dab89c1682e091dfa3780ce95359ebea9f6b7d52
braney
  Thu May 18 09:49:17 2017 -0700
add licensing info to optimalLeaf library

diff --git src/optimalLeaf/SimMat.hh src/optimalLeaf/SimMat.hh
index b9d5f1f..0f41872 100644
--- src/optimalLeaf/SimMat.hh
+++ src/optimalLeaf/SimMat.hh
@@ -1,33 +1,39 @@
+/* This code provided by Ziv Bar-Joseph with the explicit understanding that 
+ * no licensing is required for it to be used in the UCSC Genome Browser
+ * as long as reference is made to this paper:
+ * https://www.ncbi.nlm.nih.gov/pubmed/12801867
+ */
+
 // --------------------------------------------------------
 //                     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