added pipeline commands which involved change to command factory and command class...

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 6b2570c9808ab9083a06c4fc41439c6fd99b22e2..1e09dba67dc7f1d9b0b10c5a5dfa79023b04a3a6 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -36,6 +36,54 @@ inline bool compareGroup(repStruct left, repStruct right){
        return (left.group < right.group);      
 }
 //**********************************************************************************************************************
+GetOTURepCommand::GetOTURepCommand(){  
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["name"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetOTURepCommand", "GetOTURepCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetOTURepCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"fasta","list","label","name", "group", "sorted", "phylip","column","large","cutoff","precision","groups","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetOTURepCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetOTURepCommand::getRequiredParameters(){      
+       try {
+               string Array[] =  {"fasta","list"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetOTURepCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetOTURepCommand::getRequiredFiles(){   
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetOTURepCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetOTURepCommand::GetOTURepCommand(string option)  {
        try{
                globaldata = GlobalData::getInstance();
@@ -62,6 +110,11 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       outputTypes["name"] = tempOutNames;
+                       
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -378,7 +431,7 @@ int GetOTURepCommand::execute(){
                                        
                                        if (m->control_pressed) { 
                                                if (large) {  inRow.close(); remove(distFile.c_str());  }
-                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
                                                delete read; delete input; delete list; globaldata->gListVector = NULL; return 0; 
                                        }
                                        
@@ -397,7 +450,7 @@ int GetOTURepCommand::execute(){
                                        
                                        if (m->control_pressed) { 
                                                if (large) {  inRow.close(); remove(distFile.c_str());  }
-                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
                                                delete read; delete input; delete list; globaldata->gListVector = NULL; return 0; 
                                        }
                                        
@@ -437,7 +490,7 @@ int GetOTURepCommand::execute(){
                        
                        if (m->control_pressed) { 
                                        if (large) {  inRow.close(); remove(distFile.c_str());  }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
                                        delete read; delete input; delete list; globaldata->gListVector = NULL; return 0; 
                        }
                }
@@ -607,7 +660,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                if (Groups.size() == 0) { //you don't want to use groups
                        outputNamesFile  = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".rep.names";
                        m->openOutputFile(outputNamesFile, newNamesOutput);
-                       outputNames.push_back(outputNamesFile);
+                       outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile); 
                        outputNameFiles[outputNamesFile] = processList->getLabel();
                }else{ //you want to use groups
                        ofstream* temp;
@@ -617,7 +670,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                                outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".rep.names";
                                
                                m->openOutputFile(outputNamesFile, *(temp));
-                               outputNames.push_back(outputNamesFile);
+                               outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile);
                                outputNameFiles[outputNamesFile] = processList->getLabel() + "." + Groups[i];
                        }
                }
@@ -705,7 +758,7 @@ int GetOTURepCommand::processNames(string filename, string label) {
                string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + label + ".rep.fasta";
                m->openOutputFile(outputFileName, out);
                vector<repStruct> reps;
-               outputNames.push_back(outputFileName);
+               outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
                
                ofstream out2;
                string tempNameFile = filename + ".temp";