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/* @source ensmarker **********************************************************
**
** Ensembl Marker functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.61 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2013/02/17 13:02:10 $ 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 "ensmarker.h"
#include "enstable.h"
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== global variables ============================ */
/* ========================================================================= */
/* ========================================================================= */
/* ============================= private data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private constants =========================== */
/* ========================================================================= */
/* @conststatic markerKType ***************************************************
**
** The Ensembl Marker type member is enumerated in both, the SQL table
** definition and the data structure. The following strings are used for
** conversion in database operations and correspond to EnsEMarkerType.
**
******************************************************************************/
static const char *const markerKType[] =
{
"",
"est",
"microsatellite",
(const char *) NULL
};
/* @conststatic markeradaptorKTablenames **************************************
**
** Array of Ensembl Marker Adaptor SQL table names
**
******************************************************************************/
static const char *const markeradaptorKTablenames[] =
{
"marker",
"marker_synonym",
(const char *) NULL
};
/* @conststatic markeradaptorKColumnnames *************************************
**
** Array of Ensembl Marker Adaptor SQL column names
**
******************************************************************************/
static const char *const markeradaptorKColumnnames[] =
{
"marker.marker_id",
"marker.display_marker_synonym_id",
"marker.left_primer",
"marker.right_primer",
"marker.min_primer_dist",
"marker.max_primer_dist",
"marker.priority",
"marker.type",
"marker_synonym.marker_synonym_id",
"marker_synonym.name",
"marker_synonym.source",
(const char *) NULL
};
/* @conststatic markeradaptorKLeftjoins ***************************************
**
** Array of Ensembl Marker Adaptor SQL LEFT JOIN conditions
**
******************************************************************************/
static const EnsOBaseadaptorLeftjoin markeradaptorKLeftjoins[] =
{
{
"marker_synonym",
"marker.marker_id = marker_synonym.marker_id"
},
{(const char *) NULL, (const char *) NULL}
};
/* @conststatic markerfeatureadaptorKTablenames *******************************
**
** Array of Ensembl Marker Feature Adaptor SQL table names
**
******************************************************************************/
static const char *const markerfeatureadaptorKTablenames[] =
{
"marker_feature",
"marker",
"marker_synonym",
(const char *) NULL
};
/* @conststatic markerfeatureadaptorKColumnnames ******************************
**
** Array of Ensembl Marker Feature Adaptor SQL column names
**
******************************************************************************/
static const char *const markerfeatureadaptorKColumnnames[] =
{
"marker_feature.marker_feature_id",
"marker_feature.seq_region_id",
"marker_feature.seq_region_start",
"marker_feature.seq_region_end",
"marker_feature.analysis_id",
"marker_feature.map_weight",
"marker.marker_id",
"marker.left_primer",
"marker.right_primer",
"marker.min_primer_dist",
"marker.max_primer_dist",
"marker.priority",
"marker.type",
"marker_synonym.marker_synonym_id",
"marker_synonym.name",
"marker_synonym.source",
(const char *) NULL
};
/* @conststatic markerfeatureadaptorKLeftjoins ********************************
**
** Array of Ensembl Marker Feature Adaptor SQL LEFT JOIN conditions
**
******************************************************************************/
static const EnsOBaseadaptorLeftjoin markerfeatureadaptorKLeftjoins[] =
{
{
"marker_synonym",
"marker.display_marker_synonym_id = marker_synonym.marker_synonym_id"
},
{(const char *) NULL, (const char *) NULL}
};
/* @conststatic markerfeatureadaptorKDefaultcondition *************************
**
** Ensembl Marker Feature Adaptor SQL SELECT default condition
**
******************************************************************************/
static const char *markerfeatureadaptorKDefaultcondition =
"marker_feature.marker_id = marker.marker_id";
/* ========================================================================= */
/* =========================== private variables =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private functions =========================== */
/* ========================================================================= */
static AjBool markersynonymadaptorFetchAllbyStatement(
EnsPDatabaseadaptor dba,
const AjPStr statement,
AjPList mss);
static AjBool markermaplocationadaptorFetchAllbyStatement(
EnsPDatabaseadaptor dba,
const AjPStr statement,
AjPList mmls);
static AjBool markeradaptorFetchAllbyStatement(
EnsPBaseadaptor ba,
const AjPStr statement,
EnsPAssemblymapper am,
EnsPSlice slice,
AjPList markers);
static int listMarkerfeatureCompareEndAscending(
const void *item1,
const void *item2);
static int listMarkerfeatureCompareEndDescending(
const void *item1,
const void *item2);
static int listMarkerfeatureCompareIdentifierAscending(
const void *item1,
const void *item2);
static int listMarkerfeatureCompareStartAscending(
const void *item1,
const void *item2);
static int listMarkerfeatureCompareStartDescending(
const void *item1,
const void *item2);
static AjBool markerfeatureadaptorFetchAllbyStatement(
EnsPBaseadaptor ba,
const AjPStr statement,
EnsPAssemblymapper am,
EnsPSlice slice,
AjPList mfs);
/* ========================================================================= */
/* ======================= All functions by section ======================== */
/* ========================================================================= */
/* @filesection ensmarker *****************************************************
**
** @nam1rule ens Function belongs to the Ensembl library
**
******************************************************************************/
/* @datasection [EnsPMarkersynonym] Ensembl Marker Synonym ********************
**
** @nam2rule Markersynonym Functions for manipulating
** Ensembl Marker Synonym objects
**
** @cc Bio::EnsEMBL::Map::MarkerSynonym
** @cc CVS Revision: 1.7
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Marker Synonym by pointer.
** It is the responsibility of the user to first destroy any previous
** Marker Synonym. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPMarkersynonym]
**
** @nam3rule New Constructor
** @nam4rule Cpy Constructor with existing object
** @nam4rule Ini Constructor with initial values
** @nam4rule Ref Constructor by incrementing the reference counter
**
** @argrule Cpy ms [const EnsPMarkersynonym] Ensembl Marker Synonym
** @argrule Ini identifier [ajuint] SQL database-internal identifier
** @argrule Ini source [AjPStr] Source
** @argrule Ini name [AjPStr] Name
** @argrule Ref ms [EnsPMarkersynonym] Ensembl Marker Synonym
**
** @valrule * [EnsPMarkersynonym] Ensembl Marker Synonym or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensMarkersynonymNewCpy ***********************************************
**
** Object-based constructor function, which returns an independent object.
**
** @param [r] ms [const EnsPMarkersynonym] Ensembl Marker Synonym
**
** @return [EnsPMarkersynonym] Ensembl Marker Synonym or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPMarkersynonym ensMarkersynonymNewCpy(const EnsPMarkersynonym ms)
{
EnsPMarkersynonym pthis = NULL;
if (!ms)
return NULL;
AJNEW0(pthis);
pthis->Use = 1U;
pthis->Identifier = ms->Identifier;
if (ms->Source)
pthis->Source = ajStrNewRef(ms->Source);
if (ms->Name)
pthis->Name = ajStrNewRef(ms->Name);
return pthis;
}
/* @func ensMarkersynonymNewIni ***********************************************
**
** Constructor for an Ensembl Marker Synonym with initial values.
**
** @cc Bio::EnsEMBL::Map::MarkerSynonym::new
** @param [r] identifier [ajuint] SQL database-internal identifier
** @param [u] source [AjPStr] Source
** @param [u] name [AjPStr] Name
**
** @return [EnsPMarkersynonym] Ensembl Marker Synonym or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPMarkersynonym ensMarkersynonymNewIni(ajuint identifier,
AjPStr source,
AjPStr name)
{
EnsPMarkersynonym ms = NULL;
AJNEW0(ms);
ms->Use = 1U;
ms->Identifier = identifier;
if (source)
ms->Source = ajStrNewRef(source);
if (name)
ms->Name = ajStrNewRef(name);
return ms;
}
/* @func ensMarkersynonymNewRef ***********************************************
**
** Ensembl Object referencing function, which returns a pointer to the
** Ensembl Object passed in and increases its reference count.
**
** @param [u] ms [EnsPMarkersynonym] Ensembl Marker Synonym
**
** @return [EnsPMarkersynonym] Ensembl Marker Synonym or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPMarkersynonym ensMarkersynonymNewRef(EnsPMarkersynonym ms)
{
if (!ms)
return NULL;
ms->Use++;
return ms;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Marker Synonym object.
**
** @fdata [EnsPMarkersynonym]
**
** @nam3rule Del Destroy (free) an Ensembl Marker Synonym
**
** @argrule * Pms [EnsPMarkersynonym*] Ensembl Marker Synonym address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensMarkersynonymDel **************************************************
**
** Default destructor for an Ensembl Marker Synonym.
**
** @param [d] Pms [EnsPMarkersynonym*] Ensembl Marker Synonym address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensMarkersynonymDel(EnsPMarkersynonym *Pms)
{
EnsPMarkersynonym pthis = NULL;
if (!Pms)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensMarkersynonymDel"))
{
ajDebug("ensMarkersynonymDel\n"
" *Pms %p\n",
*Pms);
ensMarkersynonymTrace(*Pms, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Pms) || --pthis->Use)
{
*Pms = NULL;
return;
}
ajStrDel(&pthis->Source);
ajStrDel(&pthis->Name);
ajMemFree((void **) Pms);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Marker Synonym object.
**
** @fdata [EnsPMarkersynonym]
**
** @nam3rule Get Return Marker Synonym attribute(s)
** @nam4rule Identifier Return the SQL database-internal identifier
** @nam4rule Name Return the name
** @nam4rule Source Return the source
**
** @argrule * ms [const EnsPMarkersynonym] Ensembl Marker Synonym
**
** @valrule Identifier [ajuint] SQL database-internal identifier or 0U
** @valrule Name [AjPStr] Name or NULL
** @valrule Source [AjPStr] Source or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensMarkersynonymGetIdentifier ****************************************
**
** Get the SQL database-internal identifier member of an
** Ensembl Marker Synonym.
**
** @cc Bio::EnsEMBL::Map::MarkerSynonym::dbID
** @param [r] ms [const EnsPMarkersynonym] Ensembl Marker Synonym
**
** @return [ajuint] SQL database-internal identifier or 0U
**
** @release 6.2.0
** @@
******************************************************************************/
ajuint ensMarkersynonymGetIdentifier(const EnsPMarkersynonym ms)
{
return (ms) ? ms->Identifier : 0U;
}
/* @func ensMarkersynonymGetName **********************************************
**
** Get the name member of an Ensembl Marker Synonym.
**
** @cc Bio::EnsEMBL::Map::MarkerSynonym::name
** @param [r] ms [const EnsPMarkersynonym] Ensembl Marker Synonym
**
** @return [AjPStr] Name or NULL
**
** @release 6.3.0
** @@
******************************************************************************/
AjPStr ensMarkersynonymGetName(const EnsPMarkersynonym ms)
{
return (ms) ? ms->Name : NULL;
}
/* @func ensMarkersynonymGetSource ********************************************
**
** Get the source member of an Ensembl Marker Synonym.
**
** @cc Bio::EnsEMBL::Map::MarkerSynonym::source
** @param [r] ms [const EnsPMarkersynonym] Ensembl Marker Synonym
**
** @return [AjPStr] Source or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
AjPStr ensMarkersynonymGetSource(const EnsPMarkersynonym ms)
{
return (ms) ? ms->Source : NULL;
}
/* @section member assignment *************************************************
**
** Functions for assigning members of an Ensembl Marker Synonym object.
**
** @fdata [EnsPMarkersynonym]
**
** @nam3rule Set Set one member of an Ensembl Marker Synonym
** @nam4rule Identifier Set the SQL database-internal identifier
** @nam4rule Name Set the name
** @nam4rule Source Set the source
**
** @argrule * ms [EnsPMarkersynonym] Ensembl Marker Synonym
** @argrule Identifier identifier [ajuint] SQL database-internal identifier
** @argrule Name name [AjPStr] Name
** @argrule Source source [AjPStr] Source
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory modify
******************************************************************************/
/* @func ensMarkersynonymSetIdentifier ****************************************
**
** Set the SQL database-internal identifier member of an
** Ensembl Marker Synonym.
**
** @cc Bio::EnsEMBL::Map::MarkerSynonym::dbID
** @param [u] ms [EnsPMarkersynonym] Ensembl Marker Synonym
** @param [r] identifier [ajuint] SQL database-internal identifier
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkersynonymSetIdentifier(EnsPMarkersynonym ms, ajuint identifier)
{
if (!ms)
return ajFalse;
ms->Identifier = identifier;
return ajTrue;
