X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.h;fp=maligner.h;h=3deacfe875eb6ed266dca8514109ea515f035fc9;hb=8c1196586860f830fc9c813f2a79abab7434dc4b;hp=6ddd6acebdff359294deda6b4cc1b4c2c5ae788f;hpb=0571957d68cbbc0e425af1db8e808f826010b9e2;p=mothur.git

diff --git a/maligner.h b/maligner.h
index 6ddd6ac..3deacfe 100644
--- a/maligner.h
+++ b/maligner.h
@@ -20,7 +20,7 @@ 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*);
@@ -32,14 +32,10 @@ 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;
-		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();
@@ -53,8 +49,6 @@ class Maligner {
 		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);
 		MothurOut* m;
 		
 };