X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimera.h;h=e187bfc60d8d504d80561d4347f9a838f1ddabee;hp=e37d9f9af93cdbc808a6eb7bc7fe7f1ebe4df20a;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=7b80945ef716dd72d00563a5a4d692394f7f84c3

diff --git a/chimera.h b/chimera.h
index e37d9f9..e187bfc 100644
--- a/chimera.h
+++ b/chimera.h
@@ -45,10 +45,10 @@ struct data_struct {
 struct data_results {
 	vector<data_struct> results;
 	string flag;
-	map<int, int> spotMap;
 	Sequence trimQuery;
+	//results malignerResults;
 	
-	data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), spotMap(s), trimQuery(t) {}
+	data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), trimQuery(t) {}
 	data_results() {}
 };
 /***********************************************************************/
@@ -77,6 +77,7 @@ struct score_struct {
 	int score;
 	int row;
 	int col;
+//	int mismatches;
 };
 /***********************************************************************/
 struct trace_struct {
@@ -102,6 +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){
@@ -113,7 +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; 
@@ -122,9 +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(){}
 };
 
@@ -135,8 +146,8 @@ class Chimera {
 
 	public:
 	
-		Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
-		virtual ~Chimera(){	for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } };
+		Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false;  byGroup = false; }
+		virtual ~Chimera(){	for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } for (int i = 0; i < filteredTemplateSeqs.size(); i++) { delete filteredTemplateSeqs[i];  } };
 		virtual bool getUnaligned()				{	return unaligned;			}
 		virtual int getLength()					{   return length;	}
 		virtual vector<Sequence*> readSeqs(string);
@@ -146,13 +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&){  Sequence temp; return temp; }
+		virtual Sequence print(MPI_File&, MPI_File&, data_results, data_results, bool&){  Sequence temp; return temp; }
 		virtual int print(MPI_File&, MPI_File&, string){  return 0; }
 		#endif
 		
@@ -160,7 +173,8 @@ class Chimera {
 	protected:
 		
 		vector<Sequence*> templateSeqs;
-		bool filter, unaligned; 
+		vector<Sequence*> filteredTemplateSeqs;
+		bool filter, unaligned, byGroup; 
 		int length; 
 		string seqMask, filterString, outputDir, templateFileName; 
 		Sequence* getSequence(string);  //find sequence from name