pat's minor edits to distance calculations

[mothur.git] / fastamap.cpp

diff --git a/fastamap.cpp b/fastamap.cpp
index f5ac122112a633de7768b251568edda33623a81c..36b072121b044490332a8926f0f3f287bf816fab 100644 (file)
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -21,6 +21,8 @@ void FastaMap::readFastaFile(string inFileName) {
                string temp;
 
                while(!in.eof()){
+                       if (m->control_pressed) { break; }
+                       
                        Sequence currSeq(in);
                        name = currSeq.getName();
                        
@@ -44,7 +46,7 @@ void FastaMap::readFastaFile(string inFileName) {
                in.close();             
        }
        catch(exception& e) {
-               errorOut(e, "FastaMap", "readFastaFile");
+               m->errorOut(e, "FastaMap", "readFastaFile");
                exit(1);
        }
 }
@@ -59,6 +61,8 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
        map<string,string> oldNameMap;
        string name, list;
        while(!oldNameFile.eof()){
+               if (m->control_pressed) { break; }
+               
                oldNameFile >> name >> list;
                oldNameMap[name] = list;
                gobble(oldNameFile);
@@ -69,6 +73,8 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
        openInputFile(inFastaFile, inFASTA);
        string sequence;
        while(!inFASTA.eof()){
+               if (m->control_pressed) { break; }
+               
                Sequence currSeq(inFASTA);
                name = currSeq.getName();
                
@@ -145,12 +151,13 @@ void FastaMap::printNamesFile(string outFileName){ //prints data
                
                // two column file created with groupname and them list of identical sequence names
                for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+                       if (m->control_pressed) { break; }
                        outFile << it->second.groupname << '\t' << it->second.names << endl;
                }
                outFile.close();
        }
        catch(exception& e) {
-               errorOut(e, "FastaMap", "printNamesFile");
+               m->errorOut(e, "FastaMap", "printNamesFile");
                exit(1);
        }
 }
@@ -163,13 +170,14 @@ void FastaMap::printCondensedFasta(string outFileName){ //prints data
                openOutputFile(outFileName, out);
                //creates a fasta file
                for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+                       if (m->control_pressed) { break; }
                        out << ">" << it->second.groupname << endl;
                        out << it->first << endl;
                }
                out.close();
        }
        catch(exception& e) {
-               errorOut(e, "FastaMap", "printCondensedFasta");
+               m->errorOut(e, "FastaMap", "printCondensedFasta");
                exit(1);
        }
 }