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

[mothur.git] / consensusseqscommand.cpp

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 55ec8023270cd17d38b830f519ad9f62518e635e..d6158ba3ed3bc147027d54098aa71398182dc2f6 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -53,6 +53,28 @@ string ConsensusSeqsCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string ConsensusSeqsCommand::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 =  "cons.fasta"; }
+            else if (type == "name") {  outputFileName =  "cons.names"; }
+            else if (type == "summary") {  outputFileName =  "cons.summary"; }
+            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, "ConsensusSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************
 ConsensusSeqsCommand::ConsensusSeqsCommand(){  
@@ -194,7 +216,7 @@ int ConsensusSeqsCommand::execute(){
                if (listfile == "") {
                        
                        ofstream outSummary;
-                       string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.summary";
+                       string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
                        m->openOutputFile(outputSummaryFile, outSummary);
                        outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
                        outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
@@ -202,7 +224,7 @@ int ConsensusSeqsCommand::execute(){
                        outSummary << "PositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
                        
                        ofstream outFasta;
-                       string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.fasta";
+                       string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
                        m->openOutputFile(outputFastaFile, outFasta);
                        outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
                        
@@ -370,18 +392,18 @@ int ConsensusSeqsCommand::processList(ListVector*& list){
        try{
                
                ofstream outSummary;
-               string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.summary";
+               string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("summary");
                m->openOutputFile(outputSummaryFile, outSummary);
                outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
                outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
                
                ofstream outName;
-               string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.names";
+               string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("name");
                m->openOutputFile(outputNameFile, outName);
                outputNames.push_back(outputNameFile); outputTypes["name"].push_back(outputNameFile);
                
                ofstream outFasta;
-               string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.fasta";
+               string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("fasta");
                m->openOutputFile(outputFastaFile, outFasta);
                outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);