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/* @source ensdatabaseadaptor *************************************************
**
** Ensembl Database Adaptor functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.45 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2013/02/17 13:02:40 $ by $Author: mks $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
**
******************************************************************************/
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensdatabaseadaptor.h"
#include "ensmetainformation.h"
#include "enssoftware.h"
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* @const ensKDatabaseadaptorRegCollection ************************************
**
** Regular expression to match Ensembl collection databases.
**
******************************************************************************/
const char *ensKDatabaseadaptorRegCollection =
"^" /* Start of string assertion */
"(\\w+)" /* Genus name (1) */
"_" /* Separator */
"collection" /* Prefix */
"_" /* Separator */
"([a-z]+)" /* Ensembl Database group (2) */
"(?:_\\d+)?" /* Ensembl Genomes version */
"_" /* Separator */
"(\\d+)" /* Ensembl Software version (3) */
"_" /* Separator */
"[0-9a-z]+" /* Assembly suffix */
"$"; /* End of string assertion */
/* @const ensKDatabaseadaptorRegMulti *****************************************
**
** Regular expression to match Ensembl multi-species databases.
**
******************************************************************************/
const char *ensKDatabaseadaptorRegMulti =
"^" /* Start of string assertion */
"ensembl(?:genomes)?" /* Prefix */
"_" /* Separator */
"([a-z]+)" /* Ensembl Database group (1) */
"(_\\w+?)*?" /* Ensembl Genomes section (2) */
"(?:_\\d+)?" /* Ensembl Genomes version */
"_" /* Separator */
"(\\d+)" /* Ensembl Software version (3) */
"$"; /* End of string assertion */
/* @const ensKDatabaseadaptorRegSpecies ***************************************
**
** Regular expression to match Ensembl species-specific databases.
**
******************************************************************************/
const char *ensKDatabaseadaptorRegSpecies =
"^" /* Start of string assertion */
"([a-z]+_[0-9a-z]+(?:_[a-z0-9]+)?)" /* Species name (1) */
/* homo_sapiens or canis_lupus_familiaris */
"_" /* Separator */
"([a-z]+)" /* Database group (2) */
"(?:_\\d+)?" /* Ensembl Genomes version */
"_" /* Separator */
"(\\d+)" /* Ensembl Software version (3) */
"_" /* Separator */
"[0-9a-z]+" /* Assembly suffix */
"$"; /* End of string assertion */
/* ========================================================================= */
/* =========================== global variables ============================ */
/* ========================================================================= */
/* ========================================================================= */
/* ============================= private data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private constants =========================== */
/* ========================================================================= */
/* @conststatic databaseadaptorKGroup *****************************************
**
** The Ensembl Database Adaptor group member is enumerated in the data
** structure. The following strings are used for conversion in database
** operations and correspond to EnsEDatabaseadaptorGroup.
**
******************************************************************************/
static const char *databaseadaptorKGroup[] =
{
"",
"core",
"vega",
"otherfeatures",
"cdna",
"variation",
"funcgen",
"compara",
"ontology",
"qc",
"pipeline",
"hive",
"coreexpressionest",
"coreexpressiongnf",
"ancestral",
"website",
"production",
(const char *) NULL
};
/* ========================================================================= */
/* =========================== private variables =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private functions =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* ======================= All functions by section ======================== */
/* ========================================================================= */
/* @filesection ensdatabaseadaptor ********************************************
**
** @nam1rule ens Function belongs to the Ensembl library
**
******************************************************************************/
/* @datasection [EnsPDatabaseadaptor] Ensembl Database Adaptor ****************
**
** @nam2rule Databaseadaptor Functions for manipulating
** Ensembl Database Adaptor objects
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor
** @cc CVS Revision: 1.231.2.1
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Database Adaptor by pointer.
** It is the responsibility of the user to first destroy any previous
** Database Adaptor. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPDatabaseadaptor]
**
** @nam3rule New Constructor
** @nam4rule Databasename Constructor with a database name
** @nam4rule Ini Constructor with initial values
** @nam4rule Url Constructor with a Uniform Resource Locator (URL)
**
** @argrule Databasename dbc [EnsPDatabaseconnection]
** Ensembl Database Connection
** @argrule Databasename database [AjPStr] Database name
** @argrule Ini dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @argrule Ini database [AjPStr] Database name
** @argrule Ini species [AjPStr] Species
** @argrule Ini dbag [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration
** @argrule Ini multi [AjBool] Multiple species
** @argrule Ini identifier [ajuint] Species identifier
** @argrule Url url [const AjPStr] Uniform Resource Locator
**
** @valrule * [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensDatabaseadaptorNewDatabasename ************************************
