maligner change

[mothur.git] / maligner.h

diff --git a/maligner.h b/maligner.h
index abe18a3cb1ad6c6b65d41077b8dd1fb56d802f96..da270d6ac10c2b43a5ee6100dd9e8c33ea5c71ae 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, float, int, int); //int, int, int, , string, Database*, Database*
                ~Maligner() {};
                
                string getResults(Sequence*, DeCalculator*);
@@ -31,8 +32,7 @@ class Maligner {
                Sequence* query;
                vector<Sequence*> refSeqs;
                vector<Sequence*> db;
-               int numWanted, matchScore, misMatchPenalty, minCoverage, minSimilarity;
-               string searchMethod;
+               int minCoverage, minSimilarity, matchScore, misMatchPenalty;
                float minDivR, percentIdenticalQueryChimera;
                vector<results> outputResults;
                map<int, int> spotMap;
@@ -46,9 +46,10 @@ class Maligner {
                vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
                vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
                string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
+               string constructAntiChimericSeq(vector<trace_struct>, vector<Sequence*>);
                float computePercentID(string, string);
                string chimeraMaligner(int, DeCalculator*);
-               vector<Sequence*> getBlastSeqs(Sequence*, int);
+               MothurOut* m;
                
 };