modified mpi code to save ram by writing out every 10 seqs.

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 6ca8c2945bb4600e6c7f518b1d7c4dfa1a529225..57ed7130916b0e1d810b470fa0552dc5556a1143 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -16,7 +16,7 @@ ChimeraSlayer::ChimeraSlayer(string mode, bool r, string f) : searchMethod(mode)
        decalc = new DeCalculator();    
 }
 //***************************************************************************************************************
-void ChimeraSlayer::doPrep() {
+int ChimeraSlayer::doPrep() {
        try {
        
                string  kmerDBNameLeft;
@@ -33,6 +33,9 @@ void ChimeraSlayer::doPrep() {
                        if(!kmerFileTestLeft){  
                        
                                for (int i = 0; i < templateSeqs.size(); i++) {
+                                       
+                                       if (m->control_pressed) { return 0; } 
+                                       
                                        string leftFrag = templateSeqs[i]->getUnaligned();
                                        leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
                                        
@@ -57,6 +60,8 @@ void ChimeraSlayer::doPrep() {
                        if(!kmerFileTestRight){ 
                        
                                for (int i = 0; i < templateSeqs.size(); i++) {
+                                       if (m->control_pressed) { return 0; } 
+                                       
                                        string rightFrag = templateSeqs[i]->getUnaligned();
                                        rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
                                        
@@ -82,6 +87,8 @@ void ChimeraSlayer::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);
                        
@@ -96,14 +103,19 @@ void ChimeraSlayer::doPrep() {
                                
                for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
                
+               if (m->control_pressed) {  return 0; } 
+
+               
                //run filter on template
-               for (int i = 0; i < templateSeqs.size(); i++) {  runFilter(templateSeqs[i]);  }
+               for (int i = 0; i < templateSeqs.size(); i++) {  if (m->control_pressed) {  return 0; }  runFilter(templateSeqs[i]);  }
                
-               mothurOutEndLine(); mothurOut("It took " + toString(time(NULL) - start) + " secs to filter.");  mothurOutEndLine();
+               m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to filter.");    m->mothurOutEndLine();
+               
+               return 0;
 
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraSlayer", "doprep");
+               m->errorOut(e, "ChimeraSlayer", "doprep");
                exit(1);
        }
 }
@@ -111,14 +123,14 @@ void ChimeraSlayer::doPrep() {
 ChimeraSlayer::~ChimeraSlayer() {      delete decalc;  if (searchMethod == "kmer") {  delete databaseRight;  delete databaseLeft;  }    }
 //***************************************************************************************************************
 void ChimeraSlayer::printHeader(ostream& out) {
-       mothurOutEndLine();
-       mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
-       mothurOutEndLine();
+       m->mothurOutEndLine();
+       m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
+       m->mothurOutEndLine();
        
        out << "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 }
 //***************************************************************************************************************
-void ChimeraSlayer::print(ostream& out, ostream& outAcc) {
+int ChimeraSlayer::print(ostream& out, ostream& outAcc) {
        try {
                if (chimeraFlags == "yes") {
                        string chimeraFlag = "no";
@@ -129,7 +141,7 @@ void ChimeraSlayer::print(ostream& out, ostream& outAcc) {
                        
                        if (chimeraFlag == "yes") {     
                                if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) {
-                                       mothurOut(querySeq->getName() + "\tyes"); mothurOutEndLine();
+                                       m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine();
                                        outAcc << querySeq->getName() << endl;
                                }
                        }
@@ -138,9 +150,11 @@ void ChimeraSlayer::print(ostream& out, ostream& outAcc) {
                        out << endl;
                }else {  out << querySeq->getName() << "\tno" << endl;  }
                
+               return 0;
+               
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraSlayer", "print");
+               m->errorOut(e, "ChimeraSlayer", "print");
                exit(1);
        }
 }
@@ -158,7 +172,10 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                maligner = new Maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
                slayer = new Slayer(window, increment, minSim, divR, iters, minSNP);
                
+               if (m->control_pressed) {  return 0;  }
+               
                string chimeraFlag = maligner->getResults(query, decalc);
+               if (m->control_pressed) {  return 0;  }
                vector<results> Results = maligner->getOutput();
                                
                //found in testing realigning only made things worse
@@ -233,8 +250,11 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                                spotMap = decalc->getMaskMap();
                        }
                        
+                       if (m->control_pressed) {  for (int k = 0; k < seqs.size(); k++) {  delete seqs[k].seq;   }  return 0;  }
+                       
                        //send to slayer
                        chimeraFlags = slayer->getResults(query, seqsForSlayer);
+                       if (m->control_pressed) {  return 0;  }
                        chimeraResults = slayer->getOutput();
                        
                        //free memory
@@ -247,7 +267,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraSlayer", "getChimeras");
+               m->errorOut(e, "ChimeraSlayer", "getChimeras");
                exit(1);
        }
 }
@@ -282,7 +302,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
 
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraSlayer", "printBlock");
+               m->errorOut(e, "ChimeraSlayer", "printBlock");
                exit(1);
        }
 }