From: westcott <westcott>
Date: Tue, 8 Feb 2011 17:56:37 +0000 (+0000)
Subject: added [ERROR] flag if command aborts
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;p=mothur.git
added [ERROR] flag if command aborts
---
diff --git a/aligncommand.cpp b/aligncommand.cpp
index db4e34a..3048481 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -64,8 +64,7 @@ vector<string> AlignCommand::getRequiredFiles(){
//**********************************************************************************************************************
AlignCommand::AlignCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
@@ -79,10 +78,10 @@ AlignCommand::AlignCommand(){
//**********************************************************************************************************************
AlignCommand::AlignCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true;}
else {
@@ -279,7 +278,7 @@ void AlignCommand::help(){
int AlignCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
int longestBase = templateDB->getLongestBase();
diff --git a/aligncommand.h b/aligncommand.h
index 1410626..169b435 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -58,7 +58,8 @@ private:
vector<string> candidateFileNames;
vector<string> outputNames;
- bool abort, flip;
+ bool abort, flip, calledHelp;
+
};
#endif
diff --git a/amovacommand.cpp b/amovacommand.cpp
index c0b9aec..0a9b53b 100644
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -66,8 +66,7 @@ vector<string> AmovaCommand::getValidParameters(){
//**********************************************************************************************************************
AmovaCommand::AmovaCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["amova"] = tempOutNames;
}
@@ -105,12 +104,12 @@ vector<string> AmovaCommand::getRequiredFiles(){
AmovaCommand::AmovaCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -349,7 +348,7 @@ AmovaCommand::~AmovaCommand(){}
int AmovaCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read design file
designMap = new GroupMap(designfile);
diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index bf14d6b..81c24a3 100644
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -48,8 +48,7 @@ vector<string> BinSeqCommand::getRequiredFiles(){
//**********************************************************************************************************************
BinSeqCommand::BinSeqCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
}
@@ -62,12 +61,12 @@ BinSeqCommand::BinSeqCommand(){
BinSeqCommand::BinSeqCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -218,7 +217,7 @@ BinSeqCommand::~BinSeqCommand(){
int BinSeqCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int error = 0;
diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index b7d6c45..66a4397 100644
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -34,8 +34,7 @@ vector<string> BootSharedCommand::getValidParameters(){
//**********************************************************************************************************************
BootSharedCommand::BootSharedCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
}
@@ -71,14 +70,14 @@ vector<string> BootSharedCommand::getRequiredFiles(){
BootSharedCommand::BootSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Groups.clear();
Estimators.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -235,7 +234,7 @@ BootSharedCommand::~BootSharedCommand(){
int BootSharedCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
util = new SharedUtil();
diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index b0e5eff..a462bc7 100644
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -25,6 +25,7 @@ vector<string> CatchAllCommand::getValidParameters(){
//**********************************************************************************************************************
CatchAllCommand::CatchAllCommand(){
try {
+ abort = true; calledHelp = true;
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["csv"] = tempOutNames;
@@ -62,11 +63,11 @@ vector<string> CatchAllCommand::getRequiredFiles(){
CatchAllCommand::CatchAllCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -173,7 +174,7 @@ void CatchAllCommand::help(){
int CatchAllCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//prepare full output directory
outputDir = m->getFullPathName(outputDir);
diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 5d7d6d4..22e4fe2 100644
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -48,8 +48,7 @@ vector<string> ChimeraBellerophonCommand::getRequiredFiles(){
//**********************************************************************************************************************
ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
@@ -63,10 +62,10 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
//***************************************************************************************************************
ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -210,7 +209,7 @@ ChimeraBellerophonCommand::~ChimeraBellerophonCommand(){ /* do nothing */ }
int ChimeraBellerophonCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int i = 0; i < fastaFileNames.size(); i++) {
diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 223ddb2..8a4ccde 100644
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -25,6 +25,7 @@ vector<string> ChimeraCcodeCommand::getValidParameters(){
//**********************************************************************************************************************
ChimeraCcodeCommand::ChimeraCcodeCommand(){
try {
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["mapinfo"] = tempOutNames;
@@ -61,10 +62,10 @@ vector<string> ChimeraCcodeCommand::getRequiredFiles(){
//***************************************************************************************************************
ChimeraCcodeCommand::ChimeraCcodeCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -239,7 +240,7 @@ ChimeraCcodeCommand::~ChimeraCcodeCommand(){ /* do nothing */ }
int ChimeraCcodeCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {
diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 3104fac..c766b9a 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -47,6 +47,7 @@ vector<string> ChimeraCheckCommand::getRequiredFiles(){
//**********************************************************************************************************************
ChimeraCheckCommand::ChimeraCheckCommand(){
try {
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
}
@@ -58,10 +59,10 @@ ChimeraCheckCommand::ChimeraCheckCommand(){
//***************************************************************************************************************
ChimeraCheckCommand::ChimeraCheckCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -280,7 +281,7 @@ ChimeraCheckCommand::~ChimeraCheckCommand(){ /* do nothing */ }
int ChimeraCheckCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int i = 0; i < fastaFileNames.size(); i++) {
diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index c5e579e..a8d2d65 100644
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -25,6 +25,7 @@ vector<string> ChimeraPintailCommand::getValidParameters(){
//**********************************************************************************************************************
ChimeraPintailCommand::ChimeraPintailCommand(){
try {
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
@@ -60,10 +61,10 @@ vector<string> ChimeraPintailCommand::getRequiredFiles(){
//***************************************************************************************************************
ChimeraPintailCommand::ChimeraPintailCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -309,7 +310,7 @@ ChimeraPintailCommand::~ChimeraPintailCommand(){ /* do nothing */ }
int ChimeraPintailCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {
diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index a7ed94f..67b70f2 100644
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -27,6 +27,7 @@ vector<string> ChimeraSlayerCommand::getValidParameters(){
//**********************************************************************************************************************
ChimeraSlayerCommand::ChimeraSlayerCommand(){
try {
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
@@ -63,10 +64,10 @@ vector<string> ChimeraSlayerCommand::getRequiredFiles(){
//***************************************************************************************************************
ChimeraSlayerCommand::ChimeraSlayerCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -343,7 +344,7 @@ ChimeraSlayerCommand::~ChimeraSlayerCommand(){ /* do nothing */ }
int ChimeraSlayerCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {
diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 31fe64f..1ebb1f4 100644
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -25,8 +25,7 @@ vector<string> ChopSeqsCommand::getValidParameters(){
//**********************************************************************************************************************
ChopSeqsCommand::ChopSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
@@ -62,10 +61,10 @@ vector<string> ChopSeqsCommand::getRequiredFiles(){
//**********************************************************************************************************************
ChopSeqsCommand::ChopSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -156,7 +155,7 @@ void ChopSeqsCommand::help(){
int ChopSeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.fasta";
string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.accnos";
diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index d3d574e..8d9f177 100644
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -26,8 +26,7 @@ vector<string> ClassifyOtuCommand::getValidParameters(){
//**********************************************************************************************************************
ClassifyOtuCommand::ClassifyOtuCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["constaxonomy"] = tempOutNames;
outputTypes["taxsummary"] = tempOutNames;
@@ -63,13 +62,13 @@ vector<string> ClassifyOtuCommand::getRequiredFiles(){
//**********************************************************************************************************************
ClassifyOtuCommand::ClassifyOtuCommand(string option) {
try{
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
if (option == "help") {
- help(); abort = true;
