added sets to amova and homova commands. added oligos to make.contigs. added metadat...

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 0d8c5b03df532dc83e23f030e93d906c727842e3..441eaf8a4dc4e77beb36c7e39c102f9aa13f0d53 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -61,6 +61,28 @@ string HeatMapCommand::getHelpString(){
        }
 }
 
+//**********************************************************************************************************************
+
+string HeatMapCommand::getOutputFileNameTag(string type, string inputName=""){ 
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "svg")            {   outputFileName =  "svg";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HeatMapCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 HeatMapCommand::HeatMapCommand(){      
        try {
@@ -151,27 +173,27 @@ HeatMapCommand::HeatMapCommand(string option) {
                        
                        //check for required parameters
                        listfile = validParameter.validFile(parameters, "list", true);
-                       if (listfile == "not open") { listfile = ""; abort = true; }
+                       if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
                        else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
-                       if (sabundfile == "not open") { sabundfile = ""; abort = true; }        
+                       if (sabundfile == "not open") {  abort = true; }        
                        else if (sabundfile == "not found") { sabundfile = ""; }
                        else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
                        
                        rabundfile = validParameter.validFile(parameters, "rabund", true);
-                       if (rabundfile == "not open") { rabundfile = ""; abort = true; }        
+                       if (rabundfile == "not open") {  abort = true; }        
                        else if (rabundfile == "not found") { rabundfile = ""; }
                        else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
-                       if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
+                       if (sharedfile == "not open") { abort = true; } 
                        else if (sharedfile == "not found") { sharedfile = ""; }
                        else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
                        
                        relabundfile = validParameter.validFile(parameters, "relabund", true);
-                       if (relabundfile == "not open") { relabundfile = ""; abort = true; }    
+                       if (relabundfile == "not open") {  abort = true; }      
                        else if (relabundfile == "not found") { relabundfile = ""; }
                        else {  format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
                        
@@ -222,14 +244,14 @@ HeatMapCommand::HeatMapCommand(string option) {
                        if (groups == "not found") { groups = ""; }
                        else { 
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        string temp = validParameter.validFile(parameters, "numotu", false);            if (temp == "not found") { temp = "0"; }
-                       convert(temp, numOTU);
+                       m->mothurConvert(temp, numOTU);
                        
                        temp = validParameter.validFile(parameters, "fontsize", false);                         if (temp == "not found") { temp = "24"; }
-                       convert(temp, fontSize);
+                       m->mothurConvert(temp, fontSize);
                        
                        sorted = validParameter.validFile(parameters, "sorted", false);                         
                        if (sorted == "not found") { 
@@ -286,8 +308,8 @@ 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());  } } outputTypes.clear();
-                                       m->Groups.clear(); 
+                                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+                                       m->clearGroups(); 
                                        delete input; delete heatmap; return 0;
                                }
                
@@ -329,8 +351,8 @@ int HeatMapCommand::execute(){
                        
                        
                        if (m->control_pressed) {
-                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
-                               m->Groups.clear(); 
+                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+                               m->clearGroups(); 
                                delete input; delete heatmap; return 0;
                        }
 
@@ -359,13 +381,13 @@ int HeatMapCommand::execute(){
                        }
                
                        //reset groups parameter
-                       m->Groups.clear();  
+                       m->clearGroups();  
                        
                }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
        
                        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());  } } outputTypes.clear();
+                                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
                                        delete rabund;  delete input; delete heatmap; return 0; 
                                }
 
@@ -404,7 +426,7 @@ int HeatMapCommand::execute(){
                        }
                        
                        if (m->control_pressed) {
-                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
                                delete input; delete heatmap; return 0;
                        }
 
@@ -439,8 +461,8 @@ 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());  } } outputTypes.clear();
-                                       m->Groups.clear(); 
+                                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+                                       m->clearGroups(); 
                                        delete input; delete heatmap; return 0;
                                }
                
@@ -481,8 +503,8 @@ int HeatMapCommand::execute(){
                        
                        
                        if (m->control_pressed) {
-                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
-                               m->Groups.clear(); 
+                               for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+                               m->clearGroups(); 
                                delete input; delete heatmap; return 0;
                        }
 
@@ -511,7 +533,7 @@ int HeatMapCommand::execute(){
                        }
                
                        //reset groups parameter
-                       m->Groups.clear();  
+                       m->clearGroups();  
 
                }
                
@@ -519,7 +541,7 @@ int HeatMapCommand::execute(){
                delete heatmap;
                
                if (m->control_pressed) {
-                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear(); return 0;
+                       for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear(); return 0;
                }
                
                m->mothurOutEndLine();