fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 0d8c5b03df532dc83e23f030e93d906c727842e3..7d9b482564287916f599b0f3148ee4d6a80861f2 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -222,14 +222,14 @@ 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 +286,8 @@ 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 +329,8 @@ 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 +359,13 @@ 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 +404,7 @@ 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 +439,8 @@ 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 +481,8 @@ 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 +511,7 @@ int HeatMapCommand::execute(){
                        }
                
                        //reset groups parameter
-                       m->Groups.clear();  
+                       m->clearGroups();  
 
                }
                
@@ -519,7 +519,7 @@ 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();