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

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index bb82702e9089b04f73571be314956567fb88f40e..dc4fec28a2c6edeb799dac61a90c5ecbff247a51 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -9,7 +9,53 @@
 
 #include "heatmapcommand.h"
 
-
+//**********************************************************************************************************************
+vector<string> HeatMapCommand::getValidParameters(){   
+       try {
+               string Array[] =  {"groups","label","sorted","scale","fontsize","numotu","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HeatMapCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+HeatMapCommand::HeatMapCommand(){      
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["svg"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> HeatMapCommand::getRequiredParameters(){        
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HeatMapCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> HeatMapCommand::getRequiredFiles(){     
+       try {
+               string Array[] =  {"list","sabund","rabund","shared","relabund","or"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HeatMapCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 HeatMapCommand::HeatMapCommand(string option) {
@@ -37,6 +83,10 @@ HeatMapCommand::HeatMapCommand(string option) {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["svg"] = 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 = ""; 
@@ -168,7 +218,7 @@ int HeatMapCommand::execute(){
                        while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                if (m->control_pressed) {
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
-                                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
+                                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
                                        globaldata->Groups.clear(); 
                                        delete read; delete heatmap; return 0;
                                }
@@ -176,7 +226,8 @@ int HeatMapCommand::execute(){
                                if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
        
                                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                                       outputNames.push_back(heatmap->getPic(lookup));
+                                       string outputFileName = heatmap->getPic(lookup);
+                                       outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
                                        
                                        processedLabels.insert(lookup[0]->getLabel());
                                        userLabels.erase(lookup[0]->getLabel());
@@ -190,7 +241,8 @@ int HeatMapCommand::execute(){
                                        lookup = input->getSharedRAbundVectors(lastLabel);
                                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                        
-                                       outputNames.push_back(heatmap->getPic(lookup));
+                                       string outputFileName = heatmap->getPic(lookup);
+                                       outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
                                        
                                        processedLabels.insert(lookup[0]->getLabel());
                                        userLabels.erase(lookup[0]->getLabel());
@@ -209,7 +261,7 @@ int HeatMapCommand::execute(){
                        
                        
                        if (m->control_pressed) {
-                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
+                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
                                globaldata->Groups.clear(); 
                                delete read; delete heatmap; return 0;
                        }
@@ -233,7 +285,8 @@ int HeatMapCommand::execute(){
                                lookup = input->getSharedRAbundVectors(lastLabel);
                                
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-                               outputNames.push_back(heatmap->getPic(lookup));
+                               string outputFileName = heatmap->getPic(lookup);
+                               outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                        }
                
@@ -244,14 +297,15 @@ int HeatMapCommand::execute(){
        
                        while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                if (m->control_pressed) {   
-                                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
+                                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
                                        delete rabund;  delete read; delete heatmap; return 0;  
                                }
 
                                if(allLines == 1 || labels.count(rabund->getLabel()) == 1){                     
        
                                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
-                                       outputNames.push_back(heatmap->getPic(rabund));
+                                       string outputFileName = heatmap->getPic(rabund);
+                                       outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
                                        
                                        processedLabels.insert(rabund->getLabel());
                                        userLabels.erase(rabund->getLabel());
@@ -264,7 +318,8 @@ int HeatMapCommand::execute(){
                                        rabund = input->getRAbundVector(lastLabel);
                                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                                       outputNames.push_back(heatmap->getPic(rabund));
+                                       string outputFileName = heatmap->getPic(rabund);
+                                       outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
                                        
                                        processedLabels.insert(rabund->getLabel());
                                        userLabels.erase(rabund->getLabel());
@@ -281,7 +336,7 @@ int HeatMapCommand::execute(){
                        }
                        
                        if (m->control_pressed) {
-                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
+                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
                                delete read; delete heatmap; return 0;
                        }
 
@@ -305,7 +360,8 @@ int HeatMapCommand::execute(){
                                rabund = input->getRAbundVector(lastLabel);
                                m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                               outputNames.push_back(heatmap->getPic(rabund));
+                               string outputFileName = heatmap->getPic(rabund);
+                               outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
                                delete rabund; globaldata->rabund = NULL;
                        }
                
@@ -315,7 +371,7 @@ int HeatMapCommand::execute(){
                        while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                if (m->control_pressed) {
                                        for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
-                                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
+                                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
                                        globaldata->Groups.clear(); 
                                        delete read; delete heatmap; return 0;
                                }
@@ -323,7 +379,8 @@ int HeatMapCommand::execute(){
                                if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){                     
        
                                        m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
-                                       outputNames.push_back(heatmap->getPic(lookupFloat));
+                                       string outputFileName = heatmap->getPic(lookupFloat);
+                                       outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
                                        
                                        processedLabels.insert(lookupFloat[0]->getLabel());
                                        userLabels.erase(lookupFloat[0]->getLabel());
@@ -336,7 +393,8 @@ int HeatMapCommand::execute(){
                                        lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
                                        m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
                                        
-                                       outputNames.push_back(heatmap->getPic(lookupFloat));
+                                       string outputFileName = heatmap->getPic(lookupFloat);
+                                       outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
                                        
                                        processedLabels.insert(lookupFloat[0]->getLabel());
                                        userLabels.erase(lookupFloat[0]->getLabel());
@@ -355,7 +413,7 @@ int HeatMapCommand::execute(){
                        
                        
                        if (m->control_pressed) {
-                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
+                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
                                globaldata->Groups.clear(); 
                                delete read; delete heatmap; return 0;
                        }
@@ -379,7 +437,8 @@ int HeatMapCommand::execute(){
                                lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
                                
                                m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
-                               outputNames.push_back(heatmap->getPic(lookupFloat));
+                               string outputFileName = heatmap->getPic(lookupFloat);
+                               outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
                                for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
                        }
                
@@ -392,7 +451,7 @@ int HeatMapCommand::execute(){
                delete input; globaldata->ginput = NULL;
                
                if (m->control_pressed) {
-                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } }
+                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
                        delete read; delete heatmap; return 0;
                }