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

[mothur.git] / getrelabundcommand.cpp

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 037cd3ee70b970a7f0ecce05e2e0c073e449562e..5b9327b57bd928a5e456a7251a83be1a0664cd6c 100644 (file)
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -10,7 +10,53 @@
 #include "getrelabundcommand.h"
 
 //**********************************************************************************************************************
-
+vector<string> GetRelAbundCommand::getValidParameters(){       
+       try {
+               string Array[] =  {"groups","label","scale","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRelAbundCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+GetRelAbundCommand::GetRelAbundCommand(){      
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["relabund"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::getRequiredParameters(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRelAbundCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::getRequiredFiles(){ 
+       try {
+               string Array[] =  {"shared"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetRelAbundCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetRelAbundCommand::GetRelAbundCommand(string option) {
        try {
                globaldata = GlobalData::getInstance();
@@ -36,10 +82,14 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["relabund"] = 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->inputFileName); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it       
                        }
                        
                        //make sure the user has already run the read.otu command
@@ -52,7 +102,7 @@ GetRelAbundCommand::GetRelAbundCommand(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;  }
                        }
                        
@@ -66,7 +116,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
                        if (groups == "not found") { groups = ""; pickedGroups = false; }
                        else { 
                                pickedGroups = true;
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                        
@@ -118,9 +168,9 @@ int GetRelAbundCommand::execute(){
        
                if (abort == true) { return 0; }
                
-               string outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "relabund";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "relabund";
                ofstream out;
-               openOutputFile(outputFileName, out);
+               m->openOutputFile(outputFileName, out);
                out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
                
                read = new ReadOTUFile(globaldata->inputFileName);      
@@ -136,7 +186,7 @@ int GetRelAbundCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
        
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
 
@@ -147,7 +197,7 @@ int GetRelAbundCommand::execute(){
                                userLabels.erase(lookup[0]->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                string saveLabel = lookup[0]->getLabel();
                        
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  
@@ -167,13 +217,13 @@ int GetRelAbundCommand::execute(){
                        //prevent memory leak
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                        
-                       if (m->control_pressed) {  globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) {  outputTypes.clear();  globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
 
                        //get next line to process
                        lookup = input->getSharedRAbundVectors();                               
                }
                
-               if (m->control_pressed) { globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str());  return 0; }
+               if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str());  return 0; }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -206,11 +256,11 @@ int GetRelAbundCommand::execute(){
                delete read;
                out.close();
                
-               if (m->control_pressed) { remove(outputFileName.c_str()); return 0;}
+               if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-               m->mothurOut(outputFileName); m->mothurOutEndLine();
+               m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
                m->mothurOutEndLine();
                
                return 0;