working on removing pointers from chimera.slayer to eliminate pesky m…

…emory leaks
zhanglab · May 31, 2011 · 2e28b53 · 2e28b53
1 parent 5a7b1d4
commit 2e28b53
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Showing 16 changed files with 321 additions and 277 deletions.
diff --git a/ccode.cpp b/ccode.cpp
@@ -74,7 +74,7 @@ Ccode::~Ccode() {
 	#endif
 }	
 //***************************************************************************************************************
-Sequence* Ccode::print(ostream& out, ostream& outAcc) {
+Sequence Ccode::print(ostream& out, ostream& outAcc) {
 	try {
 
 		ofstream out2;
@@ -155,7 +155,7 @@ Sequence* Ccode::print(ostream& out, ostream& outAcc) {
 		//free memory
 		for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
 
-		return NULL;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Ccode", "print");
@@ -164,7 +164,7 @@ Sequence* Ccode::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-Sequence* Ccode::print(MPI_File& out, MPI_File& outAcc) {
+Sequence Ccode::print(MPI_File& out, MPI_File& outAcc) {
 	try {
 
 		string outMapString = "";
@@ -263,7 +263,7 @@ Sequence* Ccode::print(MPI_File& out, MPI_File& outAcc) {
 		//free memory
 		for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
 
-		return NULL;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Ccode", "print");

diff --git a/ccode.h b/ccode.h
@@ -28,10 +28,10 @@ class Ccode : public Chimera {
 		~Ccode();
 
 		int getChimeras(Sequence* query);
-		Sequence* print(ostream&, ostream&);
+		Sequence print(ostream&, ostream&);
 
 		#ifdef USE_MPI
-		Sequence* print(MPI_File&, MPI_File&);
+		Sequence print(MPI_File&, MPI_File&);
 		#endif
 	private:
 

diff --git a/chimera.h b/chimera.h
@@ -103,6 +103,12 @@ struct SeqDist {
 	float dist;
 	int index;
 };
+/***********************************************************************/
+struct SeqCompare {
+	Sequence seq;
+	float dist;
+	int index;
+};
 //********************************************************************************************************************
 //sorts lowest to highest
 inline bool compareRegionStart(results left, results right){
@@ -114,7 +120,11 @@ inline bool compareSeqDist(SeqDist left, SeqDist right){
 	return (left.dist < right.dist);	
 } 
 //********************************************************************************************************************
-
+//sorts lowest to highest
+inline bool compareSeqCompare(SeqCompare left, SeqCompare right){
+	return (left.dist < right.dist);	
+} 
+//********************************************************************************************************************
 struct sim {
 		string leftParent;
 		string rightParent; 
@@ -147,14 +157,14 @@ class Chimera {
 		virtual void printHeader(ostream&){};
 		virtual int getChimeras(Sequence*){ return 0; }
 		virtual int getChimeras(){ return 0; }
-		virtual Sequence* print(ostream&, ostream&){  return NULL; }
-		virtual Sequence* print(ostream&, ostream&, data_results, data_results) { return NULL; }
+		virtual Sequence print(ostream&, ostream&){  Sequence temp; return temp; }
+		virtual Sequence print(ostream&, ostream&, data_results, data_results) { Sequence temp; return temp; }
 		virtual int print(ostream&, ostream&, string){  return 0; }
 		virtual data_results getResults() { data_results results; return results; }
 
 		#ifdef USE_MPI
-		virtual Sequence* print(MPI_File&, MPI_File&){  return 0; }
-		virtual Sequence* print(MPI_File&, MPI_File&, data_results, data_results){  return NULL; }
+		virtual Sequence print(MPI_File&, MPI_File&){  Sequence temp; return temp; }
+		virtual Sequence print(MPI_File&, MPI_File&, data_results, data_results){  Sequence temp; return temp; }
 		virtual int print(MPI_File&, MPI_File&, string){  return 0; }
 		#endif
 

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
@@ -47,7 +47,7 @@ ChimeraCheckRDP::~ChimeraCheckRDP() {
 	}
 }	
 //***************************************************************************************************************
-Sequence* ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
+Sequence ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
 	try {
 
 		m->mothurOut("Processing: " + querySeq->getName()); m->mothurOutEndLine();
@@ -72,7 +72,7 @@ Sequence* ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
 			}
 		}
 
-		return NULL;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ChimeraCheckRDP", "print");
@@ -81,7 +81,7 @@ Sequence* ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-Sequence* ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
+Sequence ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
 	try {
 
 		cout << "Processing: " << querySeq->getName() << endl; 
@@ -115,7 +115,7 @@ Sequence* ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
 			}
 		}
 
-		return NULL;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ChimeraCheckRDP", "print");

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
@@ -29,10 +29,10 @@ class ChimeraCheckRDP : public Chimera {
 		~ChimeraCheckRDP();
 
 		int getChimeras(Sequence*);
-		Sequence* print(ostream&, ostream&);
+		Sequence print(ostream&, ostream&);
 
 		#ifdef USE_MPI
-		Sequence* print(MPI_File&, MPI_File&);
+		Sequence print(MPI_File&, MPI_File&);
 		#endif
 
 	private: