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

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index f267ba4b7859ed091f749456cb5495799ffc9ec0..08cf21e5d6b543684cfebe56c0cdaf8697139125 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -55,6 +55,29 @@ string SffInfoCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string SffInfoCommand::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 =  "fasta";   }
+            else if (type == "flow")    {   outputFileName =  "flow";   }
+            else if (type == "sfftxt")        {   outputFileName =  "sff.txt";   }
+            else if (type == "qfile")       {   outputFileName =  "qual";   }
+             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, "SffInfoCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 
 
 //**********************************************************************************************************************
@@ -365,14 +388,14 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
         string rootName = outputDir + m->getRootName(m->getSimpleName(input));
         if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
         
-               string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
-               string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
+               string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("sfftxt");
+               string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("flow");
                if (trim) {
-                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
-                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
+                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("fasta");
+                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("qfile");
                }else{
-                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
-                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
+                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw." + getOutputFileNameTag("fasta");
+                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw." + getOutputFileNameTag("qfile");
                }
                
                if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName);  outputTypes["sfftxt"].push_back(sfftxtFileName); }
@@ -940,17 +963,17 @@ int SffInfoCommand::parseSffTxt() {
                        fileRoot = m->getRootName(fileRoot);
                }
                
-               string outFlowFileName = outputDir + fileRoot + "flow";
+               string outFlowFileName = outputDir + fileRoot + getOutputFileNameTag("flow");
                if (trim) {
-                       outFastaFileName = outputDir + fileRoot + "fasta";
-                       outQualFileName = outputDir + fileRoot + "qual";
+                       outFastaFileName = outputDir + fileRoot + getOutputFileNameTag("fasta");
+                       outQualFileName = outputDir + fileRoot + getOutputFileNameTag("qfile");
                }else{
-                       outFastaFileName = outputDir + fileRoot + "raw.fasta";
-                       outQualFileName = outputDir + fileRoot + "raw.qual";
+                       outFastaFileName = outputDir + fileRoot + "raw." + getOutputFileNameTag("fasta");
+                       outQualFileName = outputDir + fileRoot + "raw." + getOutputFileNameTag("qfile");
                }
                
                if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
-               if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
+               if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
                if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName);  }
                
                //read common header