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

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index fc98e0fc45c3b576a3e2420ac415c016266b4c1c..942635ea183cedee17550fd85df3c3daa68d9979 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -64,6 +64,28 @@ string ChimeraCcodeCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ChimeraCcodeCommand::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 =  "ccode.chimeras"; }
+            else if (type == "mapinfo") {  outputFileName =  "mapinfo"; }
+            else if (type == "accnos") {  outputFileName =  "ccode.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, "ChimeraCcodeCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ChimeraCcodeCommand::ChimeraCcodeCommand(){    
        try {
                abort = true; calledHelp = true;
@@ -284,14 +306,16 @@ int ChimeraCcodeCommand::execute(){
                        if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
                        string outputFileName, accnosFileName;
                        if (maskfile != "") {
-                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos";
+                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + getOutputFileNameTag("chimera");
+                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + getOutputFileNameTag("accnos");
                        }else {
-                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "ccode.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "ccode.accnos";
+                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + getOutputFileNameTag("chimera");
+                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + getOutputFileNameTag("accnos");
+
                        }
 
-                       string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "mapinfo";
+                       string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("mapinfo");
+
                        
                        if (m->control_pressed) { delete chimera;  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        } outputTypes.clear(); return 0;        }