**
** Constructor for an Ensembl Database Adaptor with a database name.
**
** An Ensembl database name encodes all information to create an
** Ensembl Database Adaptor. This function parses the database name and sets
** the species and Ensembl Database Adaptor Group accordingly. For collection
** databases only a single Ensembl Database Adaptor representing the entire
** collection is returned, which has the multi-species member set to ajTrue and
** the species indentifier set to 0. An Ensembl Database Adaptor representing a
** collection has to be expanded into species-specific ones.
**
** Ensembl Database Adaptors are singleton objects in the sense that a single
** instance of an Ensembl Database Adaptor connected to a particular database
** is sufficient to instantiate any number of Ensembl Object Adaptors from the
** database. Each Ensembl Object Adaptor will have a weak reference to the
** Ensembl Database Adaptor that instantiated it. Therefore, Ensembl Database
** Adaptors should not be instantiated directly, but rather obtained from the
** Ensembl Registry, which will in turn call this function if neccessary.
**
** @see ensRegistryNewDatabaseadaptor
** @see ensRegistryGetDatabaseadaptor
**
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @param [u] database [AjPStr] Database name
**
** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPDatabaseadaptor ensDatabaseadaptorNewDatabasename(
EnsPDatabaseconnection dbc,
AjPStr database)
{
AjBool debug = AJFALSE;
AjPRegexp rec = NULL;
AjPRegexp rem = NULL;
AjPRegexp res = NULL;
AjPStr group = NULL;
AjPStr prefix = NULL;
AjPStr swversion = NULL;
AjPStr multi = NULL;
EnsEDatabaseadaptorGroup dbag = ensEDatabaseadaptorGroupNULL;
EnsPDatabaseadaptor dba = NULL;
debug = ajDebugTest("ensDatabaseadaptorNewDatabasename");
if (debug)
{
ajDebug("ensDatabaseadaptorNewDatabasename\n"
" dbc %p\n"
" database '%S'\n",
dbc,
database);
ensDatabaseconnectionTrace(dbc, 1);
}
if (!dbc)
return NULL;
if ((database == NULL) || (ajStrGetLen(database) == 0))
return NULL;
rec = ajRegCompC(ensKDatabaseadaptorRegCollection);
rem = ajRegCompC(ensKDatabaseadaptorRegMulti);
res = ajRegCompC(ensKDatabaseadaptorRegSpecies);
multi = ajStrNewC("default");
if (ajRegExec(rec, database))
{
/* Ensembl Collection databases have to be matched first. */
group = ajStrNew();
prefix = ajStrNew();
swversion = ajStrNew();
ajRegSubI(rec, 1, &prefix);
ajRegSubI(rec, 2, &group);
ajRegSubI(rec, 3, &swversion);
if (ajStrMatchCaseC(swversion, ensKSoftwareVersion))
{
if (debug)
ajDebug("ensDatabaseadaptorNewDatabasename matched "
"collection database '%S'.\n",
database);
dbag = ensDatabaseadaptorGroupFromStr(group);
if (dbag)
dba = ensDatabaseadaptorNewIni(dbc,
database,
prefix,
dbag,
ajTrue,
0);
else
ajDebug("ensDatabaseadaptorNewDatabasename got unexpected "
"group string '%S' for database name '%S'.\n",
group, database);
}
else
{
if (debug)
ajDebug("ensDatabaseadaptorNewDatabasename matched "
"collection database '%S', "
"but not the software version '%s'.\n",
database, ensKSoftwareVersion);
}
ajStrDel(&group);
ajStrDel(&prefix);
ajStrDel(&swversion);
}
else if (ajRegExec(rem, database))
{
/* Multi-species databases */
group = ajStrNew();
prefix = ajStrNew();
swversion = ajStrNew();
ajRegSubI(rem, 1, &group);
if (ajRegLenI(rem, 3))
{
ajRegSubI(rem, 2, &prefix);
ajRegSubI(rem, 3, &swversion);
/* Remove leading underscores from the species prefix. */
if (ajStrPrefixC(prefix, "_"))
ajStrCutStart(&prefix, 1);
}
else
ajRegSubI(rem, 2, &swversion);
if (ajStrMatchCaseC(swversion, ensKSoftwareVersion))
{
if (debug)
ajDebug("ensDatabaseadaptorNewDatabasename matched "
"multi-species database '%S'.\n",
database);
dbag = ensDatabaseadaptorGroupFromStr(group);
if (dbag)
dba = ensDatabaseadaptorNewIni(dbc,
database,
(ajStrGetLen(prefix))
? prefix : multi,
dbag,
ajFalse,
0);
else
ajDebug("ensDatabaseadaptorNewDatabasename got unexpected "
"group string '%S' for database name '%S'.\n",
group, database);
}
else
{
if (debug)
ajDebug("ensDatabaseadaptorNewDatabasename matched "
"multi-species database '%S', "
"but not the software version '%s'.\n",
database, ensKSoftwareVersion);
}
ajStrDel(&group);
ajStrDel(&prefix);
ajStrDel(&swversion);
}
else if (ajRegExec(res, database))
{
/* Species-specific databases */
prefix = ajStrNew();
group = ajStrNew();
swversion = ajStrNew();
ajRegSubI(res, 1, &prefix);
ajRegSubI(res, 2, &group);
ajRegSubI(res, 3, &swversion);
if (ajStrMatchCaseC(swversion, ensKSoftwareVersion))
{
if (debug)
ajDebug("ensDatabaseadaptorNewDatabasename matched "
"species-specific database '%S'.\n",
database);
dbag = ensDatabaseadaptorGroupFromStr(group);
if (dbag)
dba = ensDatabaseadaptorNewIni(dbc,
database,
prefix,
dbag,
ajFalse,
0);
else
ajDebug("ensDatabaseadaptorNewDatabasename got unexpected "
"group string '%S' for database name '%S'.\n",
group, database);
}
else
{
if (debug)
ajDebug("ensDatabaseadaptorNewDatabasename matched "
"species-specific database '%S', "
"but not the software version '%s'.\n",
database, ensKSoftwareVersion);
}
ajStrDel(&prefix);
ajStrDel(&group);
ajStrDel(&swversion);
}
else
ajDebug("ensDatabaseadaptorNewDatabasename no match for "
"database name '%S'.\n",
database);
ajRegFree(&rec);
ajRegFree(&rem);
ajRegFree(&res);
ajStrDel(&multi);
return dba;
