added checks for ^C to quit command instead of program

[mothur.git] / bellerophon.cpp

diff --git a/bellerophon.cpp b/bellerophon.cpp
index 02b282926bbb2dbe1eae2ed61997c2cbe4bccb8b..2c545fea5b141eff17bb9bf6aa3a8ea9745f9582 100644 (file)
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -27,12 +27,15 @@ Bellerophon::Bellerophon(string name, string o)  {
 }
 
 //***************************************************************************************************************
-void Bellerophon::print(ostream& out, ostream& outAcc) {
+int Bellerophon::print(ostream& out, ostream& outAcc) {
        try {
                int above1 = 0;
                out << "Name\tScore\tLeft\tRight\t" << endl;
                //output prefenence structure to .chimeras file
                for (int i = 0; i < pref.size(); i++) {
+                       
+                       if (m->control_pressed) {  return 0; }
+                       
                        out << pref[i].name << '\t' << setprecision(3) << pref[i].score[0] << '\t' << pref[i].leftParent[0] << '\t' << pref[i].rightParent[0] << endl;
                        
                        //calc # of seqs with preference above 1.0
@@ -62,6 +65,8 @@ void Bellerophon::print(ostream& out, ostream& outAcc) {
                m->mothurOut("97.5%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
                spot = 0;
                m->mothurOut("Maximum:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
+               
+               return 1;
 
        }
        catch(exception& e) {
@@ -89,6 +94,8 @@ int Bellerophon::getChimeras() {
                        filterSeqs->execute();
                        delete filterSeqs;
                        
+                       if (m->control_pressed) { return 0; }
+                       
                        //reset fastafile to filtered file
                        if (outputDir == "") { fastafile = getRootName(fastafile) + "filter.fasta"; }
                        else                             { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; }
@@ -96,10 +103,12 @@ int Bellerophon::getChimeras() {
                }
                
                distCalculator = new eachGapDist();
-cout << "fastafile = " << fastafile << endl;           
+               
                //read in sequences
                seqs = readSeqs(fastafile);
-       cout << "here:"<< endl; 
+               
+               if (m->control_pressed) { return 0; }
+       
                if (unaligned) { m->mothurOut("Your sequences need to be aligned when you use the bellerophon method."); m->mothurOutEndLine(); return 1;  }
                
                int numSeqs = seqs.size();
@@ -142,10 +151,15 @@ cout << "fastafile = " << fastafile << endl;
                int count = 0;
                while (count < iters) {
                                
+                               if (m->control_pressed) { return 0; }
+                               
                                //create 2 vectors of sequences, 1 for left side and one for right side
                                vector<Sequence> left;  vector<Sequence> right;
                                
                                for (int i = 0; i < seqs.size(); i++) {
+                               
+                                       if (m->control_pressed) { return 0; }
+                                       
 //cout << "midpoint = " << midpoint << "\twindow = " << window << endl;
 //cout << "whole = " << seqs[i]->getAligned().length() << endl;
                                        //save left side
@@ -176,8 +190,13 @@ cout << "fastafile = " << fastafile << endl;
                                SparseMatrix* SparseRight = new SparseMatrix();
                                
                                createSparseMatrix(0, left.size(), SparseLeft, left);
+                               
+                               if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
+                               
                                createSparseMatrix(0, right.size(), SparseRight, right);
                                
+                               if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
+                               
                                vector<SeqMap> distMapRight;
                                vector<SeqMap> distMapLeft;
                                
@@ -191,11 +210,13 @@ cout << "fastafile = " << fastafile << endl;
                                //cout << "left" << endl << endl;
                                for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) {
                                        distMapLeft[currentCell->row][currentCell->column] = currentCell->dist;
+                                       if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
                                        //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
                                }
                                //cout << "right" << endl << endl;
                                for (MatData currentCell = SparseRight->begin(); currentCell != SparseRight->end(); currentCell++) {
                                        distMapRight[currentCell->row][currentCell->column] = currentCell->dist;
+                                       if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
                                        //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
                                }
                                
@@ -246,6 +267,8 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar
                for(int i=startSeq; i<endSeq; i++){
                        
                        for(int j=0;j<i;j++){
+                               
+                               if (m->control_pressed) { return 0; }
                        
                                distCalculator->calcDist(s[i], s[j]);
                                float dist = distCalculator->getDist();
@@ -264,7 +287,7 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar
        }
 }
 /***************************************************************************************************************/
-void Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
+int Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
        try {
                
                float dme = 0.0;
@@ -288,6 +311,8 @@ void Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right,
                        SeqMap currentRight = right[i];         // same as left but with distances on the right side.
                        
                        for (int j = 0; j < i; j++) {
+                       
+                               if (m->control_pressed) {  return 0; }
                                
                                itL = currentLeft.find(j);
                                itR = currentRight.find(j);
@@ -352,6 +377,8 @@ void Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right,
 //cout << endl << "dme = " << dme << endl;
                //recalculate prefernences based on dme
                for (int i = 0; i < pref.size(); i++) {
+               
+                       if (m->control_pressed) {  return 0; }
 //cout << "unadjusted pref " << i << " = " << pref[i].score[1] << endl;        
                        // gives the actual percentage of the dme this seq adds
                        pref[i].score[1] = pref[i].score[1] / dme;
@@ -368,6 +395,8 @@ void Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right,
                //is this score bigger then the last score
                for (int i = 0; i < pref.size(); i++) {  
                        
+                       if (m->control_pressed) {  return 0; }
+                       
                        //update biggest score
                        if (pref[i].score[1] > pref[i].score[0]) {
                                pref[i].score[0] = pref[i].score[1];
@@ -379,6 +408,8 @@ void Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right,
                        }
                        
                }
+               
+               return 1;
 
        }
        catch(exception& e) {