Merge remote-tracking branch 'origin/master'

[mothur.git] / shhhseqscommand.cpp

diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 72504196039c9f337f8051ecdf54a4af1eed5c90..63de2bb5541ddbd653b90eced12b4d59a9084629 100644 (file)
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -54,6 +54,29 @@ string ShhhSeqsCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string ShhhSeqsCommand::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 == "fasta")            {   outputFileName =  "shhh_seqs.fasta";   }
+            else if (type == "name")    {   outputFileName =  "shhh_seqs.names";   }
+            else if (type == "map")        {   outputFileName =  "shhh_seqs.map";   }
+            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, "ShhhSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 
 ShhhSeqsCommand::ShhhSeqsCommand(){    
@@ -185,9 +208,9 @@ int ShhhSeqsCommand::execute() {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                if (outputDir == "") { outputDir = m->hasPath(fastafile);  }//if user entered a file with a path then preserve it                               
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.fasta";
-               string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.names";
-               string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.map";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
+               string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + getOutputFileNameTag("name");
+               string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + getOutputFileNameTag("map");
                
                if (groupfile != "") {
                        //Parse sequences by group
@@ -364,7 +387,7 @@ vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, st
                        lines.push_back(linePair(startIndex, endIndex));
                }
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)          
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)         
                
                //loop through and create all the processes you want
                while (process != processors) {
@@ -695,14 +718,15 @@ int ShhhSeqsCommand::deconvoluteResults(string fastaFile, string nameFile){
                string inputString = "fasta=" + fastaFile + ", name=" + nameFile;
                m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-               
+               m->mothurCalling = true;
+        
                Command* uniqueCommand = new DeconvoluteCommand(inputString);
                uniqueCommand->execute();
                
                map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
                
                delete uniqueCommand;
-               
+               m->mothurCalling = false;
                m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                
                string newnameFile = filenames["name"][0];