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