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

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index d27a88141534c7bf9b8115eaccb55d7966096753..cedc1f2c71c450f80ad5bcfefffe8713effab6fb 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -10,7 +10,53 @@
 #include "classifyotucommand.h"
 #include "phylotree.h"
 
-
+//**********************************************************************************************************************
+vector<string> ClassifyOtuCommand::getValidParameters(){       
+       try {
+               string AlignArray[] =  {"list","label","name","taxonomy","cutoff","probs","outputdir","inputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClassifyOtuCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ClassifyOtuCommand::ClassifyOtuCommand(){      
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["constaxonomy"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClassifyOtuCommand", "ClassifyOtuCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ClassifyOtuCommand::getRequiredParameters(){    
+       try {
+               string Array[] =  {"list","taxonomy"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClassifyOtuCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ClassifyOtuCommand::getRequiredFiles(){ 
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClassifyOtuCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
        try{
@@ -37,6 +83,10 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["constaxonomy"] = 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 = "";          }
@@ -157,7 +207,7 @@ int ClassifyOtuCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str());  }  return 0; }
+               if (m->control_pressed) { outputTypes.clear(); delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0; }
        
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
@@ -165,7 +215,7 @@ int ClassifyOtuCommand::execute(){
                        
                                        m->mothurOut(list->getLabel() + "\t" + toString(list->size())); m->mothurOutEndLine();
                                        process(list);
-                                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } delete input; delete list; return 0; }
+                                       if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } delete input; delete list; return 0; }
                                                                                
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
@@ -180,7 +230,7 @@ int ClassifyOtuCommand::execute(){
                                        process(list);
                                
                                        
-                                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } delete input; delete list; return 0; }
+                                       if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } delete input; delete list; return 0; }
                                                                                
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
@@ -216,12 +266,12 @@ int ClassifyOtuCommand::execute(){
                        process(list);
                        delete list;
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } delete input; delete list; return 0; }
+                       if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } delete input; delete list; return 0; }
                }
                
                delete input;  
                                
-               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } return 0; }
+               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -424,7 +474,9 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                ofstream out;
                string outputFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".cons.taxonomy";
                m->openOutputFile(outputFile, out);
-               outputNames.push_back(outputFile);
+               outputNames.push_back(outputFile); outputTypes["constaxonomy"].push_back(outputFile);
+               
+               out << "OTU\tSize\tTaxonomy" << endl;
                
                //for each bin in the list vector
                for (int i = 0; i < processList->getNumBins(); i++) {