X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimera.h;h=e187bfc60d8d504d80561d4347f9a838f1ddabee;hp=9c5a21995c2acd71516b4e3a9cf53732b10b54f9;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=2e28b53eb15d5dc11653247ee12aed2c7e5aac43

diff --git a/chimera.h b/chimera.h
index 9c5a219..e187bfc 100644
--- a/chimera.h
+++ b/chimera.h
@@ -133,9 +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(){}
 };
 
@@ -146,7 +146,7 @@ class Chimera {
 
 	public:
 	
-		Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false;  }
+		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;	}
@@ -160,11 +160,12 @@ class Chimera {
 		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&){  Sequence temp; return temp; }
-		virtual Sequence print(MPI_File&, MPI_File&, data_results, data_results){  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
 		
@@ -173,7 +174,7 @@ class Chimera {
 		
 		vector<Sequence*> templateSeqs;
 		vector<Sequence*> filteredTemplateSeqs;
-		bool filter, unaligned; 
+		bool filter, unaligned, byGroup; 
 		int length; 
 		string seqMask, filterString, outputDir, templateFileName; 
 		Sequence* getSequence(string);  //find sequence from name