fixes while testing

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 8a229e3cade2cff57569e16b0e4b682d8dd0be65..624aab439855f60d9072889ae2cd80b33dae320e 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -64,6 +64,7 @@ vector<string> AlignCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index a1c965bb8052bab0d2ad086e8f57622ae5abfbc0..bf14d6b07b3b6ae64c20d3072abb3c3603a9e42c 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -48,6 +48,7 @@ vector<string> BinSeqCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 BinSeqCommand::BinSeqCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index 2b7232db4dd050a663c3a5b9514b59ae058e5c4c..b7d6c45e6e0179704a0e902c7960810e65df7eca 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -34,6 +34,7 @@ vector<string> BootSharedCommand::getValidParameters(){
 //**********************************************************************************************************************
 BootSharedCommand::BootSharedCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["tree"] = tempOutNames;

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index d3c8ea562ea314a6056409671defb41d15f3e834..34096159b4e1379d5e7c61ea6094d8514d48267c 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -48,6 +48,7 @@ vector<string> ChimeraBellerophonCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["chimera"] = tempOutNames;

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 1133ff46a8620817708c72607141691d59d5c4ac..31fe64f232919ec714eecb3227e2ee946d0c9c12 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -25,6 +25,7 @@ vector<string> ChopSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ChopSeqsCommand::ChopSeqsCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index cedc1f2c71c450f80ad5bcfefffe8713effab6fb..3469c82c0c1507604e87ea05efc30ca74927e09f 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -25,6 +25,7 @@ vector<string> ClassifyOtuCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClassifyOtuCommand::ClassifyOtuCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["constaxonomy"] = tempOutNames;

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 302c4f790c0f514e80e001488bde403f941b2c1f..b8d5b8efdc1d086a556c6ff0ea07332fd4470cf8 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -30,6 +30,7 @@ vector<string> ClassifySeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClassifySeqsCommand::ClassifySeqsCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["taxonomy"] = tempOutNames;

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 025987fd04bc676cadc7a59f14b19eb9862b5620..a2d0aaa5331a402a538d253e4d1f00d7800fa77e 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -31,6 +31,7 @@ vector<string> ClearcutCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClearcutCommand::ClearcutCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["tree"] = tempOutNames;

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 8a1d120934717524c2670699c8c487c8b6c8c6bc..6043d39be8d559010e156111f41a856b716cda40 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -24,6 +24,7 @@ vector<string> ClusterCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterCommand::ClusterCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index b5681db57833ae10e9bf665b53e77bea363473c2..d24d2cae51d0610af4a9fb5517c676058a7a4af6 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -39,6 +39,7 @@ vector<string> ClusterFragmentsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterFragmentsCommand::ClusterFragmentsCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 3c957a6ce84b5e5a489faaccf18a1dc40f99a02b..6b5012abaa755ad9c72e61d4ece9ad488782b5bd 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -31,6 +31,7 @@ vector<string> ClusterSplitCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterSplitCommand::ClusterSplitCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 3dd2436a8a88cf21b8cd7705a799ed9ab6450ebf..9ea55b2d6068dfda14450d82d247a428dcb9ca56 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -72,6 +72,7 @@ vector<string> CollectCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 CollectCommand::CollectCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["sobs"] = tempOutNames;

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 87194893f3a1cc5a027646766c36f9b7db9557cb..d63930d071da178e5ddcfdb82950ae37b03718cd 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -71,6 +71,7 @@ vector<string> CollectSharedCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 CollectSharedCommand::CollectSharedCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["sharedchao"] = tempOutNames;

diff --git a/consensuscommand.cpp b/consensuscommand.cpp
index a7469902d44cb9f16b4a109f8e0bc7a0182f7f86..0671790a2152801536e3f1bf05335a86f86fca13 100644 (file)
--- a/consensuscommand.cpp
+++ b/consensuscommand.cpp
@@ -46,6 +46,7 @@ vector<string> ConcensusCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 ConcensusCommand::ConcensusCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["tree"] = tempOutNames;

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 3129ea0ad368cb8c08a5ca2e9f036c38e4b1a441..dd05afdd0243132497fdab828c384b287ff0b61c 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -24,6 +24,7 @@ vector<string> DeconvoluteCommand::getValidParameters(){
 //**********************************************************************************************************************
 DeconvoluteCommand::DeconvoluteCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index f1190c84ad58a73b66b3423cbf2d10cee907bb93..2514ae1a21bd491ffb924700b226b103ea2ca839 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -25,6 +25,7 @@ vector<string> DegapSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 DegapSeqsCommand::DegapSeqsCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index a4395a700e26d27ebd36d1151f48129f6bef045d..f6b32e68ead4b262c0c5a5c00dc07349ab2c455f 100644 (file)
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -25,6 +25,7 @@ vector<string> DeUniqueSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 DeUniqueSeqsCommand::DeUniqueSeqsCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/distancecommand.cpp b/distancecommand.cpp
index f09aa997a506076b99584228c2b2272a6530a6fc..07d7f0f957859225727e598a0ebba660efe07b7c 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -29,6 +29,7 @@ vector<string> DistanceCommand::getValidParameters(){
 //**********************************************************************************************************************
 DistanceCommand::DistanceCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 1d9ee277a9e83802e3533a949e402e59ea4adbde..c4a3a95fe7d2cff8948650ebabea4290fbaa742a 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -25,6 +25,7 @@ vector<string> FilterSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 FilterSeqsCommand::FilterSeqsCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 40bfb26c6a21cfd29368720ef91782e8cd638ac6..2847db149ac5e40defdbfdedfd9d99ae3df5d583 100644 (file)
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -24,6 +24,7 @@ vector<string> GetgroupCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetgroupCommand::GetgroupCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["bootgroup"] = tempOutNames;

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 91811fa4687202378585457d0087c2c5db973c52..eaa8d40f3d6b0ec28eb59f107ac16ba9aa0fc61e 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -27,6 +27,7 @@ vector<string> GetLineageCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetLineageCommand::GetLineageCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 31b174861c4c577659e478defcb7d0fa1d5e6c7a..1ecef653e11fe15d206b41fd958834be194455ff 100644 (file)
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -24,6 +24,7 @@ vector<string> GetListCountCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetListCountCommand::GetListCountCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["otu"] = tempOutNames;

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 1e09dba67dc7f1d9b0b10c5a5dfa79023b04a3a6..0edaf3dda753e1b590d96f07880d8dfe970da463 100644 (file)
--- 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<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index a38aeb30dea60a2fe67984fa05dc83b6fb9130e1..60f4ece3eb13de6fc68f6141c3e28ca283da694b 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -24,6 +24,7 @@ vector<string> GetRAbundCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetRAbundCommand::GetRAbundCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["rabund"] = tempOutNames;

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 5b9327b57bd928a5e456a7251a83be1a0664cd6c..8c28c47b220e1554972d3cdb97bd2218af4f1c77 100644 (file)
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -24,6 +24,7 @@ vector<string> GetRelAbundCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetRelAbundCommand::GetRelAbundCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["relabund"] = tempOutNames;

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 8ad8b4b710f0c2bba003d12f355be1dff3d5f636..3637d2903112154c6af122e1bac68a2a0ab65f1a 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -24,6 +24,7 @@ vector<string> GetSAbundCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetSAbundCommand::GetSAbundCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["sabund"] = tempOutNames;

