added hcluster command and fixed some bugs, namely one with smart distancing.

[mothur.git] / hcluster.h

diff --git a/hcluster.h b/hcluster.h
new file mode 100644 (file)
index 0000000..2688c19
--- /dev/null
+++ b/hcluster.h
@@ -0,0 +1,69 @@
+#ifndef HCLUSTER_H
+#define HCLUSTER_H
+
+/*
+ *  hcluster.h
+ *  Mothur
+ *
+ *  Created by westcott on 10/13/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "mothur.h"
+
+class RAbundVector;
+class ListVector;
+/************************************************************/
+struct clusterNode {
+       int numSeq;
+       int parent;
+       int smallChild; //used to make linkTable work with list and rabund
+       clusterNode(int num, int par, int kid) : numSeq(num), parent(par), smallChild(kid) {};
+};
+
+/***********************************************************************/
+class HCluster {
+       
+public:
+       HCluster(RAbundVector*, ListVector*);
+    bool update(int, int, float);
+       //string getTag();
+
+protected:     
+       void clusterBins();
+       void clusterNames();
+       int getUpmostParent(int);
+       int makeActive();
+       void printInfo();
+       void updateArrayandLinkTable();
+               
+       RAbundVector* rabund;
+       ListVector* list;
+       
+       vector<clusterNode> clusterArray;
+       vector< map<int, int> > linkTable;  // vector of maps - linkTable[1][6] = 2  would mean sequence in spot 1 has 2 links with sequence in 6
+       map<int, int> activeLinks;  //maps sequence to index in linkTable
+       map<int, int>::iterator it;
+       map<int, int>::iterator it2;
+       
+       int numSeqs;
+       
+       int smallRow;
+       int smallCol;
+       float smallDist;
+       
+};
+
+/***********************************************************************/
+
+
+
+
+
+
+
+#endif
+
+