e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/inc/geneSimilarities.h src/hg/inc/geneSimilarities.h
index 62a91e9..a0f5082 100644
--- src/hg/inc/geneSimilarities.h
+++ src/hg/inc/geneSimilarities.h
@@ -1,67 +1,70 @@
 /* Objects to find genePreds given similarity in genome bases annotated.  This
  * is used to relate genes between two gene sets. */
+
+/* Copyright (C) 2008 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #ifndef GENESIMILARITIES_H
 #define GENESIMILARITIES_H
 struct genePred;
 struct sqlConnection;
 
 struct geneSim
 /* a target hit and it's similarity to the query */
 {
     struct geneSim *next;
     struct genePred *gene;   // target gene
     float sim;               // similarity score (fraction)
 };
 
 
 struct geneSimilarities
 /* a genePred and associated genes and their similarity, computed by CDS or all exon
  * alignments */
 {
     struct geneSimilarities *next;
     struct genePred *query;        // the query genePred
     boolean cdsSim;                // CDS or exon similarity?
     struct geneSim *genes;         // similar genes, sorted in descending order
 };
 
 struct geneSimilarities *geneSimilaritiesNew(struct genePred *query,
                                              boolean cdsSim);
 /* construct a new geneSimilarities object. Ownership of query is passed. */
 
 void geneSimilaritiesFree(struct geneSimilarities **gssPtr);
 /* free a geneSimilarities object and all contained genePreds */
 
 void geneSimilaritiesFreeList(struct geneSimilarities **gssList);
 /* free a list of geneSimilarities objects and all contained genePreds */
 
 int geneSimCmp(const void *va, const void *vb);
 /* compare geneSim objects by descending similarity score. */
 
 struct geneSimilarities *geneSimilaritiesBuild(struct sqlConnection *conn,
                                                boolean cdsSim,
                                                struct genePred *query,
                                                char *targetGeneTbl);
 /* Construct a geneSimilarities object by finding all similar genes in
  * the specified table. Ownership of query is passed. */
 
 struct geneSimilarities *geneSimilaritiesBuildAt(struct sqlConnection *conn,
                                                  boolean cdsSim,
                                                  char *queryName,
                                                  char *queryChrom,
                                                  int queryStart,
                                                  char *queryGeneTbl,
                                                  char *targetGeneTbl);
 /* Construct a geneSimilarities object by finding the genePred named
  * queryName with txStart of queryStart in queryGeneTbl and
  * find similar genes in targetGeneTbl. */
 
 struct geneSimilarities *geneSimilaritiesBuildAll(struct sqlConnection *conn,
                                                   boolean cdsSim,
                                                   char *queryName,
                                                   char *queryGeneTbl,
                                                   char *targetGeneTbl);
 /* Construct a list of geneSimilarities objects by finding all entries
  * of queryName in queryGeneTbl and build a geneSimilarities object for each
  * one from targetGeneTbl. */
 
 #endif