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 34788b8897cca88fa06ba46a5b37f88b70df70c0..b48ba28709acfb2b0f1355743c5a860cee1c8529 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -26,6 +26,7 @@ vector<string> GetSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetSeqsCommand::GetSeqsCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index f8c245f95f8e159b61db3acda6cfa42dee9417d3..699581f4fbf7f1eb45095316147990a4836ce7ac 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -25,6 +25,7 @@ vector<string> GetSharedOTUCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetSharedOTUCommand::GetSharedOTUCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index e236d86cf2934a349500bbd2aacf2737d3f351b7..5c08320bbed66718d9fa3fb335a36af6cfaf3a44 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -24,6 +24,7 @@ vector<string> HClusterCommand::getValidParameters(){
 //**********************************************************************************************************************
 HClusterCommand::HClusterCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index dc4fec28a2c6edeb799dac61a90c5ecbff247a51..892010839f519495744e0d68518124ffa1778fae 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -24,6 +24,7 @@ vector<string> HeatMapCommand::getValidParameters(){
 //**********************************************************************************************************************
 HeatMapCommand::HeatMapCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["svg"] = tempOutNames;

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 1eb3ceedb228220f8e8d86231866c1606a50b196..7ab178c528f40b6c5b9456880545c104701debf8 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -34,6 +34,7 @@ vector<string> HeatMapSimCommand::getValidParameters(){
 //**********************************************************************************************************************
 HeatMapSimCommand::HeatMapSimCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["svg"] = tempOutNames;

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index e48cf33d7dd4a60405841e124a35c5250f76bd86..e7fb357b9bd3028fcbd32bf388af9bbb9b4c2847 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -33,6 +33,7 @@ vector<string> LibShuffCommand::getValidParameters(){
 //**********************************************************************************************************************
 LibShuffCommand::LibShuffCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["coverage"] = tempOutNames;

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index c8c82971a1cf53d0eb2ba4834c281cc310d8984b..b4b467460693ef04b07a99392bf95735690a38e1 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -26,6 +26,7 @@ vector<string> ListSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ListSeqsCommand::ListSeqsCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["accnos"] = tempOutNames;

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index 611f00f8cd54a942d6646eda9cc776933d44742b..c427db5b385c166176f3f3a5272df2f72c3400b8 100644 (file)
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -25,6 +25,7 @@ vector<string> MakeGroupCommand::getValidParameters(){
 //**********************************************************************************************************************
 MakeGroupCommand::MakeGroupCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["group"] = tempOutNames;

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 020ccff57c813168625132e83c9c198eb113a121..2ea9377f8e559cc21e107724de4c30b0b1ba9c47 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -34,6 +34,7 @@ vector<string> MatrixOutputCommand::getValidParameters(){
 //**********************************************************************************************************************
 MatrixOutputCommand::MatrixOutputCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index d431dd32ff17dcef5e267b1e93a47c8fc93b324b..c7e5b65e06b77107251b9f4164f4f722edaaeeb2 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -24,6 +24,7 @@ vector<string> MergeFileCommand::getValidParameters(){
 //**********************************************************************************************************************
 MergeFileCommand::MergeFileCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["merge"] = tempOutNames;

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index f0496b2f1f49198b813247e4d10297504e426ae1..866bc94e07553d417b38036bca46184fad973261 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -26,6 +26,7 @@ vector<string> MetaStatsCommand::getValidParameters(){
 //**********************************************************************************************************************
 MetaStatsCommand::MetaStatsCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["metastats"] = tempOutNames;

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index e5dd1a30141af8a7573f7117f5883399a3a409e4..3ed9bf2131a45ac7a4b0ac44d959b16bfe28cd36 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -25,6 +25,7 @@ vector<string> MGClusterCommand::getValidParameters(){
 //**********************************************************************************************************************
 MGClusterCommand::MGClusterCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 8fc5d3058966d896c8dbfc861591c5bbbb72316c..93bc7f29a075126c9cb70bcc6f2590bd222a574d 100644 (file)
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -24,6 +24,7 @@ vector<string> NormalizeSharedCommand::getValidParameters(){
 //**********************************************************************************************************************
 NormalizeSharedCommand::NormalizeSharedCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["shared"] = tempOutNames;