+ help(); abort = true; calledHelp = true;
} else {
//valid paramters for this command
string Array[] = {"list","label","name","taxonomy","cutoff","probs","basis","reftaxonomy","group","outputdir","inputdir"};
@@ -229,7 +228,7 @@ ClassifyOtuCommand::~ClassifyOtuCommand(){}
int ClassifyOtuCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if user gave a namesfile then use it
if (namefile != "") { readNamesFile(); }
diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 0a1ef88..2dfe05a 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -30,8 +30,7 @@ vector<string> ClassifySeqsCommand::getValidParameters(){
//**********************************************************************************************************************
ClassifySeqsCommand::ClassifySeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
outputTypes["taxsummary"] = tempOutNames;
@@ -68,10 +67,10 @@ vector<string> ClassifySeqsCommand::getRequiredFiles(){
//**********************************************************************************************************************
ClassifySeqsCommand::ClassifySeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
@@ -421,7 +420,7 @@ void ClassifySeqsCommand::help(){
int ClassifySeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if(method == "bayesian"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters); }
else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted); }
diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index a2d0aaa..767981d 100644
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -31,8 +31,7 @@ vector<string> ClearcutCommand::getValidParameters(){
//**********************************************************************************************************************
ClearcutCommand::ClearcutCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
outputTypes["matrixout"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> ClearcutCommand::getRequiredFiles(){
/**************************************************************************************/
ClearcutCommand::ClearcutCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -231,7 +230,7 @@ void ClearcutCommand::help(){
int ClearcutCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//prepare filename
string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
diff --git a/clustercommand.cpp b/clustercommand.cpp
index 6043d39..5d9225b 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -24,8 +24,7 @@ vector<string> ClusterCommand::getValidParameters(){
//**********************************************************************************************************************
ClusterCommand::ClusterCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["rabund"] = tempOutNames;
@@ -65,10 +64,10 @@ ClusterCommand::ClusterCommand(string option) {
try{
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -199,7 +198,7 @@ ClusterCommand::~ClusterCommand(){
int ClusterCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
time_t estart = time(NULL);
//int ndist = matrix->getNNodes();
diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 56fbd5c..b2b31ed 100644
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -25,8 +25,7 @@ vector<string> ClusterDoturCommand::getValidParameters(){
//**********************************************************************************************************************
ClusterDoturCommand::ClusterDoturCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["rabund"] = tempOutNames;
@@ -65,10 +64,10 @@ vector<string> ClusterDoturCommand::getRequiredFiles(){
ClusterDoturCommand::ClusterDoturCommand(string option) {
try{
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -189,7 +188,7 @@ ClusterDoturCommand::~ClusterDoturCommand(){}
int ClusterDoturCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if(namefile != ""){
nameMap = new NameAssignment(namefile);
diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 24070d2..a8277ff 100644
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -40,8 +40,7 @@ vector<string> ClusterFragmentsCommand::getValidParameters(){
//**********************************************************************************************************************
ClusterFragmentsCommand::ClusterFragmentsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
@@ -77,10 +76,10 @@ vector<string> ClusterFragmentsCommand::getRequiredFiles(){
//**********************************************************************************************************************
ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -182,7 +181,7 @@ void ClusterFragmentsCommand::help(){
int ClusterFragmentsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index c36e280..cb3fc40 100644
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -31,8 +31,7 @@ vector<string> ClusterSplitCommand::getValidParameters(){
//**********************************************************************************************************************
ClusterSplitCommand::ClusterSplitCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["rabund"] = tempOutNames;
@@ -72,11 +71,11 @@ vector<string> ClusterSplitCommand::getRequiredFiles(){
ClusterSplitCommand::ClusterSplitCommand(string option) {
try{
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
format = "";
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -290,7 +289,7 @@ ClusterSplitCommand::~ClusterSplitCommand(){}
int ClusterSplitCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
time_t estart;
vector<string> listFileNames;
diff --git a/collectcommand.cpp b/collectcommand.cpp
index 9ea55b2..4b59296 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -72,8 +72,7 @@ vector<string> CollectCommand::getRequiredFiles(){
//**********************************************************************************************************************
CollectCommand::CollectCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["sobs"] = tempOutNames;
outputTypes["chao"] = tempOutNames;
@@ -110,7 +109,7 @@ CollectCommand::CollectCommand(){
CollectCommand::CollectCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Estimators.clear();
@@ -237,7 +236,7 @@ CollectCommand::~CollectCommand(){}
int CollectCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string hadShared = "";
if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 7ab15df..21695e3 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -88,8 +88,7 @@ vector<string> CollectSharedCommand::getRequiredFiles(){
//**********************************************************************************************************************
CollectSharedCommand::CollectSharedCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["sharedchao"] = tempOutNames;
outputTypes["sharedsobs"] = tempOutNames;
@@ -141,14 +140,14 @@ CollectSharedCommand::CollectSharedCommand(){
CollectSharedCommand::CollectSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Estimators.clear();
Groups.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -439,7 +438,7 @@ CollectSharedCommand::~CollectSharedCommand(){
int CollectSharedCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if the users entered no valid calculators don't execute command
if (cDisplays.size() == 0) { return 0; }
diff --git a/command.hpp b/command.hpp
index 97701aa..ddb7763 100644
--- a/command.hpp
+++ b/command.hpp
@@ -31,6 +31,7 @@ class Command {
virtual ~Command() { }
protected:
MothurOut* m;
+ bool calledHelp;
};
#endif
diff --git a/consensuscommand.cpp b/consensuscommand.cpp
index 9b72638..9880b8d 100644
--- a/consensuscommand.cpp
+++ b/consensuscommand.cpp
@@ -46,8 +46,7 @@ vector<string> ConcensusCommand::getRequiredFiles(){
//**********************************************************************************************************************
ConcensusCommand::ConcensusCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
outputTypes["nodepairs"] = tempOutNames;
@@ -62,7 +61,7 @@ ConcensusCommand::ConcensusCommand(){
ConcensusCommand::ConcensusCommand(string fileroot) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//initialize outputTypes
vector<string> tempOutNames;
@@ -108,7 +107,7 @@ ConcensusCommand::~ConcensusCommand(){}
int ConcensusCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
else {
numNodes = t[0]->getNumNodes();
numLeaves = t[0]->getNumLeaves();
diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 513566f..482bac5 100644
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -26,8 +26,7 @@ vector<string> ConsensusSeqsCommand::getValidParameters(){
//**********************************************************************************************************************
ConsensusSeqsCommand::ConsensusSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
@@ -64,11 +63,11 @@ vector<string> ConsensusSeqsCommand::getRequiredFiles(){
//***************************************************************************************************************
ConsensusSeqsCommand::ConsensusSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -184,7 +183,7 @@ ConsensusSeqsCommand::~ConsensusSeqsCommand(){ /* do nothing */ }
int ConsensusSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
readFasta();
diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 26cdcda..58fb364 100644
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -47,8 +47,7 @@ vector<string> CorrAxesCommand::getRequiredParameters(){
//**********************************************************************************************************************
CorrAxesCommand::CorrAxesCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["corr.axes"] = tempOutNames;
}
@@ -72,11 +71,11 @@ vector<string> CorrAxesCommand::getRequiredFiles(){
//**********************************************************************************************************************
CorrAxesCommand::CorrAxesCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
globaldata = GlobalData::getInstance();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -221,7 +220,7 @@ CorrAxesCommand::~CorrAxesCommand(){}
int CorrAxesCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
/*************************************************************************************/
// use smart distancing to get right sharedRabund and convert to relabund if needed //
diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index dd05afd..6c04c12 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -24,8 +24,7 @@ vector<string> DeconvoluteCommand::getValidParameters(){
