added count parameter to chimera.slayer command

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index f402f2a8ab15a1808a461d376818d97d98c5c5c7..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 {
@@ -198,13 +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);
@@ -232,6 +253,7 @@ int PhylotypeCommand::execute(){
                                
                                ListVector list;
                                list.setLabel(level);
+                
                                //go through nodes and build listvector 
                                for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
                        
@@ -244,6 +266,7 @@ int PhylotypeCommand::execute(){
                                        //make the names compatable with listvector
                                        string name = "";
                                        for (int i = 0; i < names.size(); i++) {  
+                        
                         if (names[i] != "unknown") {
                             if (namefile != "") {      
                                 map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
@@ -255,9 +278,8 @@ int PhylotypeCommand::execute(){
                         }
                                        }
                                        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