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

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 4a9271ce94df57f99e9734ba2b4d9d30d20872e9..973e14f4fd68416bac6949a149a75bb5fbe174c4 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -30,7 +30,7 @@ SffInfoCommand::SffInfoCommand(){
                outputTypes["fasta"] = tempOutNames;
                outputTypes["flow"] = tempOutNames;
                outputTypes["sfftxt"] = tempOutNames;
-               outputTypes["qual"] = tempOutNames;
+               outputTypes["qfile"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
@@ -89,7 +89,7 @@ SffInfoCommand::SffInfoCommand(string option)  {
                        outputTypes["fasta"] = tempOutNames;
                        outputTypes["flow"] = tempOutNames;
                        outputTypes["sfftxt"] = tempOutNames;
-                       outputTypes["qual"] = tempOutNames;
+                       outputTypes["qfile"] = tempOutNames;
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
@@ -300,6 +300,18 @@ int SffInfoCommand::execute(){
                
                if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].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); }
+               }       
+               
                //report output filenames
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -336,7 +348,7 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
                
                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); }
                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);  }
                
                ifstream in;