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

[mothur.git] / libshuffcommand.cpp

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 773d8d351211f3ab9794770e72aad77235754b53..e48cf33d7dd4a60405841e124a35c5250f76bd86 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -18,6 +18,54 @@
 #include "slibshuff.h"
 #include "dlibshuff.h"
 
+//**********************************************************************************************************************
+vector<string> LibShuffCommand::getValidParameters(){  
+       try {
+               string Array[] =  {"iters","groups","step","form","cutoff","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "LibShuffCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+LibShuffCommand::LibShuffCommand(){    
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["coverage"] = tempOutNames;
+               outputTypes["libshuffsummary"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> LibShuffCommand::getRequiredParameters(){       
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "LibShuffCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> LibShuffCommand::getRequiredFiles(){    
+       try {
+               string Array[] =  {"phylip","group"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "LibShuffCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 LibShuffCommand::LibShuffCommand(string option)  {
@@ -44,6 +92,11 @@ LibShuffCommand::LibShuffCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["coverage"] = tempOutNames;
+                       outputTypes["libshuffsummary"] = 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 = ""; 
@@ -147,14 +200,14 @@ int LibShuffCommand::execute(){
                        pValueCounts[i].assign(numGroups, 0);
                }
        
-               if (m->control_pressed) {  delete form; globaldata->Groups.clear(); delete globaldata->gMatrix;  globaldata->gMatrix = NULL; return 0; }
+               if (m->control_pressed) {  outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix;  globaldata->gMatrix = NULL; return 0; }
                                
                Progress* reading = new Progress();
                
                for(int i=0;i<numGroups-1;i++) {
                        for(int j=i+1;j<numGroups;j++) {
                                
-                               if (m->control_pressed) {  delete form; globaldata->Groups.clear(); delete globaldata->gMatrix;  globaldata->gMatrix = NULL; delete reading; return 0; }
+                               if (m->control_pressed) {  outputTypes.clear();  delete form; globaldata->Groups.clear(); delete globaldata->gMatrix;  globaldata->gMatrix = NULL; delete reading; return 0; }
 
                                reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
                                int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
@@ -162,13 +215,13 @@ int LibShuffCommand::execute(){
        
                                for(int p=0;p<iters;p++) {      
                                        
-                                       if (m->control_pressed) {  delete form; globaldata->Groups.clear(); delete globaldata->gMatrix;  globaldata->gMatrix = NULL; delete reading; return 0; }
+                                       if (m->control_pressed) {  outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix;  globaldata->gMatrix = NULL; delete reading; return 0; }
                                        
                                        form->randomizeGroups(spoti,spotj); 
                                        if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj])     {       pValueCounts[i][j]++;   }
                                        if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti])     {       pValueCounts[j][i]++;   }
                                        
-                                       if (m->control_pressed) {  delete form; globaldata->Groups.clear(); delete globaldata->gMatrix;  globaldata->gMatrix = NULL; delete reading; return 0; }
+                                       if (m->control_pressed) {  outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix;  globaldata->gMatrix = NULL; delete reading; return 0; }
                                        
                                        reading->update(p);                     
                                }
@@ -177,7 +230,7 @@ int LibShuffCommand::execute(){
                        }
                }
                
-               if (m->control_pressed) {  delete form; globaldata->Groups.clear(); delete globaldata->gMatrix;  globaldata->gMatrix = NULL; delete reading; return 0; }
+               if (m->control_pressed) { outputTypes.clear();  delete form; globaldata->Groups.clear(); delete globaldata->gMatrix;  globaldata->gMatrix = NULL; delete reading; return 0; }
        
                reading->finish();
                delete reading;
@@ -193,7 +246,7 @@ int LibShuffCommand::execute(){
                //delete globaldata's copy of the gmatrix to free up memory
                delete globaldata->gMatrix;  globaldata->gMatrix = NULL;
                
-               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();
@@ -217,7 +270,7 @@ int LibShuffCommand::printCoverageFile() {
                ofstream outCov;
                summaryFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getPhylipFile())) + "libshuff.coverage";
                m->openOutputFile(summaryFile, outCov);
-               outputNames.push_back(summaryFile);
+               outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
                outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
                //cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
                
@@ -313,7 +366,7 @@ int LibShuffCommand::printSummaryFile() {
                ofstream outSum;
                summaryFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getPhylipFile())) + "libshuff.summary";
                m->openOutputFile(summaryFile, outSum);
-               outputNames.push_back(summaryFile);
+               outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);
 
                outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
                cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);