}
/* @func ensMarkersynonymSetName **********************************************
**
** Set the name member of an Ensembl Marker Synonym.
**
** @cc Bio::EnsEMBL::Map::MarkerSynonym::name
** @param [u] ms [EnsPMarkersynonym] Ensembl Marker Synonym
** @param [u] name [AjPStr] Name
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkersynonymSetName(EnsPMarkersynonym ms, AjPStr name)
{
if (!ms)
return ajFalse;
ajStrDel(&ms->Name);
ms->Name = ajStrNewRef(name);
return ajTrue;
}
/* @func ensMarkersynonymSetSource ********************************************
**
** Set the source member of an Ensembl Marker Synonym.
**
** @cc Bio::EnsEMBL::Map::MarkerSynonym::source
** @param [u] ms [EnsPMarkersynonym] Ensembl Marker Synonym
** @param [u] source [AjPStr] Source
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkersynonymSetSource(EnsPMarkersynonym ms, AjPStr source)
{
if (!ms)
return ajFalse;
ajStrDel(&ms->Source);
ms->Source = ajStrNewRef(source);
return ajTrue;
}
/* @section debugging *********************************************************
**
** Functions for reporting of an Ensembl Marker Synonym object.
**
** @fdata [EnsPMarkersynonym]
**
** @nam3rule Trace Report Ensembl Marker Synonym members to debug file.
**
** @argrule Trace ms [const EnsPMarkersynonym] Ensembl Marker Synonym
** @argrule Trace level [ajuint] Indentation level
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensMarkersynonymTrace ************************************************
**
** Trace an Ensembl Marker Synonym.
**
** @param [r] ms [const EnsPMarkersynonym] Ensembl Marker Synonym
** @param [r] level [ajuint] Indentation level
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkersynonymTrace(const EnsPMarkersynonym ms, ajuint level)
{
AjPStr indent = NULL;
if (!ms)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensMarkersynonymTrace %p\n"
"%S Use %u\n"
"%S Identifier %u\n"
"%S Source '%S'\n"
"%S Name '%S'\n",
indent, ms,
indent, ms->Use,
indent, ms->Identifier,
indent, ms->Source,
indent, ms->Name);
ajStrDel(&indent);
return ajTrue;
}
/* @section calculate *********************************************************
**
** Functions for calculating information from an Ensembl Marker Synonym object.
**
** @fdata [EnsPMarkersynonym]
**
** @nam3rule Calculate Calculate Ensembl Marker Synonym information
** @nam4rule Memsize Calculate the memory size in bytes
**
** @argrule * ms [const EnsPMarkersynonym] Ensembl Marker Synonym
**
** @valrule Memsize [size_t] Memory size in bytes or 0
**
** @fcategory misc
******************************************************************************/
/* @func ensMarkersynonymCalculateMemsize *************************************
**
** Calculate the memory size in bytes of an Ensembl Marker Synonym.
**
** @param [r] ms [const EnsPMarkersynonym] Ensembl Marker Synonym
**
** @return [size_t] Memory size in bytes or 0
**
** @release 6.4.0
** @@
******************************************************************************/
size_t ensMarkersynonymCalculateMemsize(const EnsPMarkersynonym ms)
{
size_t size = 0;
if (!ms)
return 0;
size += sizeof (EnsOMarkersynonym);
if (ms->Source)
{
size += sizeof (AjOStr);
size += ajStrGetRes(ms->Source);
}
if (ms->Name)
{
size += sizeof (AjOStr);
size += ajStrGetRes(ms->Name);
}
return size;
