added checks for ^C to quit command instead of program

[mothur.git] / taxonomyequalizer.cpp

diff --git a/taxonomyequalizer.cpp b/taxonomyequalizer.cpp
index f3ccfe45852ba8065c454d4bf42a0ad83a75d088..fc36eb643c30c549810ff462671c38ba36e118b8 100644 (file)
--- a/taxonomyequalizer.cpp
+++ b/taxonomyequalizer.cpp
@@ -19,42 +19,51 @@ TaxEqualizer::TaxEqualizer(string tfile, int c) : cutoff(c) {
                openInputFile(tfile, inTax);
        
                highestLevel = getHighestLevel(inTax);
-       
-               //if the user has specified a cutoff and it's smaller than the highest level
-               if ((cutoff != -1) && (cutoff < highestLevel)) { 
-                       highestLevel = cutoff;
-               }else if (cutoff > highestLevel) {
-                       m->mothurOut("The highest level taxonomy you have is " + toString(highestLevel) + " and your cutoff is " + toString(cutoff) + ". I will set the cutoff to " + toString(highestLevel));
-                       m->mothurOutEndLine();
-               }
-               
-               inTax.close(); 
-               ifstream in; 
-               openInputFile(tfile, in);
-               
-               ofstream out;
-               equalizedFile = getRootName(tfile) + "equalized.taxonomy";
-               openOutputFile(equalizedFile, out);
                
-               string name, tax;
-               while (in) {
-                       in >> name >> tax;   gobble(in);
+               if (!m->control_pressed) { 
                        
-                       if (containsConfidence) {  removeConfidences(tax);      }
+                       //if the user has specified a cutoff and it's smaller than the highest level
+                       if ((cutoff != -1) && (cutoff < highestLevel)) { 
+                               highestLevel = cutoff;
+                       }else if (cutoff > highestLevel) {
+                               m->mothurOut("The highest level taxonomy you have is " + toString(highestLevel) + " and your cutoff is " + toString(cutoff) + ". I will set the cutoff to " + toString(highestLevel));
+                               m->mothurOutEndLine();
+                       }
                        
-                       //is this a taxonomy that needs to be extended?
-                       if (seqLevels[name] < highestLevel) {
-                               extendTaxonomy(name, tax, highestLevel);
-                       }else if (seqLevels[name] > highestLevel) { //this can happen if the user enters a cutoff
-                               truncateTaxonomy(name, tax, highestLevel);
+                       inTax.close(); 
+                       ifstream in; 
+                       openInputFile(tfile, in);
+                       
+                       ofstream out;
+                       equalizedFile = getRootName(tfile) + "equalized.taxonomy";
+                       openOutputFile(equalizedFile, out);
+                       
+       
+                       string name, tax;
+                       while (in) {
+                       
+                               if (m->control_pressed) {  break; }
+                               
+                               in >> name >> tax;   gobble(in);
+                               
+                               if (containsConfidence) {  removeConfidences(tax);      }
+                               
+                               //is this a taxonomy that needs to be extended?
+                               if (seqLevels[name] < highestLevel) {
+                                       extendTaxonomy(name, tax, highestLevel);
+                               }else if (seqLevels[name] > highestLevel) { //this can happen if the user enters a cutoff
+                                       truncateTaxonomy(name, tax, highestLevel);
+                               }
+                               
+                               out << name << '\t' << tax << endl;
                        }
                        
-                       out << name << '\t' << tax << endl;
-               }
+                       in.close();
+                       out.close();
+                       
+                       if (m->control_pressed) { remove(equalizedFile.c_str());  }
+               }else { inTax.close(); }
                
-               in.close();
-               out.close();
-                                       
        }
        catch(exception& e) {
                m->errorOut(e, "TaxEqualizer", "TaxEqualizer");