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/ccdsInfo.c src/hg/lib/ccdsInfo.c
index bffa6f0..1678112 100644
--- src/hg/lib/ccdsInfo.c
+++ src/hg/lib/ccdsInfo.c
@@ -1,294 +1,297 @@
 /* ccdsInfo.c was originally generated by the autoSql program, which also 
  * generated ccdsInfo.h and ccdsInfo.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 "ccdsInfo.h"
 #include "genbank.h"
 
 /* FIXME: database should really have an enum column */
 
 static enum ccdsInfoSrcDb parseSrcDb(char *srcDbStr, char *mrnaAcc)
 /* parse the srcDb string to an enum */
 {
 if (sameString(srcDbStr, "N"))
     return ccdsInfoNcbi;
 else if (sameString(srcDbStr, "H"))
     {
     if (startsWith("OTT", mrnaAcc))
         return ccdsInfoVega;
     else
         return ccdsInfoEnsembl;
     }
 errAbort("invalid ccdsInfoSrcDb column \"%s\"", srcDbStr);
 return ccdsInfoNull;
 }
 
 static char *formatSrcDb(enum ccdsInfoSrcDb srcDb)
 /* format the srcDb string to an enum */
 {
 switch (srcDb)
     {
     case ccdsInfoNcbi:
         return "N";
     case ccdsInfoVega:
     case ccdsInfoEnsembl:
         return "H";
     case ccdsInfoNull:
         assert(FALSE);
     }
  return "?";
 }
 
 
 void ccdsInfoStaticLoad(char **row, struct ccdsInfo *ret)
 /* Load a row from ccdsInfo table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 strcpy(ret->ccds, row[0]);
 ret->srcDb = parseSrcDb(row[1], row[2]);
 strcpy(ret->mrnaAcc, row[2]);
 strcpy(ret->protAcc, row[3]);
 }
 
 struct ccdsInfo *ccdsInfoLoad(char **row)
 /* Load a ccdsInfo from row fetched with select * from ccdsInfo
  * from database.  Dispose of this with ccdsInfoFree(). */
 {
 struct ccdsInfo *ret;
 
 AllocVar(ret);
 strcpy(ret->ccds, row[0]);
 ret->srcDb = parseSrcDb(row[1], row[2]);
 strcpy(ret->mrnaAcc, row[2]);
 strcpy(ret->protAcc, row[3]);
 return ret;
 }
 
 struct ccdsInfo *ccdsInfoLoadAll(char *fileName) 
 /* Load all ccdsInfo from a whitespace-separated file.
  * Dispose of this with ccdsInfoFreeList(). */
 {
 struct ccdsInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = ccdsInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct ccdsInfo *ccdsInfoLoadAllByChar(char *fileName, char chopper) 
 /* Load all ccdsInfo from a chopper separated file.
  * Dispose of this with ccdsInfoFreeList(). */
 {
 struct ccdsInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = ccdsInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct ccdsInfo *ccdsInfoCommaIn(char **pS, struct ccdsInfo *ret)
 /* Create a ccdsInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new ccdsInfo */
 {
 char *s = *pS;
 char srcDbBuf[2];
 
 if (ret == NULL)
     AllocVar(ret);
 sqlFixedStringComma(&s, ret->ccds, sizeof(ret->ccds));
 sqlFixedStringComma(&s, srcDbBuf, sizeof(srcDbBuf));
 sqlFixedStringComma(&s, ret->mrnaAcc, sizeof(ret->mrnaAcc));
 ret->srcDb = parseSrcDb(srcDbBuf, ret->mrnaAcc);
 sqlFixedStringComma(&s, ret->protAcc, sizeof(ret->protAcc));
 *pS = s;
 return ret;
 }
 
 void ccdsInfoFree(struct ccdsInfo **pEl)
 /* Free a single dynamically allocated ccdsInfo such as created
  * with ccdsInfoLoad(). */
 {
 struct ccdsInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freez(pEl);
 }
 
 void ccdsInfoFreeList(struct ccdsInfo **pList)
 /* Free a list of dynamically allocated ccdsInfo's */
 {
 struct ccdsInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     ccdsInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void ccdsInfoOutput(struct ccdsInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out ccdsInfo.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ccds);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", formatSrcDb(el->srcDb));
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->mrnaAcc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->protAcc);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 static char *createSql =
     /* SQL to create ccdsInfo format table */
     "CREATE TABLE %s (\n"
     "    ccds char(12) not null,     # CCDS id\n"
     "    srcDb char(1) not null,     # source database: N=NCBI, H=Hinxton\n"
     "    mrnaAcc char(18) not null,  # mRNA accession (NCBI or Hinxton)\n"
     "    protAcc char(18) not null,  # protein accession (NCBI or Hinxton)\n"
     "              #Indices\n"
     "    INDEX(ccds),\n"
     "    INDEX(mrnaAcc)\n"
     ");\n";
 