//**********************************************************************************************************************
DeconvoluteCommand::DeconvoluteCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
@@ -61,10 +60,10 @@ vector<string> DeconvoluteCommand::getRequiredFiles(){
/**************************************************************************************/
DeconvoluteCommand::DeconvoluteCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -153,7 +152,7 @@ void DeconvoluteCommand::help(){
int DeconvoluteCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//prepare filenames and open files
string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 2514ae1..5df6188 100644
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -25,8 +25,7 @@ vector<string> DegapSeqsCommand::getValidParameters(){
//**********************************************************************************************************************
DegapSeqsCommand::DegapSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
}
@@ -61,10 +60,10 @@ vector<string> DegapSeqsCommand::getRequiredFiles(){
//***************************************************************************************************************
DegapSeqsCommand::DegapSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -189,7 +188,7 @@ DegapSeqsCommand::~DegapSeqsCommand(){ /* do nothing */ }
int DegapSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {
diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index f6b32e6..214359e 100644
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -25,8 +25,7 @@ vector<string> DeUniqueSeqsCommand::getValidParameters(){
//**********************************************************************************************************************
DeUniqueSeqsCommand::DeUniqueSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
}
@@ -61,10 +60,10 @@ vector<string> DeUniqueSeqsCommand::getRequiredFiles(){
/**************************************************************************************/
DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -153,7 +152,7 @@ void DeUniqueSeqsCommand::help(){
int DeUniqueSeqsCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//prepare filenames and open files
ofstream out;
diff --git a/distancecommand.cpp b/distancecommand.cpp
index a3cebe2..3d66722 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -30,8 +30,7 @@ vector<string> DistanceCommand::getValidParameters(){
//**********************************************************************************************************************
DistanceCommand::DistanceCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
@@ -67,11 +66,11 @@ vector<string> DistanceCommand::getRequiredFiles(){
//**********************************************************************************************************************
DistanceCommand::DistanceCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
Estimators.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -242,7 +241,7 @@ void DistanceCommand::help(){
int DistanceCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int startTime = time(NULL);
diff --git a/engine.cpp b/engine.cpp
index ad7a7ad..dd61de6 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -152,6 +152,10 @@ bool InteractEngine::getInput(){
//executes valid command
Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
+
+ //if we aborted command
+ if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+
mout->control_pressed = 0;
mout->executing = false;
@@ -291,7 +295,7 @@ bool BatchEngine::getInput(){
//CommandFactory cFactory;
int quitCommandCalled = 0;
int count = 0;
- while(quitCommandCalled == 0){
+ while(quitCommandCalled != 1){
#ifdef USE_MPI
int pid, processors;
@@ -358,6 +362,10 @@ bool BatchEngine::getInput(){
//executes valid command
Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
+
+ //if we aborted command
+ if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+
mout->control_pressed = 0;
mout->executing = false;
@@ -474,7 +482,7 @@ bool ScriptEngine::getInput(){
//CommandFactory cFactory;
int quitCommandCalled = 0;
- while(quitCommandCalled == 0){
+ while(quitCommandCalled != 1){
#ifdef USE_MPI
int pid, processors;
@@ -542,6 +550,10 @@ bool ScriptEngine::getInput(){
//executes valid command
Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
+
+ //if we aborted command
+ if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+
mout->control_pressed = 0;
mout->executing = false;
diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index f5c7bd6..6fd4e04 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -25,8 +25,7 @@ vector<string> FilterSeqsCommand::getValidParameters(){
//**********************************************************************************************************************
FilterSeqsCommand::FilterSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["filter"] = tempOutNames;
@@ -62,11 +61,11 @@ vector<string> FilterSeqsCommand::getRequiredFiles(){
/**************************************************************************************/
FilterSeqsCommand::FilterSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
filterFileName = "";
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -240,7 +239,7 @@ void FilterSeqsCommand::help(){
int FilterSeqsCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
ifstream inFASTA;
m->openInputFile(fastafileNames[0], inFASTA);
diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 2847db1..ab3ccfa 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -24,8 +24,7 @@ vector<string> GetgroupCommand::getValidParameters(){
//**********************************************************************************************************************
GetgroupCommand::GetgroupCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["bootgroup"] = tempOutNames;
}
@@ -61,10 +60,10 @@ vector<string> GetgroupCommand::getRequiredFiles(){
GetgroupCommand::GetgroupCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -135,7 +134,7 @@ GetgroupCommand::~GetgroupCommand(){
int GetgroupCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int num, inputData, count;
count = 0;
diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index 1832f96..635f68f 100644
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -27,8 +27,7 @@ vector<string> GetGroupsCommand::getValidParameters(){
//**********************************************************************************************************************
GetGroupsCommand::GetGroupsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> GetGroupsCommand::getRequiredFiles(){
//**********************************************************************************************************************
GetGroupsCommand::GetGroupsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -222,7 +221,7 @@ void GetGroupsCommand::help(){
int GetGroupsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
groupMap->readMap();
diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index fe4387a..3191d5d 100644
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -49,10 +49,10 @@ vector<string> GetlabelCommand::getRequiredFiles(){
GetlabelCommand::GetlabelCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund or rabund before you can use the get.label command."); m->mothurOutEndLine(); abort = true; }
@@ -90,7 +90,7 @@ GetlabelCommand::~GetlabelCommand(){
int GetlabelCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
filename = globaldata->inputFileName;
ifstream in;
diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 8a6f47c..eee0cca 100644
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -27,8 +27,7 @@ vector<string> GetLineageCommand::getValidParameters(){
//**********************************************************************************************************************
GetLineageCommand::GetLineageCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
@@ -68,10 +67,10 @@ vector<string> GetLineageCommand::getRequiredFiles(){
//**********************************************************************************************************************
GetLineageCommand::GetLineageCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -238,7 +237,7 @@ void GetLineageCommand::help(){
int GetLineageCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (m->control_pressed) { return 0; }
diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 1ecef65..78f2604 100644
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -24,8 +24,7 @@ vector<string> GetListCountCommand::getValidParameters(){
//**********************************************************************************************************************
GetListCountCommand::GetListCountCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["otu"] = tempOutNames;
}
@@ -61,12 +60,12 @@ vector<string> GetListCountCommand::getRequiredFiles(){
GetListCountCommand::GetListCountCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -168,7 +167,7 @@ GetListCountCommand::~GetListCountCommand(){}
int GetListCountCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
globaldata->setFormat("list");
diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 9cc9973..84d3871 100644
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -38,8 +38,7 @@ inline bool compareGroup(repStruct left, repStruct right){
//**********************************************************************************************************************
GetOTURepCommand::GetOTURepCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
@@ -88,13 +87,13 @@ vector<string> GetOTURepCommand::getRequiredFiles(){
GetOTURepCommand::GetOTURepCommand(string option) {
try{
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
if (option == "help") {
- help(); abort = true;
+ help(); abort = true; calledHelp = true;
} else {
//valid paramters for this command
string Array[] = {"fasta","list","label","name","weighted", "group", "sorted", "phylip","column","large","cutoff","precision","groups","outputdir","inputdir"};
@@ -299,7 +298,7 @@ GetOTURepCommand::~GetOTURepCommand(){}
int GetOTURepCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int error;
if (!large) {
diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index fd7c8d1..b075cb4 100644
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -27,8 +27,7 @@ vector<string> GetOtusCommand::getValidParameters(){
