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

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 7d1f4df1e95fa10241225ca20dba35c1f069d6ff..08c94ba3261c47c33d13368d9fbd84718cb5f3a2 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -11,6 +11,54 @@
 #include "metastats.h"
 #include "sharedutilities.h"
 
+//**********************************************************************************************************************
+vector<string> MetaStatsCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"groups","label","outputdir","iters","threshold","g","design","sets","processors","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MetaStatsCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+MetaStatsCommand::MetaStatsCommand(){  
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["metastats"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MetaStatsCommand", "MetaStatsCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> MetaStatsCommand::getRequiredParameters(){      
+       try {
+               string Array[] =  {"design"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MetaStatsCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> MetaStatsCommand::getRequiredFiles(){   
+       try {
+               string Array[] =  {"shared"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MetaStatsCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 MetaStatsCommand::MetaStatsCommand(string option) {
@@ -39,6 +87,10 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["metastats"] = 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 = ""; 
@@ -206,7 +258,7 @@ int MetaStatsCommand::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;  delete designMap;  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 < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); delete read;  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0; }
        
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
 
@@ -237,13 +289,13 @@ int MetaStatsCommand::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;  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); globaldata->Groups.clear(); delete read;  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0; }
 
                        //get next line to process
                        lookup = input->getSharedRAbundVectors();                               
                }
                
-               if (m->control_pressed) { globaldata->Groups.clear(); delete read; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {    remove(outputNames[i].c_str()); }  return 0; }
+               if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); }  return 0; }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -276,7 +328,7 @@ int MetaStatsCommand::execute(){
                delete read;
                delete designMap;
                
-               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();
@@ -350,7 +402,7 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                        
                        //get filename
                        string outputFileName = outputDir +  m->getRootName(m->getSimpleName(globaldata->inputFileName)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
-                       outputNames.push_back(outputFileName);
+                       outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
                        int nameLength = outputFileName.length();
                        char * output = new char[nameLength];
                        strcpy(output, outputFileName.c_str());