}
/* @func ensDatabaseadaptorNewIni *********************************************
**
** Constructor for an Ensembl Database Adaptor with initial values.
**
** If a database name has not been provided, the database name of the
** Ensembl Database Connection will be used.
**
** Ensembl Database Adaptors are singleton objects in the sense that a single
** instance of an Ensembl Database Adaptor connected to a particular database
** is sufficient to instantiate any number of Ensembl Object Adaptors from the
** database. Each Ensembl Object Adaptor will have a weak reference to the
** Ensembl Database Adaptor that instantiated it. Therefore, Ensembl Database
** Adaptors should not be instantiated directly, but rather obtained from the
** Ensembl Registry, which will in turn call this function if neccessary.
**
** @see ensRegistryNewDatabaseadaptor
** @see ensRegistryGetDatabaseadaptor
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::new
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
** @param [uN] database [AjPStr] Database name
** @param [u] species [AjPStr] Species
** @param [u] dbag [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration
** @param [r] multi [AjBool] Multiple species
** @param [r] identifier [ajuint] Species identifier
**
** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
**
** @release 6.4.0
** @@
** NOTE: The Perl API automatically registers the Ensembl Database Adaptor in
** the Ensembl Registry via Bio::EnsEMBL::Utils::ConfigRegistry::gen_load.
** In this implementation both objects are kept separate. The Ensembl Registry
** object provides a function, which generates an Ensembl Database Adaptor
** based on the same parameter set and automatically registers it.
******************************************************************************/
EnsPDatabaseadaptor ensDatabaseadaptorNewIni(
EnsPDatabaseconnection dbc,
AjPStr database,
AjPStr species,
EnsEDatabaseadaptorGroup dbag,
AjBool multi,
ajuint identifier)
{
EnsPDatabaseadaptor dba = NULL;
if (ajDebugTest("ensDatabaseadaptorNewIni"))
{
ajDebug("ensDatabaseadaptorNewIni\n"
" dbc %p\n"
" database '%S'\n"
" species '%S'\n"
" dbag %d\n"
" multi '%B'\n"
" identifier %u\n",
dbc,
database,
species,
dbag,
multi,
identifier);
ensDatabaseconnectionTrace(dbc, 1);
}
if (!dbc)
return NULL;
if (!species)
return NULL;
if (!dbag)
return NULL;
AJNEW0(dba);
dba->Databaseconnection = ensDatabaseconnectionNewCpy(dbc, database);
if (species)
dba->Species = ajStrNewRef(species);
dba->Group = dbag;
dba->Multispecies = multi;
dba->Identifier = identifier;
return dba;
}
/* @func ensDatabaseadaptorNewUrl *********************************************
**
** Constructor for an Ensembl Database Adaptor with a
** Uniform Resource Locator (URL).
**
** Ensembl Database Adaptors are singleton objects in the sense that a single
** instance of an Ensembl Database Adaptor connected to a particular database
** is sufficient to instantiate any number of Ensembl Object Adaptors from the
** database. Each Ensembl Object Adaptor will have a weak reference to the
** Ensembl Database Adaptor that instantiated it. Therefore, Ensembl Database
** Adaptors should not be instantiated directly, but rather obtained from the
** Ensembl Registry, which will in turn call this function if neccessary.
**
** @see ensRegistryNewDatabaseadaptor
** @see ensRegistryGetDatabaseadaptor
**
** @param [r] url [const AjPStr] Uniform Resource Locator
**
** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPDatabaseadaptor ensDatabaseadaptorNewUrl(const AjPStr url)
{
EnsPDatabaseadaptor dba = NULL;
EnsPDatabaseconnection dbc = NULL;
if ((url == NULL) || (ajStrGetLen(url) == 0))
return NULL;
dbc = ensDatabaseconnectionNewUrl(url);
if (!dbc)
return NULL;
dba = ensDatabaseadaptorNewDatabasename(
dbc,
ensDatabaseconnectionGetDatabasename(dbc));
ensDatabaseconnectionDel(&dbc);
return dba;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Database Adaptor object.