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 022ff3af04dcc23933b05f4b7a76d3131db20ac2..14138de30355151035a7ddca66f5bd928e534bc5 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -24,6 +24,7 @@ vector<string> OtuHierarchyCommand::getValidParameters(){
 //**********************************************************************************************************************
 OtuHierarchyCommand::OtuHierarchyCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["otuheirarchy"] = tempOutNames;

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 733c47063bad878d8a54b061cc06e28fa2c7618c..aed03cd9ea273fe5e42413fc1c709abe01983e94 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -61,6 +61,7 @@ vector<string> PairwiseSeqsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 PairwiseSeqsCommand::PairwiseSeqsCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 31de119591dc333cc71ff08305822c018af861be..1e6643162b5962eadaf1cd36cc0ead26700240ec 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -25,6 +25,7 @@ vector<string> ParseFastaQCommand::getValidParameters(){
 //**********************************************************************************************************************
 ParseFastaQCommand::ParseFastaQCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 84d91048b181ddf19fc3f2c3977541e2ccebd2bd..9cf5a73a56802b65bae10d1c28187f214ebcfb56 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -25,6 +25,7 @@ vector<string> ParseListCommand::getValidParameters(){
 //**********************************************************************************************************************
 ParseListCommand::ParseListCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;

diff --git a/parsesffcommand.cpp b/parsesffcommand.cpp
index c636ec99221d874ec6b497e2ae3965fd353c8dc0..e2f9d61f5b268644eaf1492e54e91af204439e6f 100644 (file)
--- a/parsesffcommand.cpp
+++ b/parsesffcommand.cpp
@@ -25,6 +25,7 @@ vector<string> ParseSFFCommand::getValidParameters(){
 //**********************************************************************************************************************
 ParseSFFCommand::ParseSFFCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["flow"] = tempOutNames;

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index b879395b528b845805c622acd107e637e3af74f8..3d6818b30bac00f2a7137e2f158cb0e415106a9b 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -24,6 +24,7 @@ vector<string> ParsimonyCommand::getValidParameters(){
 //**********************************************************************************************************************
 ParsimonyCommand::ParsimonyCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["parsimony"] = tempOutNames;

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 4a4e55e2c01788141dc6d1173e3e14ed768d1fec..ee0a5462de87049f6b026546492203be630ea8d7 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -25,6 +25,7 @@ vector<string> PCACommand::getValidParameters(){
 //**********************************************************************************************************************
 PCACommand::PCACommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["pcoa"] = tempOutNames;

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 1c90eca1180acc6287b0530e9c9d3e84fbea120d..efa14cd7069266ebfedb41018de0120327a145a9 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -24,6 +24,7 @@ vector<string> PhyloDiversityCommand::getValidParameters(){
 //**********************************************************************************************************************
 PhyloDiversityCommand::PhyloDiversityCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["phylodiv"] = tempOutNames;

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index c4751b5481a8c11803f3fd2582bdd013810644ff..2018170648761a91b5b9026fada7079b0b4e73e1 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -28,6 +28,7 @@ vector<string> PhylotypeCommand::getValidParameters(){
 //**********************************************************************************************************************
 PhylotypeCommand::PhylotypeCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index d928122787c965beafb78b12eb42b901367a4eb9..ae2663df8e63b117995b3442227f72343e194bbb 100644 (file)
--- 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<string, vector<string> >& 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<string> validParameters = command->getValidParameters();
                
@@ -372,6 +372,7 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt
                map<string, vector<string> >::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<string> 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<string, vector<string> >& mothurMadeFiles){
        try {
+               
                OptionParser parser(options);
                map<string, string> parameters = parser.getParameters(); 
                map<string, string>::iterator it;