 char *ccdsInfoGetCreateSql(char *table)
 /* Get sql command to create ccdsInfo table. Result should be freed. */
 {
 char sql[1024];
 sqlSafef(sql, sizeof(sql), createSql, table);
 return cloneString(sql);
 }
 
 static int cmpMRna(const void *va, const void *vb)
 /* Compare to sort based on mrnaAcc. */
 {
 const struct ccdsInfo *a = *((struct ccdsInfo **)va);
 const struct ccdsInfo *b = *((struct ccdsInfo **)vb);
 return strcmp(a->mrnaAcc, b->mrnaAcc);
 }
 
 void ccdsInfoMRnaSort(struct ccdsInfo **ccdsInfos)
 /* Sort list by mrnaAcc */
 {
 slSort(ccdsInfos, cmpMRna);
 }
 
 static int cmpCcdsMRna(const void *va, const void *vb)
 /* Compare to sort based on CCDS id and mrnaAcc. */
 {
 const struct ccdsInfo *a = *((struct ccdsInfo **)va);
 const struct ccdsInfo *b = *((struct ccdsInfo **)vb);
 
 
 int dif = strcmp(a->ccds, b->ccds);
 if (dif == 0)
     dif = strcmp(a->mrnaAcc, b->mrnaAcc);
 return dif;
 }
 
 void ccdsInfoCcdsMRnaSort(struct ccdsInfo **ccdsInfos)
 /* Sort list by CCDS id and mrnaAcc */
 {
 slSort(ccdsInfos, cmpCcdsMRna);
 }
 
 static char *getSrcDbWhere(enum ccdsInfoSrcDb srcDb)
 /* generate where expression for CCDS srcDb.  Note: static return!! */
 {
 static char extraWhere[64];
 switch (srcDb) {
 case ccdsInfoNull:
     extraWhere[0] = '\0';
     break;
 case ccdsInfoNcbi:
     safef(extraWhere, sizeof(extraWhere), " and srcDb = 'N'");
     break;
 case ccdsInfoVega:
     safef(extraWhere, sizeof(extraWhere), " and srcDb = 'H' and mrnaAcc like 'OTT%%'");
     break;
 case ccdsInfoEnsembl:
     safef(extraWhere, sizeof(extraWhere), " and srcDb = 'H' and mrnaAcc not like 'OTT%%'");
     break;
 }
 return extraWhere;
 }
 
 struct ccdsInfo *ccdsInfoSelectByCcds(struct sqlConnection *conn, char *ccdsId,
                                       enum ccdsInfoSrcDb srcDb)
 /* Obtain list of ccdsInfo object for the specified id and srcDb.  If srcDb is
  * ccdsInfoNull, return all srcDbs.  Return NULL if ccdsId it's not valid */
 {
 char query[256];
 struct sqlResult *sr;
 char **row;
 struct ccdsInfo *ccdsInfos = NULL;
 
 sqlSafef(query, sizeof(query), "select * from ccdsInfo where ccds = '%s'%-s",
       ccdsId, getSrcDbWhere(srcDb));
 sr = sqlGetResult(conn, query);
 
 while ((row = sqlNextRow(sr)) != NULL)
     slSafeAddHead(&ccdsInfos, ccdsInfoLoad(row));
 sqlFreeResult(&sr);
 
 return ccdsInfos;
 }
 
 struct ccdsInfo *ccdsInfoSelectByMrna(struct sqlConnection *conn, char *mrnaAcc)
 /* Obtain of ccdsInfo object for the specified mRNA or NULL if mrna is not
  * associated with a CCDS.  Version number is optional for RefSeq mrnaAcc */
 {
 char query[256];
 struct sqlResult *sr;
 char **row;
 struct ccdsInfo *ccdsInfo = NULL;
 
 if (genbankIsRefSeqAcc(mrnaAcc) && (strchr(mrnaAcc, '.') == NULL))
     sqlSafef(query, sizeof(query), "select * from ccdsInfo where mrnaAcc like '%s.%%'",
           mrnaAcc);
 else
     sqlSafef(query, sizeof(query), "select * from ccdsInfo where mrnaAcc = '%s'",
           mrnaAcc);
 sr = sqlGetResult(conn, query);
 
 /* should only get one, but this is easier to code */
 while ((row = sqlNextRow(sr)) != NULL)
     slSafeAddHead(&ccdsInfo, ccdsInfoLoad(row));
 sqlFreeResult(&sr);
 
 if ((ccdsInfo != NULL) && (ccdsInfo->next != NULL))
     errAbort("obtained multiple CCDSs for mRNA %s", mrnaAcc);
 
 return ccdsInfo;
 }