**
** @fdata [EnsPDatabaseadaptor]
**
** @nam3rule Del Destroy (free) an Ensembl Database Adaptor
**
** @argrule * Pdba [EnsPDatabaseadaptor*]
** Ensembl Database Adaptor address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensDatabaseadaptorDel ************************************************
**
** Default destructor for an Ensembl Database Adaptor.
**
** Ensembl Database Adaptors are singleton objects that are registered in the
** Ensembl Registry and weakly referenced by Ensembl Object Adaptors that have
** been instantiated by it. Therefore, Ensembl Database Adaptors should never
** be destroyed directly. Upon exit, the Ensembl Registry will call this
** function if required.
**
** @see ensExit
** @see ensRegistryExit
**
** @param [d] Pdba [EnsPDatabaseadaptor*] Ensembl Database Adaptor address
**
** @return [void]
**
** @release 6.2.0
** @@
** NOTE: The Perl API removes the Ensembl Database Adaptor from the
** Ensembl Registry via Bio::EnsEMBL::Registry::remove_db.
** This implementation keeps both objects independent and Ensembl Database
** Adaptors are deleted from the Ensembl Registry.
******************************************************************************/
void ensDatabaseadaptorDel(EnsPDatabaseadaptor *Pdba)
{
EnsPDatabaseadaptor pthis = NULL;
if (!Pdba)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensDatabaseadaptorDel"))
{
ajDebug("ensDatabaseadaptorDel\n"
" *Pdba %p\n",
*Pdba);
ensDatabaseadaptorTrace(*Pdba, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Pdba))
return;
ensDatabaseconnectionDel(&pthis->Databaseconnection);
ajStrDel(&pthis->Species);
ajListstrFreeData(&pthis->SpeciesNames);
ajMemFree((void **) Pdba);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Database Adaptor object.
**
** @fdata [EnsPDatabaseadaptor]
**
** @nam3rule Get Return Ensembl Database Adaptor attribute(s)
** @nam4rule Databaseconnection Return the Ensembl Database Connection
** @nam4rule Group Return the Ensembl Database Adaptor Group enumeration
** @nam4rule Identifier Return the species identifier
** @nam4rule Multispecies Return the multi-species flag
** @nam4rule Species Return the species
**
** @argrule * dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @valrule Databaseconnection [EnsPDatabaseconnection]
** Ensembl Database Connection or NULL
** @valrule Species [AjPStr] Species or NULL
** @valrule Group [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration or ensEDatabaseadaptorGroupNULL
** @valrule Multispecies [AjBool] Multiple species or ajFalse
** @valrule Identifier [ajuint] Species identifier or 0U
**
** @fcategory use
******************************************************************************/
/* @func ensDatabaseadaptorGetDatabaseconnection ******************************
**
** Get the Ensembl Database Connection member of an Ensembl Database Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::dbc
** @param [r] dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [EnsPDatabaseconnection] Ensembl Database Connection or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPDatabaseconnection ensDatabaseadaptorGetDatabaseconnection(
const EnsPDatabaseadaptor dba)
{
return (dba) ? dba->Databaseconnection : NULL;
}
/* @func ensDatabaseadaptorGetGroup *******************************************
**
** Get the group member of an Ensembl Database Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::group
** @param [r] dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration or ensEDatabaseadaptorGroupNULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsEDatabaseadaptorGroup ensDatabaseadaptorGetGroup(
const EnsPDatabaseadaptor dba)
{
return (dba) ? dba->Group : ensEDatabaseadaptorGroupNULL;
}
/* @func ensDatabaseadaptorGetIdentifier **************************************
**
** Get the species identifier member of an Ensembl Database Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::species_id
** @param [r] dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [ajuint] Species identifier or 0U, defaults to 1U
**
** @release 6.2.0
** @@
******************************************************************************/
ajuint ensDatabaseadaptorGetIdentifier(
const EnsPDatabaseadaptor dba)
{
return (dba) ? ((dba->Identifier) ? dba->Identifier : 1U) : 0U;
}
/* @func ensDatabaseadaptorGetMultispecies ************************************
**
** Get the multi-species member of an Ensembl Database Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::is_multispecies
** @param [r] dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [AjBool] ajTrue if the database contains multiple species
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorGetMultispecies(
const EnsPDatabaseadaptor dba)
{
return (dba) ? dba->Multispecies : ajFalse;
}
/* @func ensDatabaseadaptorGetSpecies *****************************************
**
** Get the species member of an Ensembl Database Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::species
** @param [r] dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [AjPStr] Species or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
AjPStr ensDatabaseadaptorGetSpecies(
const EnsPDatabaseadaptor dba)
{
return (dba) ? dba->Species : NULL;
}
/* @section load on demand ****************************************************
**
** Functions for returning members of an Ensembl Database Adaptor object,
** which may need loading from an Ensembl SQL database on demand.
**
** @fdata [EnsPDatabaseadaptor]
**
** @nam3rule Load Return Ensembl Database Adaptor attribute(s)
** loaded on demand
** @nam4rule Speciesnames Return all species names
**
** @argrule * dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @valrule Speciesnames [const AjPList]
** AJAX List of AJAX String (species name) objects or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensDatabaseadaptorLoadSpeciesnames ***********************************
**
** Load all species name objects of an Ensembl Database Adaptor.
**
** This is not a simple accessor function, it will fetch species name
** objects from the Ensembl SQL database in case the AJAX List is not defined.
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [const AjPList]
** AJAX List of AJAX String (species name) objects or NULL
**
** @release 6.5.0
** @@
******************************************************************************/
const AjPList ensDatabaseadaptorLoadSpeciesnames(EnsPDatabaseadaptor dba)
{
if (!dba)
return NULL;
if (dba->SpeciesNames)
return dba->SpeciesNames;
else
dba->SpeciesNames = ajListstrNew();
if (dba->Multispecies)
ensMetainformationadaptorRetrieveAllSpeciesnames(
ensRegistryGetMetainformationadaptor(dba),
dba->SpeciesNames);
else
ajListPushAppend(dba->SpeciesNames, (void *) ajStrNewS(dba->Species));
return dba->SpeciesNames;
}
/* @section member assignment *************************************************
**
** Functions for assigning members of an Ensembl Database Adaptor object.
**
** @fdata [EnsPDatabaseadaptor]
**
** @nam3rule Set Set one member of an Ensembl Database Adaptor
** @nam4rule Databaseconnection Set the Ensembl Database Connection
** @nam4rule Group Set the group
** @nam4rule Identifier Set the species identifier
** @nam4rule Multispecies Set the multiple-species flag
** @nam4rule Species Set the species
**
** @argrule * dba [EnsPDatabaseadaptor] Ensembl Database Adaptor object
** @argrule Databaseconnection dbc [EnsPDatabaseconnection]
** Ensembl Database Connection
** @argrule Group dbag [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration
** @argrule Identifier identifier [ajuint] Species identifier
** @argrule Multispecies multi [AjBool] Multi-species attribute
** @argrule Species species [AjPStr] Species
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory modify
******************************************************************************/
/* @func ensDatabaseadaptorSetDatabaseconnection ******************************
**
** Set the Ensembl Database Connection member of an Ensembl Database Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::dbc
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [u] dbc [EnsPDatabaseconnection] Ensembl Database Connection
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorSetDatabaseconnection(EnsPDatabaseadaptor dba,
EnsPDatabaseconnection dbc)
{
if (!dba)
return ajFalse;
ensDatabaseconnectionDel(&dba->Databaseconnection);
dba->Databaseconnection = ensDatabaseconnectionNewRef(dbc);
return ajTrue;
}
/* @func ensDatabaseadaptorSetGroup *******************************************
**
** Set the group member of an Ensembl Database Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::group
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [u] dbag [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorSetGroup(EnsPDatabaseadaptor dba,
EnsEDatabaseadaptorGroup dbag)
{
if (!dba)
return ajFalse;
dba->Group = dbag;
return ajTrue;
}
/* @func ensDatabaseadaptorSetIdentifier **************************************
**
** Set the species identifier member of an Ensembl Database Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::species_id
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [r] identifier [ajuint] Species identifier
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorSetIdentifier(EnsPDatabaseadaptor dba,
ajuint identifier)
{
if (!dba)
return ajFalse;
dba->Identifier = identifier;
return ajTrue;
}
/* @func ensDatabaseadaptorSetMultispecies ************************************
**
** Set the multi-species member of an Ensembl Database Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::is_multispecies
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [r] multi [AjBool] Multi-species attribute
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorSetMultispecies(EnsPDatabaseadaptor dba,
AjBool multi)
{
if (!dba)
return ajFalse;
dba->Multispecies = multi;
return ajTrue;
}
/* @func ensDatabaseadaptorSetSpecies *****************************************
**
** Set the species member of an Ensembl Database Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::DBAdaptor::species
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [u] species [AjPStr] Species
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorSetSpecies(EnsPDatabaseadaptor dba, AjPStr species)
{
if (!dba)
return ajFalse;
ajStrDel(&dba->Species);
if (species)
dba->Species = ajStrNewRef(species);
return ajTrue;
}
/* @section debugging *********************************************************
**
** Functions for reporting of an Ensembl Database Adaptor object.
**
** @fdata [EnsPDatabaseadaptor]
**
** @nam3rule Trace Report Ensembl Database Adaptor members to debug file
**
** @argrule Trace dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
** @argrule Trace level [ajuint] Indentation level
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensDatabaseadaptorTrace **********************************************
**
** Trace an Ensembl Database Adaptor.
**
** @param [r] dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [r] level [ajuint] Indentation level
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorTrace(const EnsPDatabaseadaptor dba, ajuint level)
{
AjIList iter = NULL;
AjPStr indent = NULL;
AjPStr name = NULL;
if (!dba)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensDatabaseadaptorTrace %p\n"
"%S Databaseconnection %p\n"
"%S Species '%S'\n"
"%S SpeciesNames %p\n"
"%S Group '%s'\n"
"%S Multispecies '%B'\n"
"%S Identifier %u\n",
indent, dba,
indent, dba->Databaseconnection,
indent, dba->Species,
indent, dba->SpeciesNames,
indent, ensDatabaseadaptorGroupToChar(dba->Group),
indent, dba->Multispecies,
indent, dba->Identifier);
ensDatabaseconnectionTrace(dba->Databaseconnection, level + 1);
/* Trace the AJAX List of AJAX String (species name) objects. */
if (dba->SpeciesNames)
{
ajDebug("%S AJAX List %p of AJAX String (species name) objects:\n",
indent, dba->SpeciesNames);
iter = ajListIterNewread(dba->SpeciesNames);
while (!ajListIterDone(iter))
{
name = (AjPStr) ajListIterGet(iter);
ajDebug("%S %S\n", indent, name);
}
ajListIterDel(&iter);
}
ajStrDel(&indent);
return ajTrue;
}
/* @section comparison ********************************************************
**
** Functions for comparing Ensembl Database Adaptor objects.
**
** @fdata [EnsPDatabaseadaptor]
**
** @nam3rule Match Compare two Ensembl Database Adaptor objects
** @nam3rule Matchcomponents Match components of an Ensembl Database Adaptor
**
** @argrule Match dba1 [const EnsPDatabaseadaptor] Ensembl Database Adaptor
** @argrule Match dba2 [const EnsPDatabaseadaptor] Ensembl Database Adaptor
** @argrule Matchcomponents dba [const EnsPDatabaseadaptor]
** Ensembl Database Adaptor
** @argrule Matchcomponents dbc [const EnsPDatabaseconnection]
** Ensembl Database Connection
** @argrule Matchcomponents species [const AjPStr] Species
** @argrule Matchcomponents dbag [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration
** @argrule Matchcomponents multi [AjBool] Multiple species
** @argrule Matchcomponents identifier [ajuint] Species identifier
**
** @valrule * [AjBool] True on success
**
** @fcategory use
******************************************************************************/
/* @func ensDatabaseadaptorMatch **********************************************
**
** Tests for matching two Ensembl Database Adaptors.
**
** @param [r] dba1 [const EnsPDatabaseadaptor] First Ensembl Database Adaptor
** @param [r] dba2 [const EnsPDatabaseadaptor] Second Ensembl Database Adaptor
**
** @return [AjBool] ajTrue if the Ensembl Database Adaptors are equal
**
** @release 6.2.0
** @@
** The comparison is based on initial pointer equality and if that fails a
** comparison of the group member, the species identifier and a
** case-insensitive string comparison of the species member.
******************************************************************************/
AjBool ensDatabaseadaptorMatch(const EnsPDatabaseadaptor dba1,
const EnsPDatabaseadaptor dba2)
{
if (!dba1)
return ajFalse;
if (!dba2)
return ajFalse;
if (dba1 == dba2)
return ajTrue;
if (!ensDatabaseconnectionMatch(dba1->Databaseconnection,
dba2->Databaseconnection))
return ajFalse;
if (dba1->Group != dba2->Group)
return ajFalse;
if (dba1->Multispecies != dba2->Multispecies)
return ajFalse;
if (dba1->Identifier != dba2->Identifier)
return ajFalse;
if (!ajStrMatchCaseS(dba1->Species, dba2->Species))
return ajFalse;
return ajTrue;
}
/* @func ensDatabaseadaptorMatchcomponents ************************************
**
** Tests whether an Ensembl Database Adaptor matches component members.
**
** @param [r] dba [const EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [r] dbc [const EnsPDatabaseconnection] Ensembl Database Connection
** @param [r] species [const AjPStr] Species
** @param [u] dbag [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration
** @param [r] multi [AjBool] Multiple species
** @param [r] identifier [ajuint] Species identifier
**
** @return [AjBool] ajTrue if all members match
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorMatchcomponents(const EnsPDatabaseadaptor dba,
const EnsPDatabaseconnection dbc,
const AjPStr species,
EnsEDatabaseadaptorGroup dbag,
AjBool multi,
ajuint identifier)
{
if (!dba)
return ajFalse;
if (!dbc)
return ajFalse;
if (!species)
return ajFalse;
if (!dbag)
return ajFalse;
if (dba->Group != dbag)
return ajFalse;
if (dba->Multispecies != multi)
return ajFalse;
if (dba->Identifier != identifier)
return ajFalse;
if (!ensDatabaseconnectionMatch(dba->Databaseconnection, dbc))
return ajFalse;
if (!ajStrMatchCaseS(dba->Species, species))
return ajFalse;
return ajTrue;
}
/* @section convenience functions *********************************************
**
** Ensembl Database Adaptor convenience functions
**
** @fdata [EnsPDatabaseadaptor]
**
** @nam3rule Disconnect Disconnect the underlying Ensembl Database Connection
** @nam3rule Escape Escape a string
** @nam4rule C Escape to an AJAX String
** @nam4rule S Escape to a C-type character string
** @nam3rule Sqlstatement AJAX SQL Statement
** @nam4rule Del Delete an AJAX SQL Statement
** @nam4rule New Run a new AJAX SQL statement
**
** @argrule * dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @argrule EscapeC Ptxt [char**] Address of the (new) SQL-escaped C string
