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

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 6f5bb979a4d45b9fc3d8201848aa9f6b2d2dddb7..6a8afd017c1e88ff1bdbde883608b5eff00b235f 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -97,6 +97,29 @@ string TrimSeqsCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string TrimSeqsCommand::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 == "qfile")            {   outputFileName =  "qual";   }
+            else if (type == "fasta")            {   outputFileName =  "fasta";   }
+            else if (type == "group")            {   outputFileName =  "groups";   }
+            else if (type == "name")            {   outputFileName =  "names";   }
+            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, "TrimSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 
 
 //**********************************************************************************************************************
@@ -336,14 +359,14 @@ int TrimSeqsCommand::execute(){
                vector<vector<string> > qualFileNames;
                vector<vector<string> > nameFileNames;
                
-               string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
+               string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("fasta");
                outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
                
-               string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
+               string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("fasta");
                outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
                
-               string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
-               string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
+               string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("qfile");
+               string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("qfile");
                
                if (qFileName != "") {
                        outputNames.push_back(trimQualFile);
@@ -352,8 +375,8 @@ int TrimSeqsCommand::execute(){
                        outputTypes["qfile"].push_back(scrapQualFile); 
                }
                
-               string trimNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "trim.names";
-               string scrapNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "scrap.names";
+               string trimNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "trim." + getOutputFileNameTag("name");
+               string scrapNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "scrap." + getOutputFileNameTag("name");
                
                if (nameFile != "") {
                        m->readNames(nameFile, nameMap);
@@ -369,7 +392,7 @@ int TrimSeqsCommand::execute(){
                if(oligoFile != ""){
                        createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
                        if (createGroup) {
-                               outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
+                               outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + getOutputFileNameTag("group");
                                outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
                        }
                }
@@ -428,7 +451,7 @@ int TrimSeqsCommand::execute(){
                                m->openInputFile(it->first, in);
                                
                                ofstream out;
-                               string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first)) + "groups";
+                               string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first)) + getOutputFileNameTag("group");
                                outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
                                m->openOutputFile(thisGroupName, out);