fixed classify.seqs output file name - had issue if reference taxonomy file did not...

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index b982b8d1deb3cbc51716cf74339b8dcaea5d136d..9c45afe95277b5c7106e3f87f64e60e53b9bf321 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -149,10 +149,10 @@ MGClusterCommand::MGClusterCommand(string option) {
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);                if (temp == "not found") { temp = "100"; }
                        precisionLength = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "0.70"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
                        
                        method = validParameter.validFile(parameters, "method", false);
@@ -162,10 +162,10 @@ MGClusterCommand::MGClusterCommand(string option) {
                        else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
 
                        temp = validParameter.validFile(parameters, "length", false);                   if (temp == "not found") { temp = "5"; }
-                       convert(temp, length); 
+                       m->mothurConvert(temp, length); 
                        
                        temp = validParameter.validFile(parameters, "penalty", false);                  if (temp == "not found") { temp = "0.10"; }
-                       convert(temp, penalty); 
+                       m->mothurConvert(temp, penalty); 
                        
                        temp = validParameter.validFile(parameters, "min", false);                              if (temp == "not found") { temp = "true"; }
                        minWanted = m->isTrue(temp); 
@@ -230,7 +230,7 @@ int MGClusterCommand::execute(){
                
                if (m->control_pressed) { 
                        delete nameMap; delete read; delete list; delete rabund; 
-                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                        outputTypes.clear();
                        return 0; 
                }
@@ -253,7 +253,7 @@ int MGClusterCommand::execute(){
                        
                        if (m->control_pressed) { 
                                delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
-                               listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                               listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                outputTypes.clear();
                                return 0; 
                        }
@@ -265,7 +265,7 @@ int MGClusterCommand::execute(){
                                
                                if (m->control_pressed) { 
                                        delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
-                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                        outputTypes.clear();
                                        return 0; 
                                }
@@ -288,7 +288,7 @@ int MGClusterCommand::execute(){
                                                
                                                if (m->control_pressed) { 
                                                        delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
-                                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                                        outputTypes.clear();
                                                        return 0; 
                                                }
@@ -319,7 +319,7 @@ int MGClusterCommand::execute(){
                                        
                                        if (m->control_pressed) { 
                                                        delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
-                                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                                        outputTypes.clear();
                                                        return 0; 
                                        }
@@ -349,7 +349,7 @@ int MGClusterCommand::execute(){
                        
                        if (m->control_pressed) { 
                                delete nameMap;  delete list; delete rabund; 
-                               listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                               listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                outputTypes.clear();
                                return 0; 
                        }
@@ -366,7 +366,7 @@ int MGClusterCommand::execute(){
                        
                        if (m->control_pressed) { 
                                delete nameMap;  delete list; delete rabund; delete hcluster;
-                               listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                               listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                                outputTypes.clear();
                                return 0; 
                        }
@@ -382,9 +382,9 @@ int MGClusterCommand::execute(){
                                
                                if (m->control_pressed) { 
                                        delete nameMap;  delete list; delete rabund; delete hcluster;
-                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
-                                       remove(distFile.c_str());
-                                       remove(overlapFile.c_str());
+                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                       m->mothurRemove(distFile);
+                                       m->mothurRemove(overlapFile);
                                        outputTypes.clear();
                                        return 0; 
                                }
@@ -397,9 +397,9 @@ int MGClusterCommand::execute(){
                                                
                                                if (m->control_pressed) { 
                                                        delete nameMap;  delete list; delete rabund; delete hcluster;
-                                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
-                                                       remove(distFile.c_str());
-                                                       remove(overlapFile.c_str());
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                       m->mothurRemove(distFile);
+                                                       m->mothurRemove(overlapFile);
                                                        outputTypes.clear();
                                                        return 0; 
                                                }
@@ -421,9 +421,9 @@ int MGClusterCommand::execute(){
                                                                
                                                                if (m->control_pressed) { 
                                                                        delete nameMap;  delete list; delete rabund; delete hcluster; delete temp;
-                                                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
-                                                                       remove(distFile.c_str());
-                                                                       remove(overlapFile.c_str());
+                                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                                       m->mothurRemove(distFile);
+                                                                       m->mothurRemove(overlapFile);
                                                                        outputTypes.clear();
                                                                        return 0; 
                                                                }
@@ -457,9 +457,9 @@ int MGClusterCommand::execute(){
                                        
                                        if (m->control_pressed) { 
                                                        delete nameMap; delete list; delete rabund; delete hcluster; delete temp;
-                                                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
-                                                       remove(distFile.c_str());
-                                                       remove(overlapFile.c_str());
+                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                       m->mothurRemove(distFile);
+                                                       m->mothurRemove(overlapFile);
                                                        outputTypes.clear();
                                                        return 0; 
                                        }
@@ -474,8 +474,8 @@ int MGClusterCommand::execute(){
                        }
                        
                        delete hcluster;
-                       remove(distFile.c_str());
-                       remove(overlapFile.c_str());
+                       m->mothurRemove(distFile);
+                       m->mothurRemove(overlapFile);
                }
                
                delete list; 
@@ -486,7 +486,7 @@ int MGClusterCommand::execute(){
        
                if (m->control_pressed) { 
                        delete nameMap; 
-                       listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
                        outputTypes.clear();
                        return 0; 
                }
@@ -658,12 +658,12 @@ void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOve
        try {
                //sort distFile
                string sortedDistFile = m->sortFile(unsortedDist, outputDir);
-               remove(unsortedDist.c_str());  //delete unsorted file
+               m->mothurRemove(unsortedDist);  //delete unsorted file
                distFile = sortedDistFile;
                
                //sort overlap file
                string sortedOverlapFile = m->sortFile(unsortedOverlap, outputDir);
-               remove(unsortedOverlap.c_str());  //delete unsorted file
+               m->mothurRemove(unsortedOverlap);  //delete unsorted file
                overlapFile = sortedOverlapFile;
        }
        catch(exception& e) {