added checks for ^C to quit command instead of program

aligncommand.cpp

@@ -213,6 +213,8 @@ int AlignCommand::execute(){
 		vector<string> outputNames;
 
 		for (int s = 0; s < candidateFileNames.size(); s++) {
+			if (m->control_pressed) { return 0; }
+
 			m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 
 			if (outputDir == "") {  outputDir += hasPath(candidateFileNames[s]); }
@@ -234,8 +236,9 @@ int AlignCommand::execute(){
 
 				lines.push_back(new linePair(0, numFastaSeqs));
 
-				int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
-				if (exitCommand == 0) { 
+				driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+
+				if (m->control_pressed) { 
 					remove(accnosFileName.c_str()); 
 					remove(alignFileName.c_str()); 
 					remove(reportFileName.c_str()); 
@@ -280,7 +283,7 @@ int AlignCommand::execute(){
 					lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 				}
 
-				int exitCommand = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); 
+				createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); 
 
 				rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
 				rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
@@ -317,7 +320,7 @@ int AlignCommand::execute(){
 					m->mothurOutEndLine();
 				}else{ hasAccnos = false;  }
 
-				if (exitCommand == 0) { 
+				if (m->control_pressed) { 
 					remove(accnosFileName.c_str()); 
 					remove(alignFileName.c_str()); 
 					remove(reportFileName.c_str()); 
@@ -332,8 +335,9 @@ int AlignCommand::execute(){
 
 			lines.push_back(new linePair(0, numFastaSeqs));
 
-			int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
-			if (exitCommand == 0) { 
+			driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+
+			if (m->control_pressed) { 
 				remove(accnosFileName.c_str()); 
 				remove(alignFileName.c_str()); 
 				remove(reportFileName.c_str()); 
@@ -494,7 +498,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 	try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		int process = 0;
-		int exitCommand;
+		int exitCommand = 1;
 		//		processIDS.resize(0);
 
 		//loop through and create all the processes you want

alignmentdb.cpp

@@ -28,6 +28,8 @@ AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, floa
 		while (!fastaFile.eof()) {
 			Sequence temp(fastaFile);  gobble(fastaFile);
 
+			if (m->control_pressed) {  templateSequences.clear(); break;  }
+
 			if (temp.getName() != "") {
 				templateSequences.push_back(temp);
 				//save longest base
@@ -67,20 +69,21 @@ AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, floa
 			search = new KmerDB(fastaFileName, 8);
 		}
 
-		if (needToGenerate) {
-
-			//add sequences to search 
-			for (int i = 0; i < templateSequences.size(); i++) {
-				search->addSequence(templateSequences[i]);
+		if (!(m->control_pressed)) {
+			if (needToGenerate) {
+				//add sequences to search 
+				for (int i = 0; i < templateSequences.size(); i++) {
+					search->addSequence(templateSequences[i]);
+				}
+				search->generateDB();
+
+			}else if ((method == "kmer") && (!needToGenerate)) {
+				ifstream kmerFileTest(kmerDBName.c_str());
+				search->readKmerDB(kmerFileTest);	
 			}
-			search->generateDB();
 
-		}else if ((method == "kmer") && (!needToGenerate)) {
-			ifstream kmerFileTest(kmerDBName.c_str());
-			search->readKmerDB(kmerFileTest);	
+			search->setNumSeqs(numSeqs);
 		}
-
-		search->setNumSeqs(numSeqs);
 	}
 	catch(exception& e) {
 		m->errorOut(e, "AlignmentDB", "AlignmentDB");

bayesian.cpp

@@ -56,6 +56,7 @@ Classify(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0), kmerSize(ksize), c
 
 			//for each word
 			for (int i = 0; i < numKmers; i++) {
+				if (m->control_pressed) { break; }
 
 				out << i << '\t';
 
@@ -114,6 +115,8 @@ string Bayesian::getTaxonomy(Sequence* seq) {
 		}
 
 		int index = getMostProbableTaxonomy(queryKmers);
+
+		if (m->control_pressed) { return tax; }
 
 		//bootstrap - to set confidenceScore
 		int numToSelect = queryKmers.size() / 8;
@@ -143,6 +146,8 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
 		map<int, int>::iterator itConvert;
 
 		for (int i = 0; i < iters; i++) {
+			if (m->control_pressed) { return "control"; }
+
 			vector<int> temp;
 
 			for (int j = 0; j < numToSelect; j++) {

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) {
@@ -89,17 +94,21 @@ 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"; }
 
 		}
 
 		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) {

bellerophon.h

@@ -29,11 +29,7 @@ class Bellerophon : public Chimera {
 		~Bellerophon() {};
 
 		int getChimeras();
-		void print(ostream&, ostream&);
-
-		void setCons(string){};
-		void setQuantiles(string) {};
-
+		int print(ostream&, ostream&);
 
 	private:
 		Dist* distCalculator;
@@ -43,7 +39,7 @@ class Bellerophon : public Chimera {
 		string fastafile;
 		int iters;
 
-		void generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
+		int generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
 		int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
 };
 

binsequencecommand.cpp

@@ -199,6 +199,8 @@ int BinSeqCommand::execute(){
 
 		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 
+			if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} return 0; }	
+
 			if(allLines == 1 || labels.count(list->getLabel()) == 1){
 
 				error = process(list);	
@@ -230,7 +232,8 @@ int BinSeqCommand::execute(){
 			list = input->getListVector();
 		}
 
-
+		if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} return 0; }	
+
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
 		bool needToRun = false;
@@ -255,6 +258,8 @@ int BinSeqCommand::execute(){
 			delete list;  
 		}
 
+		if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());		} return 0; }	
+
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}

bootstrapsharedcommand.cpp

@@ -219,7 +219,8 @@ int BootSharedCommand::execute(){
 		globaldata->gTreemap = tmap;
 
 		while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
+			if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } globaldata->Groups.clear(); return 0;	} 
+
 			if(allLines == 1 || labels.count(order->getLabel()) == 1){			
 
 				m->mothurOut(order->getLabel()); m->mothurOutEndLine();
@@ -255,6 +256,9 @@ int BootSharedCommand::execute(){
 			order = input->getSharedOrderVector();
 		}
 
+
+		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } globaldata->Groups.clear(); return 0;	} 
+
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
 		bool needToRun = false;
@@ -268,6 +272,8 @@ int BootSharedCommand::execute(){
 			}
 		}
 
+		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } globaldata->Groups.clear(); return 0;	} 
+
 		//run last line if you need to
 		if (needToRun == true)  {
 				if (order != NULL) {	delete order;	}
@@ -280,6 +286,8 @@ int BootSharedCommand::execute(){
 
 		}
 
+		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } globaldata->Groups.clear(); return 0;	} 
+
 		//reset groups parameter
 		globaldata->Groups.clear();  
 
@@ -360,6 +368,8 @@ int BootSharedCommand::createTree(ostream* out, Tree* t){
 
 		//assemble tree
 		t->assembleTree();
+
+		if (m->control_pressed) { return 1; }
 
 		//print newick file
 		t->print(*out);
@@ -454,6 +464,8 @@ int BootSharedCommand::process(SharedOrderVector* order) {
 						//creates tree from similarity matrix and write out file
 						createTree(out[i], tempTree);
 
+						if (m->control_pressed) {   delete tempTree; return 1; }
+
 						//save trees for consensus command.
 						trees[i].push_back(tempTree);
 					}