added zap method to classify.seqs and changed bayesian method name to wang.

[mothur.git] / alignnode.h

diff --git a/alignnode.h b/alignnode.h
new file mode 100755 (executable)
index 0000000..4aecca7
--- /dev/null
+++ b/alignnode.h
@@ -0,0 +1,49 @@
+#ifndef ALIGNNODE
+#define ALIGNNODE
+
+/*
+ *  alignNode.h
+ *  bayesian
+ *
+ *  Created by Pat Schloss on 10/11/11.
+ *  Copyright 2011 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "taxonomynode.h"
+
+/**************************************************************************************************/
+
+struct thetaAlign {
+       thetaAlign() : A(0), T(0), G(0), C(0), gap(0){}
+       unsigned int A;
+       unsigned int T;
+       unsigned int G;
+       unsigned int C;
+       unsigned int gap;
+};
+
+/**************************************************************************************************/
+
+class AlignNode : public TaxonomyNode {
+       
+public:
+       AlignNode(string, int);
+       int loadSequence(string&);
+       int checkTheta();
+    void printTheta();
+       double getPxGivenkj_D_j(string& query); //P(x | k_j, D, j)
+       double getSimToConsensus(string& query);
+       vector<thetaAlign> getTheta()   {       return theta;   }
+       int addThetas(vector<thetaAlign>, int);
+       
+private:
+       vector<thetaAlign> theta;
+       vector<unsigned int> columnCounts;
+       int alignLength;
+};
+
+/**************************************************************************************************/
+
+#endif
+