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index e6ccc9b70455089d5dffc1c6f512f3e17ca1d76e..3a3aafc7c44fc3385bbb3284abbbc0b09701c13f 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -26,6 +26,7 @@ vector<string> PreClusterCommand::getValidParameters(){
 //**********************************************************************************************************************
 PreClusterCommand::PreClusterCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index d430ffc01184cd505ca97ed7a46bb727ab1292b8..cb377273ebf711d1c7ef41363178a30a4add2e31 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -62,6 +62,7 @@ vector<string> RareFactCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 RareFactCommand::RareFactCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["rarefaction"] = tempOutNames;

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 0be8141636a1fffaacce16f2592e6bf8738ad400..8cf1f2fd6606f97bed2e10d0301994d769a8aa94 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -26,6 +26,7 @@ vector<string> RareFactSharedCommand::getValidParameters(){
 //**********************************************************************************************************************
 RareFactSharedCommand::RareFactSharedCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["sharedrarefaction"] = tempOutNames;

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 24a30cb5cbe925097e63639d50cdfc7163183ead..8683fc3fa80154729ea5228fcaa38fb03726603a 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -24,6 +24,7 @@ vector<string> ReadOtuCommand::getValidParameters(){
 //**********************************************************************************************************************
 ReadOtuCommand::ReadOtuCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["rabund"] = tempOutNames;

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 629416a5f01476442b3dd3e8db9cd3fadaca4165..1ea9c39af69e703f41b0aa7c9e5194eeeb0efcf0 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -26,6 +26,7 @@ vector<string> RemoveLineageCommand::getValidParameters(){
 //**********************************************************************************************************************
 RemoveLineageCommand::RemoveLineageCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index afba6514e0ea1360ef78f65d9470f89e63e18d53..c0e04d569604ee0aa67c29ceefbda06275a2df9d 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -26,6 +26,7 @@ vector<string> RemoveSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 RemoveSeqsCommand::RemoveSeqsCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/reversecommand.cpp b/reversecommand.cpp
index d179f0d89c54923de0516aceb6bf6aef9fe406c6..7b58162d20d8ac1910323c2946f7f8b4c05299af 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -25,6 +25,7 @@ vector<string> ReverseSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ReverseSeqsCommand::ReverseSeqsCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 5845b8f86ae7c718c0dbc25fe351d493faff57c3..8a7a108eb322978377a9d09ffb880a2745c54caf 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -26,6 +26,7 @@ vector<string> ScreenSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ScreenSeqsCommand::ScreenSeqsCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 36e0f609ca67bd3cd37e7c0d33a98e88cee65e6f..26bd35444d866132fd37c34fc3e0d8fd4cf84c40 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -25,6 +25,7 @@ vector<string> AlignCheckCommand::getValidParameters(){
 //**********************************************************************************************************************
 AlignCheckCommand::AlignCheckCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["aligncheck"] = tempOutNames;

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 78dce1794003457a077fe993958c75909c1020a7..045736d1021760f3afc7a772ea404def8a3e0d70 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -24,6 +24,7 @@ vector<string> SensSpecCommand::getValidParameters(){
 //**********************************************************************************************************************
 SensSpecCommand::SensSpecCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["sensspec"] = tempOutNames;

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 1f880f38cdf5c48d4dd0418c1d9c68172af7b8b7..0da4d1cd76cd51864c5442777180043f3c699fa2 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -24,6 +24,7 @@ vector<string> SeqErrorCommand::getValidParameters(){
 //**********************************************************************************************************************
 SeqErrorCommand::SeqErrorCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["error"] = tempOutNames;

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 7d074c4e05d441d350d552d2eb3796007191943a..5776b970e6475bf74252d357ff1fef028902a797 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -25,6 +25,7 @@ vector<string> SeqSummaryCommand::getValidParameters(){
 //**********************************************************************************************************************
 SeqSummaryCommand::SeqSummaryCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["summary"] = tempOutNames;