//**********************************************************************************************************************
GetOtusCommand::GetOtusCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["list"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> GetOtusCommand::getRequiredFiles(){
//**********************************************************************************************************************
GetOtusCommand::GetOtusCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -182,7 +181,7 @@ void GetOtusCommand::help(){
int GetOtusCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
groupMap->readMap();
diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 60f4ece..0b2d4ee 100644
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -24,8 +24,7 @@ vector<string> GetRAbundCommand::getValidParameters(){
//**********************************************************************************************************************
GetRAbundCommand::GetRAbundCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["rabund"] = tempOutNames;
}
@@ -62,12 +61,12 @@ vector<string> GetRAbundCommand::getRequiredFiles(){
GetRAbundCommand::GetRAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -158,7 +157,7 @@ GetRAbundCommand::~GetRAbundCommand(){}
int GetRAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read first line
read = new ReadOTUFile(globaldata->inputFileName);
diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 08e9228..5e48203 100644
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -24,8 +24,7 @@ vector<string> GetRelAbundCommand::getValidParameters(){
//**********************************************************************************************************************
GetRelAbundCommand::GetRelAbundCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["relabund"] = tempOutNames;
}
@@ -61,12 +60,12 @@ vector<string> GetRelAbundCommand::getRequiredFiles(){
GetRelAbundCommand::GetRelAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -167,7 +166,7 @@ GetRelAbundCommand::~GetRelAbundCommand(){
int GetRelAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "relabund";
ofstream out;
diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 3637d29..2ae807c 100644
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -24,8 +24,7 @@ vector<string> GetSAbundCommand::getValidParameters(){
//**********************************************************************************************************************
GetSAbundCommand::GetSAbundCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["sabund"] = tempOutNames;
}
@@ -61,12 +60,12 @@ vector<string> GetSAbundCommand::getRequiredFiles(){
GetSAbundCommand::GetSAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -152,7 +151,7 @@ GetSAbundCommand::~GetSAbundCommand(){
int GetSAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//using order vector so you don't have to distinguish between the list and rabund files
read = new ReadOTUFile(globaldata->inputFileName);
diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 9f2b506..902cc07 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -26,8 +26,7 @@ vector<string> GetSeqsCommand::getValidParameters(){
//**********************************************************************************************************************
GetSeqsCommand::GetSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
@@ -69,10 +68,10 @@ vector<string> GetSeqsCommand::getRequiredFiles(){
//**********************************************************************************************************************
GetSeqsCommand::GetSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -257,7 +256,7 @@ void GetSeqsCommand::help(){
int GetSeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get names you want to keep
readAccnos();
diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 699581f..6ca4ee2 100644
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -25,8 +25,7 @@ vector<string> GetSharedOTUCommand::getValidParameters(){
//**********************************************************************************************************************
GetSharedOTUCommand::GetSharedOTUCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
@@ -65,13 +64,13 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
unique = true;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -218,7 +217,7 @@ GetSharedOTUCommand::~GetSharedOTUCommand(){}
int GetSharedOTUCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
int error = groupMap->readMap();
diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 69dbef6..94082df 100644
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -24,8 +24,7 @@ vector<string> HClusterCommand::getValidParameters(){
//**********************************************************************************************************************
HClusterCommand::HClusterCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["rabund"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> HClusterCommand::getRequiredFiles(){
HClusterCommand::HClusterCommand(string option) {
try{
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -237,7 +236,7 @@ HClusterCommand::~HClusterCommand(){}
int HClusterCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if(namefile != ""){
globaldata->nameMap = new NameAssignment(namefile);
diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 8920108..19a320a 100644
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -24,8 +24,7 @@ vector<string> HeatMapCommand::getValidParameters(){
//**********************************************************************************************************************
HeatMapCommand::HeatMapCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["svg"] = tempOutNames;
}
@@ -62,12 +61,12 @@ vector<string> HeatMapCommand::getRequiredFiles(){
HeatMapCommand::HeatMapCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -183,7 +182,7 @@ HeatMapCommand::~HeatMapCommand(){
int HeatMapCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir);
format = globaldata->getFormat();
diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 7ab178c..28b0221 100644
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -34,8 +34,7 @@ vector<string> HeatMapSimCommand::getValidParameters(){
//**********************************************************************************************************************
HeatMapSimCommand::HeatMapSimCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["svg"] = tempOutNames;
}
@@ -71,14 +70,14 @@ vector<string> HeatMapSimCommand::getRequiredFiles(){
HeatMapSimCommand::HeatMapSimCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Groups.clear();
Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -273,7 +272,7 @@ HeatMapSimCommand::~HeatMapSimCommand(){}
int HeatMapSimCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
heatmap = new HeatMapSim(outputDir);
diff --git a/homovacommand.cpp b/homovacommand.cpp
index 86a900a..32a7765 100644
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -66,8 +66,7 @@ vector<string> HomovaCommand::getValidParameters(){
//**********************************************************************************************************************
HomovaCommand::HomovaCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["homova"] = tempOutNames;
}
@@ -105,12 +104,12 @@ vector<string> HomovaCommand::getRequiredFiles(){
HomovaCommand::HomovaCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -349,7 +348,7 @@ HomovaCommand::~HomovaCommand(){}
int HomovaCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read design file
designMap = new GroupMap(designfile);
diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 143135f..239a4bc 100644
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -37,8 +37,7 @@ vector<string> IndicatorCommand::getRequiredParameters(){
//**********************************************************************************************************************
IndicatorCommand::IndicatorCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
outputTypes["summary"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> IndicatorCommand::getRequiredFiles(){
IndicatorCommand::IndicatorCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -199,7 +198,7 @@ IndicatorCommand::~IndicatorCommand(){}
int IndicatorCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read designfile if given and set up globaldatas groups for read of sharedfiles
if (designfile != "") {
diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index e7fb357..129c970 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -33,8 +33,7 @@ vector<string> LibShuffCommand::getValidParameters(){
//**********************************************************************************************************************
LibShuffCommand::LibShuffCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["coverage"] = tempOutNames;
outputTypes["libshuffsummary"] = tempOutNames;
@@ -72,11 +71,11 @@ vector<string> LibShuffCommand::getRequiredFiles(){
LibShuffCommand::LibShuffCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
Groups.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -189,7 +188,7 @@ void LibShuffCommand::help(){
int LibShuffCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
savedDXYValues = form->evaluateAll();
savedMinValues = form->getSavedMins();
diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 1488cda..360e195 100644
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -26,8 +26,7 @@ vector<string> ListSeqsCommand::getValidParameters(){
//**********************************************************************************************************************
ListSeqsCommand::ListSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["accnos"] = tempOutNames;
}
@@ -63,10 +62,10 @@ vector<string> ListSeqsCommand::getRequiredFiles(){
ListSeqsCommand::ListSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -206,7 +205,7 @@ void ListSeqsCommand::help(){
int ListSeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read functions fill names vector
if (fastafile != "") { inputFileName = fastafile; readFasta(); }
diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index 12be826..1c04fec 100644
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -25,8 +25,7 @@ vector<string> MakeGroupCommand::getValidParameters(){
//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["group"] = tempOutNames;
