added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index b982b8d1deb3cbc51716cf74339b8dcaea5d136d..870536d4640e5a0de07d24d4fd8799e218359a34 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -61,6 +61,28 @@ string MGClusterCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string MGClusterCommand::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 == "list") {  outputFileName =  "list"; }
+            else if (type == "rabund") {  outputFileName =  "rabund"; }
+            else if (type == "sabund") {  outputFileName =  "sabund"; }
+            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, "MGClusterCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 MGClusterCommand::MGClusterCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -149,10 +171,10 @@ 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 +184,10 @@ 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); 
@@ -223,14 +245,17 @@ int MGClusterCommand::execute(){
                else if (method == "nearest")   { tag = "nn";  }
                else                                                    { tag = "an";  }
                
-               //open output files
-               m->openOutputFile(fileroot+ tag + ".list",  listFile);
-               m->openOutputFile(fileroot+ tag + ".rabund",  rabundFile);
-               m->openOutputFile(fileroot+ tag + ".sabund",  sabundFile);
+        string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
+        string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
+        string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+        
+               m->openOutputFile(sabundFileName,       sabundFile);
+               m->openOutputFile(rabundFileName,       rabundFile);
+               m->openOutputFile(listFileName, listFile);
                
                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 +278,7 @@ 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 +290,7 @@ 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 +313,7 @@ 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 +344,7 @@ 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 +374,7 @@ 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 +391,7 @@ 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 +407,9 @@ 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 +422,9 @@ 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 +446,9 @@ 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 +482,9 @@ 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 +499,8 @@ int MGClusterCommand::execute(){
                        }
                        
                        delete hcluster;
-                       remove(distFile.c_str());
-                       remove(overlapFile.c_str());
+                       m->mothurRemove(distFile);
+                       m->mothurRemove(overlapFile);
                }
                
                delete list; 
@@ -486,16 +511,16 @@ 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; 
                }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-               m->mothurOut(fileroot+ tag + ".list"); m->mothurOutEndLine();   outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
-               m->mothurOut(fileroot+ tag + ".rabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
-               m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
+               m->mothurOut(listFileName); m->mothurOutEndLine();      outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
+               m->mothurOut(rabundFileName); m->mothurOutEndLine();    outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+               m->mothurOut(sabundFileName); m->mothurOutEndLine();    outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
                m->mothurOutEndLine();
                
                if (saveCutoff != cutoff) { 
@@ -658,12 +683,12 @@ 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) {