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 11754469fc3543c2ac544304606c507755f7ac41..d0ec9e2a93b5109c91e4a940f8b3bbaa64bdfe41 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -25,6 +25,7 @@ vector<string> SffInfoCommand::getValidParameters(){
 //**********************************************************************************************************************
 SffInfoCommand::SffInfoCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 454bb0558cce6080cdd1859fc0382ed3d47360e3..c252b4fecc9cebad935e0970fa88aaf5d43e7ac0 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -26,7 +26,8 @@ vector<string> SharedCommand::getValidParameters(){
 }
 //**********************************************************************************************************************
 SharedCommand::SharedCommand(){        
-       try {
+       try {           
+
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["rabund"] = tempOutNames;

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index f2d8e07f81320d58b500287dc66df8e068246ee5..0f4042fd1a44f040a64aec06de5a2c831985b759 100644 (file)
--- 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<hold;i++){
                        f >> 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 607009129b3c13ec8b7adfafd66e4d3fb006c486..fb0326a479efbc64d09bf946316355ce8dc44bac 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -24,6 +24,7 @@ vector<string> SplitAbundCommand::getValidParameters(){
 //**********************************************************************************************************************
 SplitAbundCommand::SplitAbundCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 4be7a0ec8a82133a9eb4def8ee78bd47e0ecbe44..1cbc2fcc6810913b5f85636c7de96fa281c1b5d0 100644 (file)
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -48,6 +48,7 @@ vector<string> SplitGroupCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 SplitGroupCommand::SplitGroupCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 17258159b7562dbee9830a03746602d935bb43a6..d68d00ac6258e0ac10346ce5b67b7d10a2de7495 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -49,6 +49,7 @@ vector<string> SummaryCommand::getValidParameters(){
 //**********************************************************************************************************************
 SummaryCommand::SummaryCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["summary"] = tempOutNames;

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 99c62a53c0580d51859673288a7955b7347442ae..5df448fc45c43656b56e8d0a54e42f089c16adf9 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -47,6 +47,7 @@ vector<string> SummarySharedCommand::getValidParameters(){
 //**********************************************************************************************************************
 SummarySharedCommand::SummarySharedCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["summary"] = tempOutNames;

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index a36e599fb3b04c01d2651423382566a26e7ac6d7..64bcd36764e044a911295870025095016be7fcc3 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -34,6 +34,8 @@ vector<string> TreeGroupCommand::getValidParameters(){
 //**********************************************************************************************************************
 TreeGroupCommand::TreeGroupCommand(){  
        try {
+               abort = true;
+               globaldata = GlobalData::getInstance();
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["tree"] = tempOutNames;

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 56fd8c54b53aaff9f4e43e8e694fc71f6987fd7c..f684b66a8e72d18f98172579197fac7cc5a2f543 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -26,6 +26,7 @@ vector<string> TrimSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 TrimSeqsCommand::TrimSeqsCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index b2d439b4e1b5481f87dc244df980c5a8c475eea2..24c7b548946a0715e49a7d3818142d50032691fc 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -24,6 +24,8 @@ vector<string> UnifracUnweightedCommand::getValidParameters(){
 //**********************************************************************************************************************
 UnifracUnweightedCommand::UnifracUnweightedCommand(){  
        try {
+               globaldata = GlobalData::getInstance();
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["unweighted"] = tempOutNames;

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 2646ede2643feef23477167cb9d627c884cd884c..33a0e6dd9a3128541ab57777125251a97effdefc 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -24,6 +24,7 @@ vector<string> UnifracWeightedCommand::getValidParameters(){
 //**********************************************************************************************************************
 UnifracWeightedCommand::UnifracWeightedCommand(){      
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["weighted"] = tempOutNames;

diff --git a/venncommand.cpp b/venncommand.cpp
index ab4f7a2fbff2da7e79ad8f5021dc10d074d8b688..7601ed8e667b10e2b2cd6eaf48c8f5ce365cc6f0 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -33,6 +33,7 @@ vector<string> VennCommand::getValidParameters(){
 //**********************************************************************************************************************
 VennCommand::VennCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["svg"] = tempOutNames;