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

[mothur.git] / slayer.h

diff --git a/slayer.h b/slayer.h
new file mode 100644 (file)
index 0000000..e898989
--- /dev/null
+++ b/slayer.h
@@ -0,0 +1,58 @@
+#ifndef SLAYER_H
+#define SLAYER_H
+/*
+ *  slayer.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/25/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+ 
+#include "sequence.hpp"
+
+/***********************************************************************/
+//This class was modeled after the chimeraSlayer written by the Broad Institute
+/***********************************************************************/
+struct data_struct { //not right needs work...
+       int regionStart;
+       int regionEnd;
+       string parent;
+       float queryToParent;
+       float queryToParentLocal;
+       float divR;
+};
+/***********************************************************************/
+
+
+class Slayer {
+
+       public:
+               
+               Slayer(int, int, int, float);
+               ~Slayer() {};
+               
+               void getResults(Sequence*, vector<Sequence*>);
+               //float getPercentID() {        return percentIdenticalQueryChimera;    }
+               //vector<results> getOutput()  {        return outputResults;                   }
+               
+                               
+       private:
+               
+               int windowSize, windowStep, parentFragmentThreshold;
+               float divRThreshold; 
+               
+               void verticalFilter(vector<Sequence*>);
+               float computePercentID(string, string, int, int);
+               
+               vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*);
+               
+                               
+};
+
+/***********************************************************************/
+
+#endif
+
+