added checks for ^C to quit command instead of program

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 66efd469fcf8631d8537b6c7e90ea066ef72c028..215b5bd07981a39b79af57bff95da745b3aa0632 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -117,6 +117,8 @@ int PreClusterCommand::execute(){
                
                //reads fasta file and return number of seqs
                int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
+               
+               if (m->control_pressed) { return 0; }
        
                if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0;  }
                if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0;  }
@@ -139,6 +141,9 @@ int PreClusterCommand::execute(){
                                
                                //try to merge it with all smaller seqs
                                for (int j = i+1; j < numSeqs; j++) {
+                                       
+                                       if (m->control_pressed) { return 0; }
+                                       
                                        if (alignSeqs[j].active) {  //this sequence has not been merged yet
                                                //are you within "diff" bases
                                                int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
@@ -166,11 +171,14 @@ int PreClusterCommand::execute(){
                string newFastaFile = fileroot + "precluster" + getExtension(fastafile);
                string newNamesFile = fileroot + "precluster.names";
                
+               if (m->control_pressed) { return 0; }
                
                m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
                m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); 
                printData(newFastaFile, newNamesFile);
                
+               if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(newFastaFile); m->mothurOutEndLine();      
@@ -202,7 +210,9 @@ int PreClusterCommand::readFASTA(){
                length = 0;
                
                while (!inFasta.eof()) {
-       
+                       
+                       if (m->control_pressed) { inFasta.close(); return 0; }
+                       
                        //inNames >> firstCol >> secondCol;
                        //nameString = secondCol;