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

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 24142e0cf4aa6174a8006f1e0a7a85c82f10ab24..ee50ab14e6183af4b2fe9979c97336ac1d9b75a5 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -45,6 +45,26 @@ string AlignCheckCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string AlignCheckCommand::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 == "aligncheck")            {   outputFileName =  "align.check";   }
+            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, "AlignCheckCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 AlignCheckCommand::AlignCheckCommand(){        
        try {
                abort = true; calledHelp = true; 
@@ -170,7 +190,7 @@ int AlignCheckCommand::execute(){
                m->openInputFile(fastafile, in);
                
                ofstream out;
-               string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
+               string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("aligncheck");
                m->openOutputFile(outfile, out);