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

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index b1d996b0f8d971c0fca0124b29031f2c88e5fecb..bd31c193e82aa0725cc8920336ec310cc19db820 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -98,6 +98,28 @@ string ChimeraUchimeCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ChimeraUchimeCommand::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 =  "uchime.chimeras"; }
+            else if (type == "accnos") {  outputFileName =  "uchime.accnos"; }
+            else if (type == "alns") {  outputFileName =  "uchime.alns"; }
+            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, "ChimeraUchimeCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ChimeraUchimeCommand::ChimeraUchimeCommand(){  
        try {
                abort = true; calledHelp = true;
@@ -522,9 +544,9 @@ int ChimeraUchimeCommand::execute(){
                        int start = time(NULL); 
                        string nameFile = "";
                        if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it                               
-                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.chimera";
-                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "uchime.accnos";
-                       string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "uchime.alns";
+                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
+                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
+                       string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + getOutputFileNameTag("alns");
                        string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
                                
                        //you provided a groupfile