85bd10da37f403d155c4434d90edcd146e682948
braney
  Mon May 15 13:03:32 2017 -0700
add sorting to composite wiggles.

diff --git src/optimalLeaf/SimMat.hh src/optimalLeaf/SimMat.hh
new file mode 100644
index 0000000..b9d5f1f
--- /dev/null
+++ src/optimalLeaf/SimMat.hh
@@ -0,0 +1,33 @@
+// --------------------------------------------------------
+//                     SimMat.hh
+// Computes the similarity matrix, and writes ordered trees 
+// to a .CDT files.
+// --------------------------------------------------------
+#ifndef SIMMAT_HH
+#define SIMMAT_HH
+
+
+
+class SimMat {
+ private:
+  float **mat,**cMat; // similarity matrix
+  int genes,exp; // number of genes and experiments
+  int *order,meanZ;
+  float **in,*means,*std;
+  char **geneNames,**geneDesc,**expNames;
+ public:
+  SimMat( int igenes, int iexp, int imeanZ, float **iin, char **igeneNames, char **igeneDesc, char **iexpNames);
+  SimMat(char *filename,int orfL,int descL,int mZ);
+  //SimMat(int genes,int exp);
+  void generateMat();
+  void generateCols(char *name); // generating similarity matrix for columns
+  float **giveMat() {return mat;}
+  float **giveCols() {return cMat;}
+  int giveGenes() {return genes;}
+  int giveExp() {return exp;}
+  float *compMean(int tot,int c,int isGene);
+  float *compStd(int tot,int c,int isGene);
+  float compSim(int g1,int g2,int c,int isGene);
+  void printOrder(int *arr,int *arrC,char *name);
+};
+#endif