Merge remote-tracking branch 'origin/master'

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index ef23375df9425f11816acbf8594f46e613e9e148..38d3bdf929f4ffc110f76ab0a55b12d66ef4ad08 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -53,7 +53,28 @@ string PhylotypeCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string PhylotypeCommand::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, "PhylotypeCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 PhylotypeCommand::PhylotypeCommand(){  
        try {
@@ -128,11 +149,11 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                        m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine(); 
                                        abort = true; 
                                }
-                       }else if (taxonomyFileName == "not open") { abort = true; }     
+                       }else if (taxonomyFileName == "not open") { taxonomyFileName = ""; abort = true; }      
                        else { m->setTaxonomyFile(taxonomyFileName); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }
+                       if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
                        else { readNamesFile(); m->setNameFile(namefile); }     
                        
@@ -144,7 +165,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "-1"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; allLines = 1; }
@@ -153,6 +174,11 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                else { allLines = 1;  }
                        }
                        
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(taxonomyFileName);
+                               parser.getNameFile(files);
+                       }
+                       
                }
        }
        catch(exception& e) {
@@ -193,13 +219,13 @@ int PhylotypeCommand::execute(){
                string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
                
                ofstream outList;
-               string outputListFile = fileroot + "tx.list";
+               string outputListFile = fileroot + "tx." + getOutputFileNameTag("list");
                m->openOutputFile(outputListFile, outList);
                ofstream outSabund;
-               string outputSabundFile = fileroot + "tx.sabund";
+               string outputSabundFile = fileroot + "tx." + getOutputFileNameTag("sabund");
                m->openOutputFile(outputSabundFile, outSabund);
                ofstream outRabund;
-               string outputRabundFile = fileroot + "tx.rabund";
+               string outputRabundFile = fileroot + "tx." + getOutputFileNameTag("rabund");
                m->openOutputFile(outputRabundFile, outRabund);
                
                outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
@@ -215,7 +241,7 @@ int PhylotypeCommand::execute(){
                        
                        if (m->control_pressed) { 
                                outRabund.close(); outSabund.close(); outList.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
                                delete tree; return 0; 
                        }
                        
@@ -227,6 +253,7 @@ int PhylotypeCommand::execute(){
                                
                                ListVector list;
                                list.setLabel(level);
+                
                                //go through nodes and build listvector 
                                for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
                        
@@ -239,18 +266,20 @@ int PhylotypeCommand::execute(){
                                        //make the names compatable with listvector
                                        string name = "";
                                        for (int i = 0; i < names.size(); i++) {  
-                                               if (namefile != "") {   
-                                                       map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
-               
-                                                       if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
-                                                       else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
-                                                       
-                                               }else{   name += names[i] + ",";        }
+                        
+                        if (names[i] != "unknown") {
+                            if (namefile != "") {      
+                                map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
+                                
+                                if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
+                                else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
+                                
+                            }else{   name += names[i] + ",";   }
+                        }
                                        }
                                        name = name.substr(0, name.length()-1);  //rip off extra ','
-                                       
                                        //add bin to list vector
-                                       list.push_back(name);
+                                       if (name != "") { list.push_back(name); } //caused by unknown
                                }       
                                
                                //print listvector
@@ -286,7 +315,7 @@ int PhylotypeCommand::execute(){
                delete tree;
                
                if (m->control_pressed) { 
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
                        return 0; 
                }