added checks for ^C to quit command instead of program

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 1b5c7cf1416f9a8d4fe68ac3a1c6d7e751eb7d18..3d80f9e8ea23a2cbcf0456b230d69005940d12a9 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -184,8 +184,6 @@ int TrimSeqsCommand::execute(){
        
                if (abort == true) { return 0; }
                
-               vector<string> outputNames;
-               
                numFPrimers = 0;  //this needs to be initialized
                numRPrimers = 0;
                
@@ -217,6 +215,22 @@ int TrimSeqsCommand::execute(){
                bool success;
 
                while(!inFASTA.eof()){
+               
+                       if (m->control_pressed) { 
+                               inFASTA.close(); 
+                               outFASTA.close();
+                               scrapFASTA.close();
+                               outGroups.close();
+                               if(qFileName != "")     {       qFile.close();  }
+                               for(int i=0;i<fastaFileNames.size();i++){
+                                       fastaFileNames[i]->close();
+                                       delete fastaFileNames[i];
+                               }       
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                               return 0;
+                       }
+
+                       
                        Sequence currSeq(inFASTA);
 
                        string origSeq = currSeq.getUnaligned();
@@ -311,6 +325,11 @@ int TrimSeqsCommand::execute(){
                        inFASTA.close();
                }
                
+               if (m->control_pressed) { 
+                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                       return 0;
+               }
+
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
@@ -365,6 +384,7 @@ void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
                                        
                                        if(allFiles){
                                                outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
+                                               outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
                                        }
                                }
                        }