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/lib/hgnc.c src/hg/lib/hgnc.c
index f770cc7..c0ec7ff 100644
--- src/hg/lib/hgnc.c
+++ src/hg/lib/hgnc.c
@@ -1,435 +1,438 @@
 /* hgnc.c was originally generated by the autoSql program, which also 
  * generated hgnc.h and hgnc.sql.  This module links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "hgnc.h"
 
 
 void hgncStaticLoadWithNull(char **row, struct hgnc *ret)
 /* Load a row from hgnc table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->hgncId = row[0];
 ret->symbol = row[1];
 ret->name = row[2];
 ret->status = row[3];
 ret->locusType = row[4];
 ret->locusGroup = row[5];
 ret->prvSymbols = row[6];
 ret->prvNames = row[7];
 ret->synonyms = row[8];
 ret->nameSyns = row[9];
 ret->chrom = row[10];
 ret->dateApprv = row[11];
 ret->dateMod = row[12];
 ret->dateSymChange = row[13];
 ret->dateNmChange = row[14];
 ret->accession = row[15];
 ret->enzymeIds = row[16];
 ret->entrezId = row[17];
 ret->ensId = row[18];
 ret->mgdId = row[19];
 ret->miscDbs = row[20];
 ret->miscIds = row[21];
 ret->pubMed = row[22];
 ret->refSeqIds = row[23];
 ret->geneFamilyNm = row[24];
 ret->geneFamilyDesc = row[25];
 ret->recType = row[26];
 ret->primaryId = row[27];
 ret->secondaryId = row[28];
 ret->ccdsId = row[29];
 ret->vegaId = row[30];
 ret->locusDbs = row[31];
 ret->gdbMapped = row[32];
 ret->entrezMapped = row[33];
 ret->omimMapped = row[34];
 ret->refSeqMapped = row[35];
 ret->uniProtMapped = row[36];
 ret->ensMapped = row[37];
 ret->ucscMapped = row[38];
 ret->mgiMapped = row[39];
 ret->rgdMapped = row[40];
 }
 
 struct hgnc *hgncLoadWithNull(char **row)
 /* Load a hgnc from row fetched with select * from hgnc
  * from database.  Dispose of this with hgncFree(). */
 {
 struct hgnc *ret;
 
 AllocVar(ret);
 ret->hgncId = cloneString(row[0]);
 ret->symbol = cloneString(row[1]);
 ret->name = cloneString(row[2]);
 ret->status = cloneString(row[3]);
 ret->locusType = cloneString(row[4]);
 ret->locusGroup = cloneString(row[5]);
 ret->prvSymbols = cloneString(row[6]);
 ret->prvNames = cloneString(row[7]);
 ret->synonyms = cloneString(row[8]);
 ret->nameSyns = cloneString(row[9]);
 ret->chrom = cloneString(row[10]);
 ret->dateApprv = cloneString(row[11]);
 ret->dateMod = cloneString(row[12]);
 ret->dateSymChange = cloneString(row[13]);
 ret->dateNmChange = cloneString(row[14]);
 ret->accession = cloneString(row[15]);
 ret->enzymeIds = cloneString(row[16]);
 ret->entrezId = cloneString(row[17]);
 ret->ensId = cloneString(row[18]);
 ret->mgdId = cloneString(row[19]);
 ret->miscDbs = cloneString(row[20]);
 ret->miscIds = cloneString(row[21]);
 ret->pubMed = cloneString(row[22]);
 ret->refSeqIds = cloneString(row[23]);
 ret->geneFamilyNm = cloneString(row[24]);
 ret->geneFamilyDesc = cloneString(row[25]);
 ret->recType = cloneString(row[26]);
 ret->primaryId = cloneString(row[27]);
 ret->secondaryId = cloneString(row[28]);
 ret->ccdsId = cloneString(row[29]);
 ret->vegaId = cloneString(row[30]);
 ret->locusDbs = cloneString(row[31]);
 ret->gdbMapped = cloneString(row[32]);
 ret->entrezMapped = cloneString(row[33]);
 ret->omimMapped = cloneString(row[34]);
 ret->refSeqMapped = cloneString(row[35]);
 ret->uniProtMapped = cloneString(row[36]);
 ret->ensMapped = cloneString(row[37]);
 ret->ucscMapped = cloneString(row[38]);
 ret->mgiMapped = cloneString(row[39]);
 ret->rgdMapped = cloneString(row[40]);
 return ret;
 }
 
 struct hgnc *hgncLoadAll(char *fileName) 
 /* Load all hgnc from a whitespace-separated file.
  * Dispose of this with hgncFreeList(). */
 {
 struct hgnc *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[41];
 
