Ejemplo n.º 1
0
unsigned shouldHaveDesc(struct gbSelect* select)
/* determine orgcats that should be descriptions */
{
struct dbLoadAttr* attr;
unsigned descOrgCats = 0;

attr = dbLoadOptionsGetAttr(&gOptions, select->release->srcDb,
                            select->type, GB_NATIVE);
if (attr->load && attr->loadDesc)
    descOrgCats |= GB_NATIVE;
attr = dbLoadOptionsGetAttr(&gOptions, select->release->srcDb,
                            select->type, GB_XENO);
if (attr->load && attr->loadDesc)
    descOrgCats |= GB_XENO;
return descOrgCats;
}
Ejemplo n.º 2
0
static void chkRefSeqAlignTables(struct gbSelect* select,
                                 struct sqlConnection* conn,
                                 struct metaDataTbls* metaDataTbls,
                                 struct dbLoadOptions *options)
/* Verify all of the refseq alignment tables, including checking the count of
 * genePred. */
{
if ((select->orgCats & GB_NATIVE)
    && dbLoadOptionsGetAttr(options, GB_REFSEQ, select->type, GB_NATIVE)->load)
    {
    chkNativeRefSeqAlignTables(select, conn, metaDataTbls, options);
    }
if ((select->orgCats & GB_XENO)
    && dbLoadOptionsGetAttr(options, GB_REFSEQ, select->type, GB_XENO)->load)
    {
    chkXenoRefSeqAlignTables(select, conn, metaDataTbls, options);
    }
}
Ejemplo n.º 3
0
static void chkGenBankAlignTables(struct gbSelect* select,
                                  struct sqlConnection* conn,
                                  struct metaDataTbls* metaDataTbls,
                                  struct dbLoadOptions *options)
/* Verify all of the PSL tables, including checking the count of
 * alignments for either mRNA or ESTs. */
{
if ((select->orgCats & GB_NATIVE)
    && dbLoadOptionsGetAttr(options, GB_GENBANK, select->type, GB_NATIVE)->load)
    {
    chkNativeGenBankAlignTables(select, conn, metaDataTbls, options);
    }
if ((select->orgCats & GB_XENO)
    && dbLoadOptionsGetAttr(options, GB_GENBANK, select->type, GB_XENO)->load)
    {
    chkXenoGenBankAlignTables(select, conn, metaDataTbls, options);
    }
}
Ejemplo n.º 4
0
static boolean loadEnabled(unsigned srcDb, unsigned type,
                           unsigned orgCat)
/* is load enabled for (srcDb, type, orgCat) */
{
struct dbLoadAttr* attr
    = dbLoadOptionsGetAttr(&gOptions, srcDb, type, orgCat);
verbose(1, "%s %s %s: %s\n", gbSrcDbName(srcDb), gbTypeName(type),
        gbOrgCatName(orgCat), (attr->load ? "enabled" : "disabled"));
return attr->load;
}
Ejemplo n.º 5
0
static boolean keepDesc(struct gbStatus* status)
/* Check if description should be stored. */
{
return dbLoadOptionsGetAttr(gOptions, status->srcDb, status->type, status->orgCat)->loadDesc;
}