}
@@ -63,10 +62,10 @@ vector<string> MakeGroupCommand::getRequiredFiles(){
MakeGroupCommand::MakeGroupCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
@@ -198,7 +197,7 @@ void MakeGroupCommand::help(){
int MakeGroupCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 02b30e3..baf449e 100644
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -64,8 +64,7 @@ vector<string> MatrixOutputCommand::getValidParameters(){
//**********************************************************************************************************************
MatrixOutputCommand::MatrixOutputCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
}
@@ -102,14 +101,14 @@ vector<string> MatrixOutputCommand::getRequiredFiles(){
MatrixOutputCommand::MatrixOutputCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Groups.clear();
Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -312,7 +311,7 @@ MatrixOutputCommand::~MatrixOutputCommand(){
int MatrixOutputCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if the users entered no valid calculators don't execute command
if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index c7e5b65..2b34a00 100644
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -24,8 +24,7 @@ vector<string> MergeFileCommand::getValidParameters(){
//**********************************************************************************************************************
MergeFileCommand::MergeFileCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["merge"] = tempOutNames;
}
@@ -61,11 +60,11 @@ vector<string> MergeFileCommand::getRequiredFiles(){
MergeFileCommand::MergeFileCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
if(option == "help") {
help();
- abort = true;
+ abort = true; calledHelp = true;
}
else {
//valid paramters for this command
@@ -137,7 +136,7 @@ MergeFileCommand::~MergeFileCommand() { /* do nothing */ }
int MergeFileCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
ofstream outputFile;
m->openOutputFile(outputFileName, outputFile);
diff --git a/mergegroupscommand.cpp b/mergegroupscommand.cpp
index 4738389..c54cd1c 100644
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -25,8 +25,7 @@ vector<string> MergeGroupsCommand::getValidParameters(){
//**********************************************************************************************************************
MergeGroupsCommand::MergeGroupsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["shared"] = tempOutNames;
}
@@ -64,12 +63,12 @@ vector<string> MergeGroupsCommand::getRequiredFiles(){
MergeGroupsCommand::MergeGroupsCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -180,7 +179,7 @@ MergeGroupsCommand::~MergeGroupsCommand(){}
int MergeGroupsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "merge" + m->getExtension(sharedfile);
diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 81715e0..e13e37c 100644
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -26,8 +26,7 @@ vector<string> MetaStatsCommand::getValidParameters(){
//**********************************************************************************************************************
MetaStatsCommand::MetaStatsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["metastats"] = tempOutNames;
}
@@ -65,12 +64,12 @@ vector<string> MetaStatsCommand::getRequiredFiles(){
MetaStatsCommand::MetaStatsCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -206,7 +205,7 @@ MetaStatsCommand::~MetaStatsCommand(){}
int MetaStatsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
designMap = new GroupMap(designfile);
designMap->readDesignMap();
diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 3ed9bf2..4809964 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -25,8 +25,7 @@ vector<string> MGClusterCommand::getValidParameters(){
//**********************************************************************************************************************
MGClusterCommand::MGClusterCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["rabund"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> MGClusterCommand::getRequiredFiles(){
MGClusterCommand::MGClusterCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -202,7 +201,7 @@ MGClusterCommand::~MGClusterCommand(){}
int MGClusterCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read names file
if (namefile != "") {
diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 28bf397..6596859 100644
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -25,8 +25,7 @@ vector<string> NMDSCommand::getValidParameters(){
//**********************************************************************************************************************
NMDSCommand::NMDSCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["nmds"] = tempOutNames;
outputTypes["stress"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> NMDSCommand::getRequiredFiles(){
NMDSCommand::NMDSCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -178,7 +177,7 @@ NMDSCommand::~NMDSCommand(){}
int NMDSCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
cout.setf(ios::fixed, ios::floatfield);
cout.setf(ios::showpoint);
diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 8526501..c0e7c1f 100644
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -24,8 +24,7 @@ vector<string> NormalizeSharedCommand::getValidParameters(){
//**********************************************************************************************************************
NormalizeSharedCommand::NormalizeSharedCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["shared"] = tempOutNames;
}
@@ -62,12 +61,12 @@ vector<string> NormalizeSharedCommand::getRequiredFiles(){
NormalizeSharedCommand::NormalizeSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -185,7 +184,7 @@ NormalizeSharedCommand::~NormalizeSharedCommand(){}
int NormalizeSharedCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "norm.shared";
ofstream out;
diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 14138de..b49af32 100644
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -24,8 +24,7 @@ vector<string> OtuHierarchyCommand::getValidParameters(){
//**********************************************************************************************************************
OtuHierarchyCommand::OtuHierarchyCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["otuheirarchy"] = tempOutNames;
}
@@ -60,10 +59,10 @@ vector<string> OtuHierarchyCommand::getRequiredFiles(){
//**********************************************************************************************************************
OtuHierarchyCommand::OtuHierarchyCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -157,7 +156,7 @@ OtuHierarchyCommand::~OtuHierarchyCommand(){}
int OtuHierarchyCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector)
vector<ListVector> lists = getListVectors();
diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 7a1ba4d..0a4edea 100644
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -61,8 +61,7 @@ vector<string> PairwiseSeqsCommand::getRequiredFiles(){
//**********************************************************************************************************************
PairwiseSeqsCommand::PairwiseSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
@@ -75,10 +74,10 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(){
//**********************************************************************************************************************
PairwiseSeqsCommand::PairwiseSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
@@ -268,7 +267,7 @@ void PairwiseSeqsCommand::help(){
int PairwiseSeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int longestBase = 2000; //will need to update this in driver if we find sequences with more bases. hardcoded so we don't have the pre-read user fasta file.
diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index f0a7abc..7f4fbba 100644
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -25,8 +25,7 @@ vector<string> ParseFastaQCommand::getValidParameters(){
//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qual"] = tempOutNames;
@@ -62,9 +61,9 @@ vector<string> ParseFastaQCommand::getRequiredFiles(){
//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(string option){
try {
- abort = false;
+ abort = false; calledHelp = false;
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -140,7 +139,7 @@ ParseFastaQCommand::~ParseFastaQCommand() { /* do nothing */ }
int ParseFastaQCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//open Output Files
string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 9cf5a73..fdacc3a 100644
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -25,8 +25,7 @@ vector<string> ParseListCommand::getValidParameters(){
//**********************************************************************************************************************
ParseListCommand::ParseListCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
}
@@ -61,11 +60,11 @@ vector<string> ParseListCommand::getRequiredFiles(){
//**********************************************************************************************************************
ParseListCommand::ParseListCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -170,7 +169,7 @@ ParseListCommand::~ParseListCommand(){}
int ParseListCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//set fileroot
string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index c97e92e..c0de504 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -24,8 +24,7 @@ vector<string> ParsimonyCommand::getValidParameters(){
//**********************************************************************************************************************
ParsimonyCommand::ParsimonyCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["parsimony"] = tempOutNames;
outputTypes["psummary"] = tempOutNames;
@@ -61,11 +60,11 @@ vector<string> ParsimonyCommand::getRequiredFiles(){
ParsimonyCommand::ParsimonyCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
Groups.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -186,7 +185,7 @@ void ParsimonyCommand::help(){
int ParsimonyCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
Progress* reading;
reading = new Progress("Comparing to random:", iters);
diff --git a/pcacommand.cpp b/pcacommand.cpp
index 8fb4121..2e8f132 100644
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -25,8 +25,7 @@ vector<string> PCACommand::getValidParameters(){
