added count parameter to chimera.slayer command

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 1fc87db562bf2994465ee3b9e043f4a961c4e844..82400112bc8770ca2ded637853028d86e6aede99 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -15,7 +15,7 @@ vector<string> ChimeraBellerophonCommand::setParameters(){
        try {
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none","none","none",false,true); parameters.push_back(pfasta);
                CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
-               CommandParameter pcorrection("filter", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcorrection);
+               CommandParameter pcorrection("correction", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcorrection);
                CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
                CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
@@ -57,6 +57,27 @@ string ChimeraBellerophonCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ChimeraBellerophonCommand::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 == "chimera") {  outputFileName =  "bellerophon.chimeras"; }
+            else if (type == "accnos") {  outputFileName =  "bellerophon.accnos"; }
+            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, "ChimeraBellerophonCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(){        
        try {
                abort = true; calledHelp = true; 
@@ -222,8 +243,8 @@ int ChimeraBellerophonCommand::execute(){
                        chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);     
                        
                        if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it               
-                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) +  "bellerophon.chimeras";
-                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.accnos";
+                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) +  getOutputFileNameTag("chimera");
+                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) +  getOutputFileNameTag("accnos");
                        
                        chimera->getChimeras();