working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 3f4eb4ef9f430ed9191f7de78e41df3427c4bec4..1df4d6b2122d88318193a74d906e601e9cd214a1 100644 (file)
--- 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