X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.h;h=1df4d6b2122d88318193a74d906e601e9cd214a1;hb=ae57e166b2ed7b475ec3f466106bd76fabadd063;hp=3f4eb4ef9f430ed9191f7de78e41df3427c4bec4;hpb=8c1196586860f830fc9c813f2a79abab7434dc4b;p=mothur.git

diff --git a/chimera.h b/chimera.h
index 3f4eb4e..1df4d6b 100644
--- 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; 
@@ -123,9 +133,9 @@ struct sim {
 };
 
 struct linePair {
-			unsigned long int start;
-			unsigned long int end;
-			linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+			unsigned long long start;
+			unsigned long long end;
+			linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
 			linePair(){}
 };
 
@@ -147,14 +157,15 @@ 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 int getNumNoParents(){  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