 while (lineFileRow(lf, row))
     {
     el = hgncLoadWithNull(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hgnc *hgncLoadAllByChar(char *fileName, char chopper) 
 /* Load all hgnc from a chopper separated file.
  * Dispose of this with hgncFreeList(). */
 {
 struct hgnc *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[41];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hgncLoadWithNull(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hgnc *hgncCommaIn(char **pS, struct hgnc *ret)
 /* Create a hgnc out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hgnc */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->hgncId = sqlStringComma(&s);
 ret->symbol = sqlStringComma(&s);
 ret->name = sqlStringComma(&s);
 ret->status = sqlStringComma(&s);
 ret->locusType = sqlStringComma(&s);
 ret->locusGroup = sqlStringComma(&s);
 ret->prvSymbols = sqlStringComma(&s);
 ret->prvNames = sqlStringComma(&s);
 ret->synonyms = sqlStringComma(&s);
 ret->nameSyns = sqlStringComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->dateApprv = sqlStringComma(&s);
 ret->dateMod = sqlStringComma(&s);
 ret->dateSymChange = sqlStringComma(&s);
 ret->dateNmChange = sqlStringComma(&s);
 ret->accession = sqlStringComma(&s);
 ret->enzymeIds = sqlStringComma(&s);
 ret->entrezId = sqlStringComma(&s);
 ret->ensId = sqlStringComma(&s);
 ret->mgdId = sqlStringComma(&s);
 ret->miscDbs = sqlStringComma(&s);
 ret->miscIds = sqlStringComma(&s);
 ret->pubMed = sqlStringComma(&s);
 ret->refSeqIds = sqlStringComma(&s);
 ret->geneFamilyNm = sqlStringComma(&s);
 ret->geneFamilyDesc = sqlStringComma(&s);
 ret->recType = sqlStringComma(&s);
 ret->primaryId = sqlStringComma(&s);
 ret->secondaryId = sqlStringComma(&s);
 ret->ccdsId = sqlStringComma(&s);
 ret->vegaId = sqlStringComma(&s);
 ret->locusDbs = sqlStringComma(&s);
 ret->gdbMapped = sqlStringComma(&s);
 ret->entrezMapped = sqlStringComma(&s);
 ret->omimMapped = sqlStringComma(&s);
 ret->refSeqMapped = sqlStringComma(&s);
 ret->uniProtMapped = sqlStringComma(&s);
 ret->ensMapped = sqlStringComma(&s);
 ret->ucscMapped = sqlStringComma(&s);
 ret->mgiMapped = sqlStringComma(&s);
 ret->rgdMapped = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void hgncFree(struct hgnc **pEl)
 /* Free a single dynamically allocated hgnc such as created
  * with hgncLoad(). */
 {
 struct hgnc *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->hgncId);
 freeMem(el->symbol);
 freeMem(el->name);
 freeMem(el->status);
 freeMem(el->locusType);
 freeMem(el->locusGroup);
 freeMem(el->prvSymbols);
 freeMem(el->prvNames);
 freeMem(el->synonyms);
 freeMem(el->nameSyns);
 freeMem(el->chrom);
 freeMem(el->dateApprv);
 freeMem(el->dateMod);
 freeMem(el->dateSymChange);
 freeMem(el->dateNmChange);
 freeMem(el->accession);
 freeMem(el->enzymeIds);
 freeMem(el->entrezId);
 freeMem(el->ensId);
 freeMem(el->mgdId);
 freeMem(el->miscDbs);
 freeMem(el->miscIds);
 freeMem(el->pubMed);
 freeMem(el->refSeqIds);
 freeMem(el->geneFamilyNm);
 freeMem(el->geneFamilyDesc);
 freeMem(el->recType);
 freeMem(el->primaryId);
 freeMem(el->secondaryId);
 freeMem(el->ccdsId);
 freeMem(el->vegaId);
 freeMem(el->locusDbs);
 freeMem(el->gdbMapped);
 freeMem(el->entrezMapped);
 freeMem(el->omimMapped);
 freeMem(el->refSeqMapped);
 freeMem(el->uniProtMapped);
 freeMem(el->ensMapped);
 freeMem(el->ucscMapped);
 freeMem(el->mgiMapped);
 freeMem(el->rgdMapped);
 freez(pEl);
 }
 
 void hgncFreeList(struct hgnc **pList)
 /* Free a list of dynamically allocated hgnc's */
 {
 struct hgnc *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hgncFree(&el);
     }
 *pList = NULL;
 }
 
 void hgncOutput(struct hgnc *el, FILE *f, char sep, char lastSep) 
 /* Print out hgnc.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->hgncId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->symbol);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->status);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->locusType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->locusGroup);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->prvSymbols);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->prvNames);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->synonyms);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nameSyns);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->dateApprv);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->dateMod);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->dateSymChange);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->dateNmChange);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->accession);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->enzymeIds);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->entrezId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ensId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->mgdId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->miscDbs);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->miscIds);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->pubMed);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->refSeqIds);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneFamilyNm);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneFamilyDesc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->recType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->primaryId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->secondaryId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ccdsId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->vegaId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->locusDbs);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gdbMapped);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->entrezMapped);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->omimMapped);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->refSeqMapped);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->uniProtMapped);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ensMapped);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ucscMapped);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->mgiMapped);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rgdMapped);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */