fixes while testing 1.33.0

[mothur.git] / maligner.h

diff --git a/maligner.h b/maligner.h
index 13aa917afb5b39ac238dda69b6032bb509e1345e..fc00e99faf3ad3931f76606c34ffb65b69eb4de7 100644 (file)
--- a/maligner.h
+++ b/maligner.h
@@ -20,40 +20,36 @@ class Maligner {
 
        public:
                
-               Maligner(vector<Sequence*>, int, int, int, float, int, int, string, Database*, Database*);
+               Maligner(vector<Sequence>, int, int, float, int, int); //int, int, int, , string, Database*, Database*
                ~Maligner() {};
                
-               string getResults(Sequence*, DeCalculator*);
+               string getResults(Sequence, DeCalculator);
                float getPercentID() {  return percentIdenticalQueryChimera;    }
                vector<results> getOutput()  {  return outputResults;                   }
                
                                
        private:
-               Sequence* query;
-               vector<Sequence*> refSeqs;
-               vector<Sequence*> db;
-               int numWanted, matchScore, misMatchPenalty, minCoverage, minSimilarity;
-               string searchMethod;
+               Sequence query;
+               vector<Sequence> refSeqs;
+               vector<Sequence> db;
+               int minCoverage, minSimilarity, matchScore, misMatchPenalty;
                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.
+               vector<int> unalignedMap;
+               vector<Sequence> minCoverageFilter(vector<Sequence>);  //removes top matches that do not have minimum coverage with query.
                int computeChimeraPenalty();
-               void verticalFilter(vector<Sequence*>);
+               vector<Sequence> verticalFilter(vector<Sequence>);
                
                vector< vector<score_struct> > buildScoreMatrix(int, int);
-               void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
+               void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence>, int);
                vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
-               vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
-               string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
+               vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>);
+               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);
-               vector<Sequence*> getKmerSeqs(Sequence*, int);
+               string chimeraMaligner(int, DeCalculator);
+               MothurOut* m;
                
 };