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

[mothur.git] / deuniqueseqscommand.cpp

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index a4395a700e26d27ebd36d1151f48129f6bef045d..1d87204abd165396a20f99cbef0e3440eadbcd95 100644 (file)
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -25,7 +25,7 @@ vector<string> DeUniqueSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 DeUniqueSeqsCommand::DeUniqueSeqsCommand(){    
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
        }
@@ -60,10 +60,10 @@ vector<string> DeUniqueSeqsCommand::getRequiredFiles(){
 /**************************************************************************************/
 DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {     
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -152,7 +152,7 @@ void DeUniqueSeqsCommand::help(){
 int DeUniqueSeqsCommand::execute() {   
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
                //prepare filenames and open files
                ofstream out;
@@ -215,6 +215,13 @@ int DeUniqueSeqsCommand::execute() {
                outputNames.push_back(outFastaFile);  outputTypes["fasta"].push_back(outFastaFile);  
                m->mothurOutEndLine();
                
+               //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); }
+               }
+               
                return 0;
        }
        catch(exception& e) {