added [ERROR] flag if command aborts

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 033cd52e9e323e1707f603f8c20aaf22f50d4ecc..81c24a33713a6a0a732f3c9e6b7cbe99e10dc02d 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -9,16 +9,64 @@
 
 #include "binsequencecommand.h"
 
+//**********************************************************************************************************************
+vector<string> BinSeqCommand::getValidParameters(){    
+       try {
+               string AlignArray[] =  {"fasta","label","name", "group","outputdir","inputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BinSeqCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> BinSeqCommand::getRequiredParameters(){ 
+       try {
+               string AlignArray[] =  {"fasta"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BinSeqCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> BinSeqCommand::getRequiredFiles(){      
+       try {
+               string AlignArray[] =  {"list"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BinSeqCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+BinSeqCommand::BinSeqCommand(){        
+       try {
+               abort = true; calledHelp = true; 
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 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
@@ -36,10 +84,14 @@ BinSeqCommand::BinSeqCommand(string option) {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(globaldata->getListFile()); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(globaldata->getListFile()); //if user entered a file with a path then preserve it       
                        }
 
                        
@@ -58,7 +110,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                it = parameters.find("fasta");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
                                }
@@ -66,7 +118,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                it = parameters.find("name");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
@@ -74,7 +126,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                it = parameters.find("group");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }
@@ -92,7 +144,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -111,7 +163,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                        else if (groupfile == "not found") { groupfile = ""; }
                        
                        if (abort == false) { 
-//                             openInputFile(fastafile, in);
+//                             m->openInputFile(fastafile, in);
                                fasta = new FastaMap();
                                if (groupfile != "") {
                                        groupMap = new GroupMap(groupfile);
@@ -165,7 +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;
                
@@ -181,7 +233,6 @@ int BinSeqCommand::execute(){
                        readNamesFile();
                }
                
-               
                //read list file
                read = new ReadOTUFile(globaldata->getListFile());      
                read->read(&*globaldata); 
@@ -210,7 +261,7 @@ int BinSeqCommand::execute(){
                                userLabels.erase(list->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                string saveLabel = list->getLabel();
                                
                                delete list;
@@ -278,7 +329,7 @@ int BinSeqCommand::execute(){
 void BinSeqCommand::readNamesFile() {
        try {
                vector<string> dupNames;
-               openInputFile(namesfile, inNames);
+               m->openInputFile(namesfile, inNames);
                
                string name, names, sequence;
        
@@ -289,7 +340,7 @@ void BinSeqCommand::readNamesFile() {
                        dupNames.clear();
                        
                        //parse names into vector
-                       splitAtComma(names, dupNames);
+                       m->splitAtComma(names, dupNames);
                        
                        //store names in fasta map
                        sequence = fasta->getSequence(name);
@@ -297,7 +348,7 @@ void BinSeqCommand::readNamesFile() {
                                fasta->push_back(dupNames[i], sequence);
                        }
                
-                       gobble(inNames);
+                       m->gobble(inNames);
                }
                inNames.close();
 
@@ -313,11 +364,11 @@ int BinSeqCommand::process(ListVector* list) {
        try {
                                string binnames, name, sequence;
                                
-                               string outputFileName = outputDir + getRootName(getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta";
-                               openOutputFile(outputFileName, out);
+                               string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta";
+                               m->openOutputFile(outputFileName, out);
                                
                                //save to output list of output file names
-                               outputNames.push_back(outputFileName);
+                               outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 
                                m->mothurOut(list->getLabel()); m->mothurOutEndLine();