** @argrule EscapeC str [const AjPStr] AJAX String to be escaped
** @argrule EscapeS Pstr [AjPStr*] Address of the (new) SQL-escaped AJAX String
** @argrule EscapeS str [const AjPStr] AJAX String to be escaped
** @argrule SqlstatementDel Psqls [AjPSqlstatement*] AJAX SQL Statement address
** @argrule SqlstatementNew statement [const AjPStr] SQL statement
**
** @valrule Disconnect [AjBool] ajTrue upon success, ajFalse otherwise
** @valrule EscapeC [AjBool] ajTrue upon success, ajFalse otherwise
** @valrule EscapeS [AjBool] ajTrue upon success, ajFalse otherwise
** @valrule Speciesnames [const AjPList] AJAX List of
** AJAX String (species name) objects
** @valrule SqlstatementDel [AjBool] ajTrue upon success, ajFalse otherwise
** @valrule SqlstatementNew [AjPSqlstatement] AJAX SQL Statement
**
** @fcategory use
******************************************************************************/
/* @func ensDatabaseadaptorDisconnect *****************************************
**
** Disconnect the Ensembl Database Connection this Ensembl Database Adaptor
** is based on.
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.3.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorDisconnect(EnsPDatabaseadaptor dba)
{
if (!dba)
return ajFalse;
return ensDatabaseconnectionDisconnect(dba->Databaseconnection);
}
/* @func ensDatabaseadaptorEscapeC ********************************************
**
** Escape special characters in an AJAX String for use in an SQL statement,
** taking into account the current character set of the AJAX SQL Connection
** and return a C-type character string.
**
** The caller is responsible for deleting the escaped C-type character string.
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [wP] Ptxt [char**] Address of the (new) SQL-escaped C string
** @param [r] str [const AjPStr] AJAX String to be escaped
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorEscapeC(EnsPDatabaseadaptor dba,
char **Ptxt,
const AjPStr str)
{
if (!dba)
return ajFalse;
if (!Ptxt)
return ajFalse;
if (!str)
return ajFalse;
if (ajDebugTest("ensDatabaseadaptorEscapeC"))
{
ajDebug("ensDatabaseadaptorEscapeC\n"
" dba %p\n"
" Ptxt %p\n"
" str '%S'\n",
dba,
Ptxt,
str);
ensDatabaseadaptorTrace(dba, 1);
}
return ensDatabaseconnectionEscapeC(dba->Databaseconnection, Ptxt, str);
}
/* @func ensDatabaseadaptorEscapeS ********************************************
**
** Escape special characters in an AJAX String for use in an SQL statement,
** taking into account the current character set of the AJAX SQL Connection
** and return an AJAX String.
**
** The caller is responsible for deleting the escaped AJAX String.
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [wP] Pstr [AjPStr*] Address of the (new) SQL-escaped AJAX String
** @param [r] str [const AjPStr] AJAX String to be escaped
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorEscapeS(EnsPDatabaseadaptor dba,
AjPStr *Pstr,
const AjPStr str)
{
if (!dba)
return ajFalse;
if (!Pstr)
return ajFalse;
if (!str)
return ajFalse;
if (ajDebugTest("ensDatabaseadaptorEscapeS"))
{
ajDebug("ensDatabaseadaptorEscapeS\n"
" dba %p\n"
" Pstr %p\n"
" str '%S'\n",
dba,
Pstr,
str);
ensDatabaseadaptorTrace(dba, 1);
}
return ensDatabaseconnectionEscapeS(dba->Databaseconnection, Pstr, str);
}
/* @func ensDatabaseadaptorSqlstatementDel ************************************
**
** Delete an AJAX SQL Statement associated with an
** Ensembl Database Adaptor.
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [d] Psqls [AjPSqlstatement*] AJAX SQL Statement address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.3.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorSqlstatementDel(EnsPDatabaseadaptor dba,
AjPSqlstatement *Psqls)
{
if (!dba)
return ajFalse;
if (!Psqls)
return ajFalse;
if (ajDebugTest("ensDatabaseadaptorSqlstatementDel"))
ajDebug("ensDatabaseadaptorSqlstatementDel\n"
" dba %p\n"
" PSqls %p\n",
dba,
Psqls);
return ensDatabaseconnectionSqlstatementDel(dba->Databaseconnection,
Psqls);
}
/* @func ensDatabaseadaptorSqlstatementNew ************************************
**
** Constructor for an AJAX SQL statement via an Ensembl Database Adaptor.
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [r] statement [const AjPStr] SQL statement
**
** @return [AjPSqlstatement] AJAX SQL Statement or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
AjPSqlstatement ensDatabaseadaptorSqlstatementNew(EnsPDatabaseadaptor dba,
const AjPStr statement)
{
if (!dba)
return NULL;
if (!statement)
return NULL;
return ensDatabaseconnectionSqlstatementNew(dba->Databaseconnection,
statement);
