sffinfocommand.cpp +++ b/sffinfocommand.cpp @@ -25,6 +25,7 @@ vector SffInfoCommand::getValidParameters(){ //********************************************************************************************************************** SffInfoCommand::SffInfoCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/sharedcommand.cpp b/sharedcommand.cpp index 454bb05..c252b4f 100644 --- a/sharedcommand.cpp +++ b/sharedcommand.cpp @@ -26,7 +26,8 @@ vector SharedCommand::getValidParameters(){ } //********************************************************************************************************************** SharedCommand::SharedCommand(){ - try { + try { + //initialize outputTypes vector tempOutNames; outputTypes["rabund"] = tempOutNames; diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp index f2d8e07..0f4042f 100644 --- a/sharedlistvector.cpp +++ b/sharedlistvector.cpp @@ -36,12 +36,12 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB f >> label >> hold; data.assign(hold, ""); - + for(int i=0;i> inputData; set(i, inputData); } - + } catch(exception& e) { m->errorOut(e, "SharedListVector", "SharedListVector"); @@ -61,6 +61,8 @@ void SharedListVector::set(int binNumber, string seqNames){ if(nNames_new > maxRank) { maxRank = nNames_new; } numSeqs += (nNames_new - nNames_old); + + } catch(exception& e) { m->errorOut(e, "SharedListVector", "set"); diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp index 6070091..fb0326a 100644 --- a/splitabundcommand.cpp +++ b/splitabundcommand.cpp @@ -24,6 +24,7 @@ vector SplitAbundCommand::getValidParameters(){ //********************************************************************************************************************** SplitAbundCommand::SplitAbundCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["list"] = tempOutNames; diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp index 4be7a0e..1cbc2fc 100644 --- a/splitgroupscommand.cpp +++ b/splitgroupscommand.cpp @@ -48,6 +48,7 @@ vector SplitGroupCommand::getRequiredFiles(){ //********************************************************************************************************************** SplitGroupCommand::SplitGroupCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/summarycommand.cpp b/summarycommand.cpp index 1725815..d68d00a 100644 --- a/summarycommand.cpp +++ b/summarycommand.cpp @@ -49,6 +49,7 @@ vector SummaryCommand::getValidParameters(){ //********************************************************************************************************************** SummaryCommand::SummaryCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["summary"] = tempOutNames; diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index 99c62a5..5df448f 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -47,6 +47,7 @@ vector SummarySharedCommand::getValidParameters(){ //********************************************************************************************************************** SummarySharedCommand::SummarySharedCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["summary"] = tempOutNames; diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp index a36e599..64bcd36 100644 --- a/treegroupscommand.cpp +++ b/treegroupscommand.cpp @@ -34,6 +34,8 @@ vector TreeGroupCommand::getValidParameters(){ //********************************************************************************************************************** TreeGroupCommand::TreeGroupCommand(){ try { + abort = true; + globaldata = GlobalData::getInstance(); //initialize outputTypes vector tempOutNames; outputTypes["tree"] = tempOutNames; diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp index 56fd8c5..f684b66 100644 --- a/trimseqscommand.cpp +++ b/trimseqscommand.cpp @@ -26,6 +26,7 @@ vector TrimSeqsCommand::getValidParameters(){ //********************************************************************************************************************** TrimSeqsCommand::TrimSeqsCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["fasta"] = tempOutNames; diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp index b2d439b..24c7b54 100644 --- a/unifracunweightedcommand.cpp +++ b/unifracunweightedcommand.cpp @@ -24,6 +24,8 @@ vector UnifracUnweightedCommand::getValidParameters(){ //********************************************************************************************************************** UnifracUnweightedCommand::UnifracUnweightedCommand(){ try { + globaldata = GlobalData::getInstance(); + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["unweighted"] = tempOutNames; diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index 2646ede..33a0e6d 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -24,6 +24,7 @@ vector UnifracWeightedCommand::getValidParameters(){ //********************************************************************************************************************** UnifracWeightedCommand::UnifracWeightedCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["weighted"] = tempOutNames; diff --git a/venncommand.cpp b/venncommand.cpp index ab4f7a2..7601ed8 100644 --- a/venncommand.cpp +++ b/venncommand.cpp @@ -33,6 +33,7 @@ vector VennCommand::getValidParameters(){ //********************************************************************************************************************** VennCommand::VennCommand(){ try { + abort = true; //initialize outputTypes vector tempOutNames; outputTypes["svg"] = tempOutNames; -- 2.39.2