chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector...

[mothur.git] / maligner.h

diff --git a/maligner.h b/maligner.h
index abe18a3cb1ad6c6b65d41077b8dd1fb56d802f96..13aa917afb5b39ac238dda69b6032bb509e1345e 100644 (file)
--- a/maligner.h
+++ b/maligner.h
@@ -11,6 +11,7 @@
  
 #include "decalc.h"
 #include "chimera.h"
+#include "database.hpp"
 
 /***********************************************************************/
 //This class was modeled after the chimeraMaligner written by the Broad Institute
@@ -19,7 +20,7 @@ class Maligner {
 
        public:
                
-               Maligner(vector<Sequence*>, int, int, int, float, int, int, string);
+               Maligner(vector<Sequence*>, int, int, int, float, int, int, string, Database*, Database*);
                ~Maligner() {};
                
                string getResults(Sequence*, DeCalculator*);
@@ -35,7 +36,10 @@ class Maligner {
                string searchMethod;
                float minDivR, percentIdenticalQueryChimera;
                vector<results> outputResults;
+               vector<int> indexes;  //stores index into template seqs of the refSeqs, so we can return the whole sequence rather than the trimmed and filtered one
                map<int, int> spotMap;
+               Database* databaseLeft;
+               Database* databaseRight;
                
                vector<Sequence*> minCoverageFilter(vector<Sequence*>);  //removes top matches that do not have minimum coverage with query.
                int computeChimeraPenalty();
@@ -49,6 +53,7 @@ class Maligner {
                float computePercentID(string, string);
                string chimeraMaligner(int, DeCalculator*);
                vector<Sequence*> getBlastSeqs(Sequence*, int);
+               vector<Sequence*> getKmerSeqs(Sequence*, int);
                
 };