started adding chimeraslayer method and fixed minor bug in treegroupscommand deconstr...

[mothur.git] / maligner.h

diff --git a/maligner.h b/maligner.h
new file mode 100644 (file)
index 0000000..6277e73
--- /dev/null
+++ b/maligner.h
@@ -0,0 +1,77 @@
+#ifndef MALIGNER_H
+#define MALIGNER_H
+/*
+ *  maligner.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/23/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "decalc.h"
+
+/***********************************************************************/
+//This class was modeled after the chimeraMaligner written by the Broad Institute
+/***********************************************************************/
+struct score_struct {
+       int prev;
+       int score;
+       int row;
+       int col;
+};
+/***********************************************************************/
+struct trace_struct {
+       int col;
+       int oldCol;
+       int row;
+};
+/***********************************************************************/
+struct results {
+       int regionStart;
+       int regionEnd;
+       string parent;
+       float queryToParent;
+       float queryToParentLocal;
+       float divR;
+};
+
+/**********************************************************************/
+class Maligner {
+
+       public:
+               
+               Maligner(vector<Sequence*>, int, int, int, float, int);
+               ~Maligner() {};
+               
+               string getResults(Sequence*);
+               float getPercentID() {  return percentIdenticalQueryChimera;    }
+               vector<results> getOutput()  {  return outputResults;                   }
+               
+                               
+       private:
+               DeCalculator* decalc;
+               Sequence* query;
+               vector<Sequence*> refSeqs;
+               vector<Sequence*> db;
+               int numWanted, matchScore, misMatchPenalty, minCoverage;
+               float minDivR, percentIdenticalQueryChimera;
+               vector<results> outputResults;
+               
+               vector<Sequence*> minCoverageFilter(vector<Sequence*>);  //removes top matches that do not have minimum coverage with query.
+               int computeChimeraPenalty();
+               void verticalFilter(vector<Sequence*>);
+               
+               vector< vector<score_struct> > buildScoreMatrix(int, 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*>);
+               float computePercentID(string, string);
+               
+};
+
+/***********************************************************************/
+
+#endif
+