added set.current and get.current commands and modified existing commands to update...

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 7f4fbbab1096101aa8f09931e4c9ac40e04052b1..87ec2d26651749f20153b7854ba7c3930eebd70c 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -28,7 +28,7 @@ ParseFastaQCommand::ParseFastaQCommand(){
                abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
-               outputTypes["qual"] = tempOutNames;
+               outputTypes["qfile"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand");
@@ -84,7 +84,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
                        //initialize outputTypes
                        vector<string> tempOutNames;
                        outputTypes["fasta"] = tempOutNames;
-                       outputTypes["qual"] = tempOutNames;
+                       outputTypes["qfile"] = 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);              
@@ -146,7 +146,7 @@ int ParseFastaQCommand::execute(){
                string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
                ofstream outFasta, outQual;
                m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);
-               m->openOutputFile(qualFile, outQual);   outputNames.push_back(qualFile);  outputTypes["qual"].push_back(qualFile);
+               m->openOutputFile(qualFile, outQual);   outputNames.push_back(qualFile);  outputTypes["qfile"].push_back(qualFile);
                
                ifstream in;
                m->openInputFile(fastaQFile, in);
@@ -194,6 +194,18 @@ int ParseFastaQCommand::execute(){
                
                if (m->control_pressed) { outputTypes.clear(); remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
                
+               //set fasta file as new current fastafile
+               string current = "";
+               itTypes = outputTypes.find("fasta");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+               }
+               
+               itTypes = outputTypes.find("qfile");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+               }               
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }