4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/protein/inc/spMapper.h src/hg/protein/inc/spMapper.h
index 1b76f7a..fa2a099 100644
--- src/hg/protein/inc/spMapper.h
+++ src/hg/protein/inc/spMapper.h
@@ -1,81 +1,81 @@
 /* spMapper - map swissprot accessions to KnownGene ids.  Intended to use in
  * building gene sorter tables.  Can optionally map uniref entry ids.  Used
  * to collect results so that duplication of entries can be avoided.  */
 
 /* Copyright (C) 2005 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #ifndef SPMAPPER_H
 #define SPMAPPER_H
 
 struct sqlConnection *conn;
 
 struct spMapper
 /* mapper object */
 {
     struct spKgMap *spKgMap;      /* hash of swissprot id to kg id. */
     struct unirefTbl *unirefTbl;  /* table of uniref entries. */
     struct hash *noMapTbl;        /* table of ids that could not be mapped,
                                    * value is code indicating the reasons */
 
     /* counts of ids that count not be found, only counted once */
     int noSpIdMapCnt;       /* couldn't map a sp id */
     int noUnirefMapCnt;     /* couldn't map a uniref entry id */
 
     /* counts of swissprot query/target pair mappings */
     int qtMapCnt;           /* pairs successfuly mapped */
     int qtNoSpIdMapCnt;     /* pairs not mapped due to no sp mapping */
     int qtNoUnirefMapCnt;   /* pairs not mapped due to no uniref entry mapping */
 
     int scoreDir;           /* 1 if higher score is better, -1 if lower score
                              * is better */
 
     /* hash table of best score for query and target ids.  A naive
      * implementation would have the pair as a single string, but this greatly
      * increase the memory usage.  Instead, both are entered separately, point
      * to the same struct. */
     struct hash *kgPairMap;      /* hash to kgEntry objects, which are chained
                                   * together for a given id */
     struct kgPair *kgPairList;   /* list of all spPair objects. */
 };
 
 struct kgEntry
 /* struct used to store a known gene id with a link to the next entry
  * and the associated spPairScore struct. */
 {
     struct kgEntry *next;
     char *id;                /* kd id, memory not owned by this struct */
     struct kgPair *kgPair;   /* containing shared score */
 };
 
 struct kgPair
 /* structure used to keep the best e-value of a pair of kg ids. */
 {
     struct kgPair *next;
     struct kgEntry *kg1Entry;   /* pointers back to each entry */
     struct kgEntry *kg2Entry;
     float score;                 /* best score for the pair */
 };
 
   
 struct spMapper *spMapperNew(struct sqlConnection *conn, int scoreDir,
                              char *unirefFile, char *orgFilter);
 /* construct a new spMapper object. scoreDir is 1 if higher score is better,
  * -1 if lower score is better If unirefFile is not null, this is a tab file
  * reformatting of the uniref xml file with member data extracted (see
  * uniref.h).  If orgFilter is not null, then only uniref members from this
  * organism are loaded.
  */
 
 void spMapperFree(struct spMapper **smPtr);
 /* free smMapper object */
 
 void spMapperMapPair(struct spMapper *sm, char *qSpId, char *tSpId, float score);
 /* map a pair of swissprot/uniprot ids to one or more pairs of known gene
  * ids and add them to the table */
 
 void spMapperPrintNoMapInfo(struct spMapper *sm, char *outFile);
 /* Print missed id table. First column is id, second column is R if it wasn't
  * found in uniref, or K if it couldn't be associated with a known gene */
 
 
 #endif