added checks for ^C to quit command instead of program

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index f3710c9e4d0aabd728c0714d0f8b7d41c0b73c24..d23949f497e65b262e3067d74d566d4665124412 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -151,6 +151,8 @@ int ListSeqsCommand::execute(){
                else if (alignfile != "")       {       inputFileName = alignfile;      readAlign();    }
                else if (listfile != "")        {       inputFileName = listfile;       readList();             }
                
+               if (m->control_pressed) { return 0; }
+               
                //sort in alphabetical order
                sort(names.begin(), names.end());
                
@@ -163,10 +165,15 @@ int ListSeqsCommand::execute(){
                
                //output to .accnos file
                for (int i = 0; i < names.size(); i++) {
+                       
+                       if (m->control_pressed) { out.close(); remove(outputFileName.c_str()); return 0; }
+                       
                        out << names[i] << endl;
                }
                out.close();
                
+               if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
                m->mothurOut(outputFileName); m->mothurOutEndLine();    
@@ -182,7 +189,7 @@ int ListSeqsCommand::execute(){
 }
 
 //**********************************************************************************************************************
-void ListSeqsCommand::readFasta(){
+int ListSeqsCommand::readFasta(){
        try {
                
                ifstream in;
@@ -190,6 +197,9 @@ void ListSeqsCommand::readFasta(){
                string name;
                
                while(!in.eof()){
+                       
+                       if (m->control_pressed) { in.close(); return 0; }
+                       
                        Sequence currSeq(in);
                        name = currSeq.getName();
                        
@@ -197,7 +207,9 @@ void ListSeqsCommand::readFasta(){
                        
                        gobble(in);
                }
-               in.close();             
+               in.close();     
+               
+               return 0;
 
        }
        catch(exception& e) {
@@ -206,7 +218,7 @@ void ListSeqsCommand::readFasta(){
        }
 }
 //**********************************************************************************************************************
-void ListSeqsCommand::readList(){
+int ListSeqsCommand::readList(){
        try {
                ifstream in;
                openInputFile(listfile, in);
@@ -219,6 +231,8 @@ void ListSeqsCommand::readList(){
                        for (int i = 0; i < list.getNumBins(); i++) {
                                string binnames = list.get(i);
                                
+                               if (m->control_pressed) { in.close(); return 0; }
+                               
                                while (binnames.find_first_of(',') != -1) { 
                                        string name = binnames.substr(0,binnames.find_first_of(','));
                                        binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
@@ -230,6 +244,8 @@ void ListSeqsCommand::readList(){
                }
                in.close();     
                
+               return 0;
+               
        }
        catch(exception& e) {
                m->errorOut(e, "ListSeqsCommand", "readList");
@@ -238,7 +254,7 @@ void ListSeqsCommand::readList(){
 }
 
 //**********************************************************************************************************************
-void ListSeqsCommand::readName(){
+int ListSeqsCommand::readName(){
        try {
                
                ifstream in;
@@ -246,6 +262,8 @@ void ListSeqsCommand::readName(){
                string name, firstCol, secondCol;
                
                while(!in.eof()){
+               
+                       if (m->control_pressed) { in.close(); return 0; }
 
                        in >> firstCol;                         
                        in >> secondCol;                        
@@ -263,6 +281,7 @@ void ListSeqsCommand::readName(){
                        gobble(in);
                }
                in.close();
+               return 0;
                
        }
        catch(exception& e) {
@@ -272,7 +291,7 @@ void ListSeqsCommand::readName(){
 }
 
 //**********************************************************************************************************************
-void ListSeqsCommand::readGroup(){
+int ListSeqsCommand::readGroup(){
        try {
        
                ifstream in;
@@ -280,7 +299,9 @@ void ListSeqsCommand::readGroup(){
                string name, group;
                
                while(!in.eof()){
-
+                       
+                       if (m->control_pressed) { in.close(); return 0; }
+                       
                        in >> name;                             //read from first column
                        in >> group;                    //read from second column
                        
@@ -289,6 +310,7 @@ void ListSeqsCommand::readGroup(){
                        gobble(in);
                }
                in.close();
+               return 0;
 
        }
        catch(exception& e) {
@@ -299,7 +321,7 @@ void ListSeqsCommand::readGroup(){
 
 //**********************************************************************************************************************
 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
-void ListSeqsCommand::readAlign(){
+int ListSeqsCommand::readAlign(){
        try {
        
                ifstream in;
@@ -314,6 +336,8 @@ void ListSeqsCommand::readAlign(){
                
                
                while(!in.eof()){
+               
+                       if (m->control_pressed) { in.close(); return 0; }
 
                        in >> name;                             //read from first column
                        
@@ -328,6 +352,8 @@ void ListSeqsCommand::readAlign(){
                        gobble(in);
                }
                in.close();
+               
+               return 0;
 
                
        }