//**********************************************************************************************************************
PCACommand::PCACommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["pca"] = tempOutNames;
outputTypes["loadings"] = tempOutNames;
@@ -63,12 +62,12 @@ vector<string> PCACommand::getRequiredFiles(){
PCACommand::PCACommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
globaldata = GlobalData::getInstance();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -150,7 +149,7 @@ PCACommand::~PCACommand(){}
int PCACommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
cout.setf(ios::fixed, ios::floatfield);
cout.setf(ios::showpoint);
diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index fbcb7e0..d8efb25 100644
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -26,8 +26,7 @@ vector<string> PCOACommand::getValidParameters(){
//**********************************************************************************************************************
PCOACommand::PCOACommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["pcoa"] = tempOutNames;
outputTypes["loadings"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> PCOACommand::getRequiredFiles(){
PCOACommand::PCOACommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -149,7 +148,7 @@ PCOACommand::~PCOACommand(){}
int PCOACommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
cout.setf(ios::fixed, ios::floatfield);
cout.setf(ios::showpoint);
diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 4eb652c..a987594 100644
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -24,8 +24,7 @@ vector<string> PhyloDiversityCommand::getValidParameters(){
//**********************************************************************************************************************
PhyloDiversityCommand::PhyloDiversityCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["phylodiv"] = tempOutNames;
outputTypes["rarefy"] = tempOutNames;
@@ -63,10 +62,10 @@ vector<string> PhyloDiversityCommand::getRequiredFiles(){
PhyloDiversityCommand::PhyloDiversityCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -169,7 +168,7 @@ PhyloDiversityCommand::~PhyloDiversityCommand(){}
int PhyloDiversityCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
for (int i = 0; i < globaldata->Groups.size(); i++) { if (globaldata->Groups[i] == "xxx") { globaldata->Groups.erase(globaldata->Groups.begin()+i); break; } }
diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 2018170..4b524dd 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -28,8 +28,7 @@ vector<string> PhylotypeCommand::getValidParameters(){
//**********************************************************************************************************************
PhylotypeCommand::PhylotypeCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["sabund"] = tempOutNames;
@@ -66,10 +65,10 @@ vector<string> PhylotypeCommand::getRequiredFiles(){
/**********************************************************************************************************************/
PhylotypeCommand::PhylotypeCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
@@ -181,7 +180,7 @@ PhylotypeCommand::~PhylotypeCommand(){}
int PhylotypeCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//reads in taxonomy file and makes all the taxonomies the same length
//by appending the last taxon to a given taxonomy as many times as needed to
diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index f95b928..84282dc 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -49,10 +49,10 @@ vector<string> PipelineCommand::getRequiredFiles(){
PipelineCommand::PipelineCommand(string option) {
try {
cFactory = CommandFactory::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
@@ -235,7 +235,7 @@ PipelineCommand::~PipelineCommand(){}
int PipelineCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
diff --git a/pipelinepdscommand.h b/pipelinepdscommand.h
index a506159..289a909 100644
--- a/pipelinepdscommand.h
+++ b/pipelinepdscommand.h
@@ -20,7 +20,7 @@ class PipelineCommand : public Command {
public:
PipelineCommand(string);
- PipelineCommand() {}
+ PipelineCommand() { abort = true; calledHelp = true; }
~PipelineCommand();
vector<string> getRequiredParameters();
vector<string> getValidParameters();
diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 3a3aafc..14409f5 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -26,8 +26,7 @@ vector<string> PreClusterCommand::getValidParameters(){
//**********************************************************************************************************************
PreClusterCommand::PreClusterCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> PreClusterCommand::getRequiredFiles(){
PreClusterCommand::PreClusterCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -167,7 +166,7 @@ void PreClusterCommand::help(){
int PreClusterCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
diff --git a/quitcommand.cpp b/quitcommand.cpp
index 0dd2dec..462fe8f 100644
--- a/quitcommand.cpp
+++ b/quitcommand.cpp
@@ -45,10 +45,10 @@ vector<string> QuitCommand::getRequiredFiles(){
//**********************************************************************************************************************
QuitCommand::QuitCommand(string option) {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
}
//**********************************************************************************************************************
diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index cb37727..4ab81ea 100644
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -62,8 +62,7 @@ vector<string> RareFactCommand::getRequiredFiles(){
//**********************************************************************************************************************
RareFactCommand::RareFactCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["rarefaction"] = tempOutNames;
outputTypes["r_chao"] = tempOutNames;
@@ -90,13 +89,13 @@ RareFactCommand::RareFactCommand(){
RareFactCommand::RareFactCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -214,7 +213,7 @@ RareFactCommand::~RareFactCommand(){}
int RareFactCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string hadShared = "";
if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 8cf1f2f..ea460c0 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -26,8 +26,7 @@ vector<string> RareFactSharedCommand::getValidParameters(){
//**********************************************************************************************************************
RareFactSharedCommand::RareFactSharedCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["sharedrarefaction"] = tempOutNames;
outputTypes["sharedr_nseqs"] = tempOutNames;
@@ -66,14 +65,14 @@ RareFactSharedCommand::RareFactSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Estimators.clear();
Groups.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -217,7 +216,7 @@ RareFactSharedCommand::~RareFactSharedCommand(){
int RareFactSharedCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if the users entered no valid calculators don't execute command
if (rDisplays.size() == 0) { return 0; }
diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index c600eb8..630f649 100644
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -51,10 +51,10 @@ vector<string> ReadDistCommand::getRequiredFiles(){
ReadDistCommand::ReadDistCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -239,7 +239,7 @@ ReadDistCommand::~ReadDistCommand(){
int ReadDistCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
time_t start = time(NULL);
size_t numDists = 0;
diff --git a/readdistcommand.h b/readdistcommand.h
index 984b4a7..2f05ddb 100644
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -27,7 +27,7 @@ class GlobalData;
class ReadDistCommand : public Command {
public:
ReadDistCommand(string);
- ReadDistCommand() {}
+ ReadDistCommand() { abort = true; calledHelp = true; }
~ReadDistCommand();
vector<string> getRequiredParameters();
vector<string> getValidParameters();
diff --git a/readotucommand.cpp b/readotucommand.cpp
index 8683fc3..6757556 100644
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -24,8 +24,7 @@ vector<string> ReadOtuCommand::getValidParameters(){
//**********************************************************************************************************************
ReadOtuCommand::ReadOtuCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["rabund"] = tempOutNames;
outputTypes["shared"] = tempOutNames;
@@ -62,11 +61,11 @@ vector<string> ReadOtuCommand::getRequiredFiles(){
ReadOtuCommand::ReadOtuCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -290,7 +289,7 @@ ReadOtuCommand::~ReadOtuCommand(){}
int ReadOtuCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (globaldata->getFormat() == "shared") {
diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index edfdf3b..05a65b7 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -48,10 +48,10 @@ vector<string> ReadTreeCommand::getRequiredFiles(){
ReadTreeCommand::ReadTreeCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -178,7 +178,7 @@ ReadTreeCommand::~ReadTreeCommand(){
int ReadTreeCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int readOk;
diff --git a/readtreecommand.h b/readtreecommand.h
index 97391d0..464a825 100644
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -19,7 +19,7 @@ class GlobalData;
class ReadTreeCommand : public Command {
public:
ReadTreeCommand(string);
- ReadTreeCommand() {}
+ ReadTreeCommand() { abort = true; calledHelp = true; }
~ReadTreeCommand();
vector<string> getRequiredParameters();
vector<string> getValidParameters();
diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 2c98e81..4462b52 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -27,8 +27,7 @@ vector<string> RemoveGroupsCommand::getValidParameters(){
//**********************************************************************************************************************
RemoveGroupsCommand::RemoveGroupsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> RemoveGroupsCommand::getRequiredFiles(){
//**********************************************************************************************************************
RemoveGroupsCommand::RemoveGroupsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -222,7 +221,7 @@ void RemoveGroupsCommand::help(){
int RemoveGroupsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
groupMap->readMap();
diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 0a5c5c7..6e43b10 100644
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -26,8 +26,7 @@ vector<string> RemoveLineageCommand::getValidParameters(){
//**********************************************************************************************************************
RemoveLineageCommand::RemoveLineageCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> RemoveLineageCommand::getRequiredFiles(){
//**********************************************************************************************************************
RemoveLineageCommand::RemoveLineageCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -237,7 +236,7 @@ void RemoveLineageCommand::help(){
int RemoveLineageCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (m->control_pressed) { return 0; }
diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 1a7d3bd..347bb08 100644
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -27,8 +27,7 @@ vector<string> RemoveOtusCommand::getValidParameters(){
//**********************************************************************************************************************
RemoveOtusCommand::RemoveOtusCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["list"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> RemoveOtusCommand::getRequiredFiles(){
//**********************************************************************************************************************
RemoveOtusCommand::RemoveOtusCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -182,7 +181,7 @@ void RemoveOtusCommand::help(){
int RemoveOtusCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
groupMap->readMap();
diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index 0ba90f3..0c656a0 100644
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -28,8 +28,7 @@ vector<string> RemoveRareCommand::getValidParameters(){
//**********************************************************************************************************************
RemoveRareCommand::RemoveRareCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["rabund"] = tempOutNames;
outputTypes["sabund"] = tempOutNames;
@@ -69,11 +68,11 @@ vector<string> RemoveRareCommand::getRequiredFiles(){
RemoveRareCommand::RemoveRareCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -227,7 +226,7 @@ void RemoveRareCommand::help(){
int RemoveRareCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (m->control_pressed) { return 0; }
diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 17de5a8..81c42f6 100644
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -26,8 +26,7 @@ vector<string> RemoveSeqsCommand::getValidParameters(){
//**********************************************************************************************************************
RemoveSeqsCommand::RemoveSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
@@ -68,10 +67,10 @@ vector<string> RemoveSeqsCommand::getRequiredFiles(){
//**********************************************************************************************************************
RemoveSeqsCommand::RemoveSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -249,7 +248,7 @@ void RemoveSeqsCommand::help(){
int RemoveSeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get names you want to keep
readAccnos();
diff --git a/reversecommand.cpp b/reversecommand.cpp
index 7b58162..d20f4af 100644
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -25,8 +25,7 @@ vector<string> ReverseSeqsCommand::getValidParameters(){
//**********************************************************************************************************************
ReverseSeqsCommand::ReverseSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
}
@@ -62,10 +61,10 @@ vector<string> ReverseSeqsCommand::getRequiredFiles(){
ReverseSeqsCommand::ReverseSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -144,7 +143,7 @@ ReverseSeqsCommand::~ReverseSeqsCommand(){ /* do nothing */ }
int ReverseSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
ifstream inFASTA;
m->openInputFile(fasta, inFASTA);
diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 65b5956..150a27e 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -26,8 +26,7 @@ vector<string> ScreenSeqsCommand::getValidParameters(){
//**********************************************************************************************************************
ScreenSeqsCommand::ScreenSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> ScreenSeqsCommand::getRequiredFiles(){
ScreenSeqsCommand::ScreenSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -247,7 +246,7 @@ ScreenSeqsCommand::~ScreenSeqsCommand(){ /* do nothing */ }
int ScreenSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if the user want to optimize we need to no the 90% mark
vector<unsigned long int> positions;
diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 26bd354..c9002ca 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -25,8 +25,7 @@ vector<string> AlignCheckCommand::getValidParameters(){
//**********************************************************************************************************************
AlignCheckCommand::AlignCheckCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["aligncheck"] = tempOutNames;
}
@@ -62,11 +61,11 @@ vector<string> AlignCheckCommand::getRequiredFiles(){
AlignCheckCommand::AlignCheckCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
haderror = 0;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -155,7 +154,7 @@ void AlignCheckCommand::help(){
int AlignCheckCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get secondary structure info.
readMap();
diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 045736d..6a22fd6 100644
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -24,8 +24,7 @@ vector<string> SensSpecCommand::getValidParameters(){
//**********************************************************************************************************************
SensSpecCommand::SensSpecCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["sensspec"] = tempOutNames;
}
@@ -62,10 +61,10 @@ vector<string> SensSpecCommand::getRequiredFiles(){
SensSpecCommand::SensSpecCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
string temp;
@@ -208,7 +207,7 @@ SensSpecCommand::~SensSpecCommand(){ /* do nothing */ }
int SensSpecCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
setUpOutput();
outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index d2c0fcb..00f7862 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -27,8 +27,7 @@ vector<string> SeqErrorCommand::getValidParameters(){
//**********************************************************************************************************************
SeqErrorCommand::SeqErrorCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["error.summary"] = tempOutNames;
outputTypes["error.seq"] = tempOutNames;
@@ -73,10 +72,10 @@ vector<string> SeqErrorCommand::getRequiredFiles(){
SeqErrorCommand::SeqErrorCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
string temp;
@@ -231,7 +230,7 @@ SeqErrorCommand::~SeqErrorCommand(){
int SeqErrorCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
m->openOutputFile(errorSummaryFileName, errorSummaryFile);
diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 7edb717..7da424c 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -25,8 +25,7 @@ vector<string> SeqSummaryCommand::getValidParameters(){
//**********************************************************************************************************************
SeqSummaryCommand::SeqSummaryCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
}
@@ -62,10 +61,10 @@ vector<string> SeqSummaryCommand::getRequiredFiles(){
SeqSummaryCommand::SeqSummaryCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -148,7 +147,7 @@ SeqSummaryCommand::~SeqSummaryCommand(){ /* do nothing */ }
int SeqSummaryCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
diff --git a/setdircommand.cpp b/setdircommand.cpp
index 214bd17..a76db24 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -47,10 +47,10 @@ vector<string> SetDirectoryCommand::getRequiredFiles(){
SetDirectoryCommand::SetDirectoryCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -117,7 +117,7 @@ SetDirectoryCommand::~SetDirectoryCommand(){}
int SetDirectoryCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
commandFactory = CommandFactory::getInstance();
diff --git a/setdircommand.h b/setdircommand.h
index 1afab07..6263c5e 100644
--- a/setdircommand.h
+++ b/setdircommand.h
@@ -20,7 +20,7 @@ class SetDirectoryCommand : public Command {
public:
SetDirectoryCommand(string);
- SetDirectoryCommand() {}
+ SetDirectoryCommand() { abort = true; calledHelp = true; }
~SetDirectoryCommand();
vector<string> getRequiredParameters();
vector<string> getValidParameters();
diff --git a/setlogfilecommand.cpp b/setlogfilecommand.cpp
index b99b833..f57dfaf 100644
--- a/setlogfilecommand.cpp
+++ b/setlogfilecommand.cpp
@@ -48,10 +48,10 @@ vector<string> SetLogFileCommand::getRequiredFiles(){
SetLogFileCommand::SetLogFileCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -103,7 +103,7 @@ SetLogFileCommand::~SetLogFileCommand(){}
int SetLogFileCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
commandFactory = CommandFactory::getInstance();
diff --git a/setlogfilecommand.h b/setlogfilecommand.h
index d2b5c3d..e0555d0 100644
--- a/setlogfilecommand.h
+++ b/setlogfilecommand.h
@@ -19,7 +19,7 @@ class SetLogFileCommand : public Command {
public:
SetLogFileCommand(string);
- SetLogFileCommand() {}
+ SetLogFileCommand() { abort = true; calledHelp = true; }
~SetLogFileCommand();
vector<string> getRequiredParameters();
vector<string> getValidParameters();
diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index c9bc469..4a9271c 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -25,8 +25,7 @@ vector<string> SffInfoCommand::getValidParameters(){
//**********************************************************************************************************************
SffInfoCommand::SffInfoCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["flow"] = tempOutNames;
@@ -65,11 +64,11 @@ vector<string> SffInfoCommand::getRequiredFiles(){
SffInfoCommand::SffInfoCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
hasAccnos = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -279,7 +278,7 @@ SffInfoCommand::~SffInfoCommand(){}
int SffInfoCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < filenames.size(); s++) {
diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index c252b4f..ec6b1d3 100644
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -27,7 +27,7 @@ vector<string> SharedCommand::getValidParameters(){
//**********************************************************************************************************************
SharedCommand::SharedCommand(){
try {
-
+
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["rabund"] = tempOutNames;
diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index ffddb8c..e2f2636 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -48,7 +48,7 @@ vector<string> ShhherCommand::getValidParameters(){
ShhherCommand::ShhherCommand(){
try {
- abort = true;
+ abort = true; calledHelp = true;
//initialize outputTypes
vector<string> tempOutNames;
@@ -101,11 +101,11 @@ ShhherCommand::ShhherCommand(string option) {
#endif
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
@@ -237,6 +237,8 @@ void ShhherCommand::help(){
#ifdef USE_MPI
int ShhherCommand::execute(){
try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
int tag = 1976;
MPI_Status status;
diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index a8ca812..d0f925e 100644
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -24,8 +24,7 @@ vector<string> SplitAbundCommand::getValidParameters(){
//**********************************************************************************************************************
SplitAbundCommand::SplitAbundCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["name"] = tempOutNames;
@@ -64,11 +63,11 @@ vector<string> SplitAbundCommand::getRequiredFiles(){
//**********************************************************************************************************************
SplitAbundCommand::SplitAbundCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -233,7 +232,7 @@ SplitAbundCommand::~SplitAbundCommand(){
int SplitAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (listfile != "") { //you are using a listfile to determine abundance
if (outputDir == "") { outputDir = m->hasPath(listfile); }
diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 3fa7d04..d389d89 100644
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -48,8 +48,7 @@ vector<string> SplitGroupCommand::getRequiredFiles(){
//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
@@ -62,10 +61,10 @@ SplitGroupCommand::SplitGroupCommand(){
//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -171,7 +170,7 @@ SplitGroupCommand::~SplitGroupCommand(){ }
int SplitGroupCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
groupMap->readMap();
diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 2a3d138..6b0e4f9 100644
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -25,8 +25,7 @@ vector<string> SubSampleCommand::getValidParameters(){
//**********************************************************************************************************************
SubSampleCommand::SubSampleCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["shared"] = tempOutNames;
outputTypes["list"] = tempOutNames;
@@ -68,12 +67,12 @@ vector<string> SubSampleCommand::getRequiredFiles(){
SubSampleCommand::SubSampleCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -279,7 +278,7 @@ SubSampleCommand::~SubSampleCommand(){}
int SubSampleCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (sharedfile != "") { getSubSampleShared(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } }
diff --git a/summarycommand.cpp b/summarycommand.cpp
index e67659f..fbe7964 100644
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -49,8 +49,7 @@ vector<string> SummaryCommand::getValidParameters(){
//**********************************************************************************************************************
SummaryCommand::SummaryCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
}
@@ -87,13 +86,13 @@ vector<string> SummaryCommand::getRequiredFiles(){
SummaryCommand::SummaryCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -194,7 +193,7 @@ SummaryCommand::~SummaryCommand(){}
int SummaryCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string hadShared = "";
if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 1211ea9..b521444 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -65,8 +65,7 @@ vector<string> SummarySharedCommand::getValidParameters(){
//**********************************************************************************************************************
SummarySharedCommand::SummarySharedCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
}
@@ -103,13 +102,13 @@ vector<string> SummarySharedCommand::getRequiredFiles(){
SummarySharedCommand::SummarySharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -317,7 +316,7 @@ SummarySharedCommand::~SummarySharedCommand(){
int SummarySharedCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
ofstream outputFileHandle, outAll;
string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "shared.summary";
diff --git a/systemcommand.cpp b/systemcommand.cpp
index fb250d7..abc07d0 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -46,10 +46,10 @@ vector<string> SystemCommand::getRequiredFiles(){
SystemCommand::SystemCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
@@ -92,7 +92,7 @@ void SystemCommand::help(){
int SystemCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
system(command.c_str());
diff --git a/systemcommand.h b/systemcommand.h
index 3b48642..55b772b 100644
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -18,7 +18,7 @@ class SystemCommand : public Command {
public:
SystemCommand(string);
- SystemCommand() {}
+ SystemCommand() { abort = true; calledHelp = true; }
~SystemCommand(){}
vector<string> getRequiredParameters();
vector<string> getValidParameters();
diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index adf140a..a31c151 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -65,7 +65,7 @@ vector<string> TreeGroupCommand::getValidParameters(){
//**********************************************************************************************************************
TreeGroupCommand::TreeGroupCommand(){
try {
- abort = true;
+ abort = true; calledHelp = true;
globaldata = GlobalData::getInstance();
//initialize outputTypes
vector<string> tempOutNames;
@@ -104,14 +104,14 @@ vector<string> TreeGroupCommand::getRequiredFiles(){
TreeGroupCommand::TreeGroupCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Groups.clear();
Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -380,7 +380,7 @@ TreeGroupCommand::~TreeGroupCommand(){
int TreeGroupCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (format == "sharedfile") {
//if the users entered no valid calculators don't execute command
diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index e4d0165..5c5d28b 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -65,8 +65,7 @@ vector<string> TrimFlowsCommand::getRequiredFiles(){
TrimFlowsCommand::TrimFlowsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["flow"] = tempOutNames;
outputTypes["fasta"] = tempOutNames;
@@ -101,11 +100,11 @@ void TrimFlowsCommand::help(){
TrimFlowsCommand::TrimFlowsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
comboStarts = 0;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -250,7 +249,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option) {
int TrimFlowsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 7267b91..45de8d6 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -31,8 +31,7 @@ vector<string> TrimSeqsCommand::getValidParameters(){
TrimSeqsCommand::TrimSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qual"] = tempOutNames;
@@ -76,11 +75,11 @@ vector<string> TrimSeqsCommand::getRequiredFiles(){
TrimSeqsCommand::TrimSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
comboStarts = 0;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -316,7 +315,7 @@ TrimSeqsCommand::~TrimSeqsCommand(){ /* do nothing */ }
int TrimSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
numFPrimers = 0; //this needs to be initialized
numRPrimers = 0;
diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 79ee042..ccd5aa4 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -25,8 +25,7 @@ vector<string> UnifracUnweightedCommand::getValidParameters(){
UnifracUnweightedCommand::UnifracUnweightedCommand(){
try {
globaldata = GlobalData::getInstance();
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["unweighted"] = tempOutNames;
outputTypes["uwsummary"] = tempOutNames;
@@ -66,11 +65,11 @@ vector<string> UnifracUnweightedCommand::getRequiredFiles(){
UnifracUnweightedCommand::UnifracUnweightedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
Groups.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -191,7 +190,7 @@ void UnifracUnweightedCommand::help(){
int UnifracUnweightedCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index bee10cb..8745a89 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -24,8 +24,7 @@ vector<string> UnifracWeightedCommand::getValidParameters(){
//**********************************************************************************************************************
UnifracWeightedCommand::UnifracWeightedCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["weighted"] = tempOutNames;
outputTypes["wsummary"] = tempOutNames;
@@ -65,11 +64,11 @@ vector<string> UnifracWeightedCommand::getRequiredFiles(){
UnifracWeightedCommand::UnifracWeightedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
Groups.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -181,7 +180,7 @@ void UnifracWeightedCommand::help(){
int UnifracWeightedCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
diff --git a/venncommand.cpp b/venncommand.cpp
index 7601ed8..5cc0fea 100644
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -33,8 +33,7 @@ vector<string> VennCommand::getValidParameters(){
//**********************************************************************************************************************
VennCommand::VennCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["svg"] = tempOutNames;
}
@@ -71,12 +70,12 @@ vector<string> VennCommand::getRequiredFiles(){
VennCommand::VennCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
@@ -243,7 +242,7 @@ VennCommand::~VennCommand(){
int VennCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string lastLabel;