}
/* @section fetch *************************************************************
**
** Functions for fetching objects of an Ensembl Database Adaptor object.
**
** @fdata [EnsPDatabaseadaptor]
**
** @nam3rule Fetch Fetch Ensembl Database Adaptor-related objects
** @nam4rule All Fetch all objects
** @nam4rule Schemabuild Fetch the schema build
**
** @argrule Schemabuild dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @argrule Schemabuild Pbuild [AjPStr*] Schema build
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensDatabaseadaptorFetchSchemabuild ***********************************
**
** Fetch the schema build of an Ensembl database, which is the software version
** and the data version separated by an underscore.
** So for database homo_sapiens_core_50_36l the schema build would be 50_36l.
** The caller is responsible for deleting the AJAX String.
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [u] Pbuild [AjPStr*] Schema build
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensDatabaseadaptorFetchSchemabuild(EnsPDatabaseadaptor dba,
AjPStr *Pbuild)
{
register ajuint i = 0U;
ajuint tokens = 0U;
AjPStr database = NULL;
AjPStr temp = NULL;
AjPStrTok token = NULL;
if (!dba)
return ajFalse;
if (!Pbuild)
return ajFalse;
if (*Pbuild)
ajStrAssignClear(Pbuild);
else
*Pbuild = ajStrNew();
database = ensDatabaseconnectionGetDatabasename(dba->Databaseconnection);
tokens = ajStrParseCountC(database, "_");
if (tokens < 2U)
return ajFalse;
token = ajStrTokenNewC(database, "_");
/* Parse all string tokens but the last two. */
temp = ajStrNew();
for (i = 0U; i < (tokens - 2U); i++)
ajStrTokenNextParse(token, &temp);
ajStrDel(&temp);
ajStrTokenRestParse(token, Pbuild);
ajStrTokenDel(&token);
return ajTrue;
}
/* @datasection [EnsEDatabaseadaptorGroup] Ensembl Database Adaptor Group *****
**
** @nam2rule Databaseadaptor Functions for manipulating
** Ensembl Database Adaptor objects
** @nam3rule DatabaseadaptorGroup Functions for manipulating
** Ensembl Database Adaptor Group enumerations
**
******************************************************************************/
/* @section Misc **************************************************************
**
** Functions for returning an Ensembl Database Adaptor Group enumeration.
**
** @fdata [EnsEDatabaseadaptorGroup]
**
** @nam4rule From Ensembl Database Adaptor Group query
** @nam5rule Str AJAX String object query
**
** @argrule Str group [const AjPStr] Group string
**
** @valrule * [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration or ensEDatabaseadaptorGroupNULL
**
** @fcategory misc
******************************************************************************/
/* @func ensDatabaseadaptorGroupFromStr ***************************************
**
** Convert an AJAX String into an Ensembl Database Adaptor Group enumeration.
**
** @param [r] group [const AjPStr] Group string
**
** @return [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration or ensEDatabaseadaptorGroupNULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsEDatabaseadaptorGroup ensDatabaseadaptorGroupFromStr(const AjPStr group)
{
register EnsEDatabaseadaptorGroup i = ensEDatabaseadaptorGroupNULL;
EnsEDatabaseadaptorGroup dbag = ensEDatabaseadaptorGroupNULL;
for (i = ensEDatabaseadaptorGroupNULL;
databaseadaptorKGroup[i];
i++)
if (ajStrMatchCaseC(group, databaseadaptorKGroup[i]))
dbag = i;
if (!dbag)
ajDebug("ensDatabaseadaptorGroupFromStr encountered "
"unexpected string '%S'.\n", group);
return dbag;
}
/* @section Cast **************************************************************
**
** Functions for returning attributes of an
** Ensembl Database Adaptor Group enumeration.
**
** @fdata [EnsEDatabaseadaptorGroup]
**
** @nam4rule To Return Ensembl Database Adaptor Group enumeration
** @nam5rule Char Return C character string value
**
** @argrule To dbag [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration
**
** @valrule Char [const char*]
** Ensembl Database Adaptor Group C-type (char *) string
**
** @fcategory cast
******************************************************************************/
/* @func ensDatabaseadaptorGroupToChar ****************************************
**
** Convert an Ensembl Database Adaptor Group enumeration into a
** C-type (char *) string.
**
** @param [u] dbag [EnsEDatabaseadaptorGroup]
** Ensembl Database Adaptor Group enumeration
**
** @return [const char*] Ensembl Database Adaptor Group C-type (char *) string
**
** @release 6.2.0
** @@
******************************************************************************/
const char* ensDatabaseadaptorGroupToChar(EnsEDatabaseadaptorGroup dbag)
{
register EnsEDatabaseadaptorGroup i = ensEDatabaseadaptorGroupNULL;
for (i = ensEDatabaseadaptorGroupNULL;
databaseadaptorKGroup[i] && (i < dbag);
i++);
if (!databaseadaptorKGroup[i])
ajDebug("ensDatabaseadaptorGroupToChar "
"encountered an out of boundary error on "
"Ensembl Databaseadaptor Group "
"enumeration %d.\n",
dbag);
return databaseadaptorKGroup[i];
}
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