added checks for ^C to quit command instead of program

[mothur.git] / chimera.cpp

diff --git a/chimera.cpp b/chimera.cpp
index 820b475ef32575a1d690d568b73ce4936a8f603b..7eeca96316511531532232d56519e1900cd7a9c6 100644 (file)
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -28,6 +28,8 @@ string Chimera::createFilter(vector<Sequence*> seqs, float t) {
                //for each sequence
                for (int i = 0; i < seqs.size(); i++) {
                
+                       if (m->control_pressed) { return filterString; }
+               
                        string seqAligned = seqs[i]->getAligned();
                
                        for (int j = 0; j < seqAligned.length(); j++) {
@@ -44,6 +46,9 @@ string Chimera::createFilter(vector<Sequence*> seqs, float t) {
                //zero out spot where all sequences have blanks
                int numColRemoved = 0;
                for(int i = 0;i < seqs[0]->getAligned().length(); i++){
+               
+                       if (m->control_pressed) { return filterString; }
+                       
                        if(gaps[i] == seqs.size())      {       filterString[i] = '0';  numColRemoved++;  }
                        
                        else if (((a[i] < threshold) && (t[i] < threshold) && (g[i] < threshold) && (c[i] < threshold))) {      filterString[i] = '0';  numColRemoved++;  }
@@ -100,6 +105,8 @@ vector<Sequence*> Chimera::readSeqs(string file) {
                //read in seqs and store in vector
                while(!in.eof()){
                        
+                       if (m->control_pressed) { return container; }
+                       
                        Sequence* current = new Sequence(in);  gobble(in);
                        
                        if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length