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

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 0557c71bda3453068175fe3d405ff87972df80e1..d45f20cae1f0516c014d42cf7e6afaef57d2a1a2 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -56,7 +56,28 @@ string TrimFlowsCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string TrimFlowsCommand::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 == "flow")            {   outputFileName =  "flow";   }
+            else if (type == "fasta")            {   outputFileName =  "flow.fasta";   }
+            else if (type == "file")            {   outputFileName =  "flow.files";   }
+            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, "TrimFlowsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 TrimFlowsCommand::TrimFlowsCommand(){  
@@ -66,6 +87,7 @@ TrimFlowsCommand::TrimFlowsCommand(){
                vector<string> tempOutNames;
                outputTypes["flow"] = tempOutNames;
                outputTypes["fasta"] = tempOutNames;
+        outputTypes["file"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
@@ -103,6 +125,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        vector<string> tempOutNames;
                        outputTypes["flow"] = tempOutNames;
                        outputTypes["fasta"] = tempOutNames;
+            outputTypes["file"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -225,13 +248,13 @@ int TrimFlowsCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
-               string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
+               string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim." + getOutputFileNameTag("flow");
                outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
                
-               string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap.flow";
+               string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap." + getOutputFileNameTag("flow");;
                outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 
-               string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.fasta";
+               string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
                if(fasta){
                        outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
                }
@@ -284,7 +307,7 @@ int TrimFlowsCommand::execute(){
                
                if(allFiles){
                        set<string> namesAlreadyProcessed;
-                       flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
+                       flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
                        m->openOutputFile(flowFilesFileName, output);
 
                        for(int i=0;i<barcodePrimerComboFileNames.size();i++){
@@ -317,7 +340,7 @@ int TrimFlowsCommand::execute(){
                        output.close();
                }
                else{
-                       flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
+                       flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
                        m->openOutputFile(flowFilesFileName, output);
                        
                        output << m->getFullPathName(trimFlowFileName) << endl;