added checks for ^C to quit command instead of program

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index a2c72702cc7f766501f705226fe4441abcf7ed24..6e9e95c9f7eaf20f91ba312b93a52be67c82b828 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -37,7 +37,7 @@ Pintail::~Pintail() {
        }
 }
 //***************************************************************************************************************
-void Pintail::doPrep() {
+int Pintail::doPrep() {
        try {
                
                mergedFilterString = "";
@@ -70,6 +70,7 @@ void Pintail::doPrep() {
                if (consfile == "") { 
                        m->mothurOut("Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    "); cout.flush();
                        probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFileName)); 
+                       if (m->control_pressed) {  return 0;  }
                        m->mothurOut("Done."); m->mothurOutEndLine();
                }else                           {   probabilityProfile = readFreq();    m->mothurOut("Done.");            }
                m->mothurOutEndLine();
@@ -87,6 +88,11 @@ void Pintail::doPrep() {
                        
                        vector<Sequence*> tempQuerySeqs;
                        while(!in.eof()){
+                               if (m->control_pressed) {  
+                                       for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
+                                       return 0; 
+                               }
+                               
                                Sequence* s = new Sequence(in);
                                gobble(in);
                                
@@ -103,12 +109,21 @@ void Pintail::doPrep() {
                            reRead = true;
                                //mask templates
                                for (int i = 0; i < temp.size(); i++) {
+                                       if (m->control_pressed) {  
+                                               for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
+                                               return 0; 
+                                       }
                                        decalc->runMask(temp[i]);
                                }
                        }
 
                        mergedFilterString = createFilter(temp, 0.5);
                        
+                       if (m->control_pressed) {  
+                               for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
+                               return 0; 
+                       }
+                       
                        //reread template seqs
                        for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
                }
@@ -124,6 +139,7 @@ void Pintail::doPrep() {
                                reRead = true;
                                //mask templates
                                for (int i = 0; i < templateSeqs.size(); i++) {
+                                       if (m->control_pressed) {  return 0;  }
                                        decalc->runMask(templateSeqs[i]);
                                }
                        }
@@ -131,6 +147,7 @@ void Pintail::doPrep() {
                        if (filter) { 
                                reRead = true;
                                for (int i = 0; i < templateSeqs.size(); i++) {
+                                       if (m->control_pressed) {  return 0;  }
                                        runFilter(templateSeqs[i]);
                                }
                        }
@@ -140,6 +157,7 @@ void Pintail::doPrep() {
                                quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
                        }else {         createProcessesQuan();          }
                
+                       if (m->control_pressed) {  return 0;  }
                        
                        ofstream out4, out5;
                        string noOutliers, outliers;
@@ -154,11 +172,10 @@ void Pintail::doPrep() {
                                noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "quan";
                        }
 
-
-
-                                               
                        decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
                        
+                       if (m->control_pressed) {  return 0;  }
+                       
                        openOutputFile(noOutliers, out5);                       
                        //adjust quantiles
                        for (int i = 0; i < quantilesMembers.size(); i++) {
@@ -210,6 +227,8 @@ void Pintail::doPrep() {
                //free memory
                for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i];  }
                
+               return 0;
+               
        }
        catch(exception& e) {
                m->errorOut(e, "Pintail", "doPrep");
@@ -217,7 +236,7 @@ void Pintail::doPrep() {
        }
 }
 //***************************************************************************************************************
-void Pintail::print(ostream& out, ostream& outAcc) {
+int Pintail::print(ostream& out, ostream& outAcc) {
        try {
                int index = ceil(deviation);
                
@@ -247,6 +266,7 @@ void Pintail::print(ostream& out, ostream& outAcc) {
                for (int m = 0; m < expectedDistance.size(); m++) {  out << expectedDistance[m] << '\t';  }
                out << endl;
                
+               return 0;
                
        }
        catch(exception& e) {
@@ -265,6 +285,8 @@ int Pintail::getChimeras(Sequence* query) {
                //find pairs has to be done before a mask
                bestfit = findPairs(query);
                
+               if (m->control_pressed) {  return 0; } 
+               
                //if they mask  
                if (seqMask != "") {
                        decalc->runMask(query);
@@ -286,8 +308,12 @@ int Pintail::getChimeras(Sequence* query) {
 
                //find observed distance
                obsDistance = decalc->calcObserved(query, bestfit, windowsForeachQuery, windowSizes);
+               
+               if (m->control_pressed) {  return 0; } 
                                
                Qav = decalc->findQav(windowsForeachQuery, windowSizes, probabilityProfile);
+               
+               if (m->control_pressed) {  return 0; } 
 
                //find alpha                    
                seqCoef = decalc->getCoef(obsDistance, Qav);
@@ -295,9 +321,13 @@ int Pintail::getChimeras(Sequence* query) {
                //calculating expected distance
                expectedDistance = decalc->calcExpected(Qav, seqCoef);
                
+               if (m->control_pressed) {  return 0; } 
+               
                //finding de
                DE = decalc->calcDE(obsDistance, expectedDistance);
                
+               if (m->control_pressed) {  return 0; } 
+               
                //find distance between query and closest match
                it = trimmed.begin();
                deviation = decalc->calcDist(query, bestfit, it->first, it->second);