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

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index ec4d35ceef2d37172d21d4d40a2ca6cfb9737404..47136938a19e6c5d4b8dd2b8110849249ac50b06 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -182,14 +182,14 @@ HClusterCommand::HClusterCommand(string option)  {
                        if (temp == "not found") { temp = "100"; }
                        //saves precision legnth for formatting below
                        length = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0)); 
                        
                        method = validParameter.validFile(parameters, "method", false);
@@ -260,7 +260,7 @@ int HClusterCommand::execute(){
                                sabundFile.close();
                                rabundFile.close();
                                listFile.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                return 0;  
                        }
                        
@@ -276,7 +276,7 @@ int HClusterCommand::execute(){
                        sabundFile.close();
                        rabundFile.close();
                        listFile.close();
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                        return 0;  
                }
 
@@ -306,7 +306,7 @@ int HClusterCommand::execute(){
                                sabundFile.close();
                                rabundFile.close();
                                listFile.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                return 0;  
                }
 
@@ -326,7 +326,7 @@ int HClusterCommand::execute(){
                                sabundFile.close();
                                rabundFile.close();
                                listFile.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                return 0;  
                        }
 
@@ -340,7 +340,7 @@ int HClusterCommand::execute(){
                                                sabundFile.close();
                                                rabundFile.close();
                                                listFile.close();
-                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                                return 0;  
                                        }
 
@@ -373,7 +373,7 @@ int HClusterCommand::execute(){
                        sabundFile.close();
                        rabundFile.close();
                        listFile.close();
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                        return 0;  
                }
                                        
@@ -390,7 +390,7 @@ int HClusterCommand::execute(){
                delete cluster;
                
                if (m->control_pressed) {  
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                        return 0;  
                }