}
/* @datasection [EnsPMarkersynonymadaptor] Ensembl Marker Synonym Adaptor *****
**
** @nam2rule Markersynonymadaptor Functions for manipulating
** Ensembl Marker Synonym Adaptor objects
**
******************************************************************************/
/* @funcstatic markersynonymadaptorFetchAllbyStatement ************************
**
** Run a SQL statement against an Ensembl Database Adaptor and consolidate the
** results into an AJAX List of Ensembl Marker Synonym objects.
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [r] statement [const AjPStr] SQL statement
** @param [u] mss [AjPList] AJAX List of Ensembl Marker Synonym objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
static AjBool markersynonymadaptorFetchAllbyStatement(
EnsPDatabaseadaptor dba,
const AjPStr statement,
AjPList mss)
{
ajuint identifier = 0U;
AjPSqlstatement sqls = NULL;
AjISqlrow sqli = NULL;
AjPSqlrow sqlr = NULL;
AjPStr name = NULL;
AjPStr source = NULL;
EnsPMarkersynonym ms = NULL;
if (!dba)
return ajFalse;
if (!statement)
return ajFalse;
if (!mss)
return ajFalse;
sqls = ensDatabaseadaptorSqlstatementNew(dba, statement);
sqli = ajSqlrowiterNew(sqls);
while (!ajSqlrowiterDone(sqli))
{
identifier = 0;
name = ajStrNew();
source = ajStrNew();
sqlr = ajSqlrowiterGet(sqli);
ajSqlcolumnToUint(sqlr, &identifier);
ajSqlcolumnToStr(sqlr, &name);
ajSqlcolumnToStr(sqlr, &source);
ms = ensMarkersynonymNewIni(identifier, source, name);
ajListPushAppend(mss, (void *) ms);
ajStrDel(&name);
ajStrDel(&source);
}
ajSqlrowiterDel(&sqli);
ensDatabaseadaptorSqlstatementDel(dba, &sqls);
return ajTrue;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an
** Ensembl Marker Synonym Adaptor object.
**
** @fdata [EnsPMarkersynonymadaptor]
**
** @nam3rule Get Return Marker Synonym Adaptor attribute(s)
** @nam4rule Databaseadaptor Return the Ensembl Database Adaptor
**
** @argrule * msa [EnsPMarkersynonymadaptor] Ensembl Marker Synonym Adaptor
**
** @valrule Databaseadaptor [EnsPDatabaseadaptor]
** Ensembl Database Adaptor or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensMarkersynonymadaptorGetDatabaseadaptor ****************************
**
** Get the Ensembl Database Adaptor member of an
** Ensembl Marker Synonym Adaptor.
**
** @param [u] msa [EnsPMarkersynonymadaptor] Ensembl Marker Synonym Adaptor
**
** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
**
** @release 6.5.0
** @@
******************************************************************************/
EnsPDatabaseadaptor ensMarkersynonymadaptorGetDatabaseadaptor(
EnsPMarkersynonymadaptor msa)
{
return msa;
}
/* @section object retrieval **************************************************
**
** Functions for fetching Ensembl Marker Synonym Adaptor objects from an
** Ensembl SQL database.
**
** @fdata [EnsPMarkersynonymadaptor]
**
** @nam3rule Fetch Fetch Ensembl Marker Synonym object(s)
** @nam4rule All Fetch all Ensembl Marker Synonym objects
** @nam4rule Allby Fetch all Ensembl Marker Synonym objects matching a
** criterion
** @nam5rule Markeridentifier Fetch all by an Ensembl Marker identifier
** @nam4rule By Fetch one Ensembl Marker Synonym object matching a criterion
** @nam5rule Identifier Fetch by an SQL database-internal identifier
**
** @argrule * msa [EnsPMarkersynonymadaptor] Ensembl Marker Synonym Adaptor
** @argrule AllbyMarkeridentifier markerid [ajuint] Ensembl Marker identifier
** @argrule AllbyMarkeridentifier mss [AjPList]
** AJAX List of Ensembl Marker Synonym objects
** @argrule ByIdentifier identifier [ajuint] SQL database-internal identifier
** @argrule ByIdentifier Pms [EnsPMarkersynonym*]
** Ensembl Marker Synonym address
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensMarkersynonymadaptorFetchAllbyMarkeridentifier ********************
**
** Fetch all Ensembl Marker Synonym objects by an Ensembl Marker identifier.
**
** The caller is responsible for deleting the Ensembl Marker Synonym objects
** before deleting the AJAX List.
**
** @param [u] msa [EnsPMarkersynonymadaptor] Ensembl MArker Synonym Adaptor
** @param [r] markerid [ajuint] Ensembl Marker identifier
** @param [u] mss [AjPList] AJAX List of Ensembl Marker Synonym objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkersynonymadaptorFetchAllbyMarkeridentifier(
EnsPMarkersynonymadaptor msa,
ajuint markerid,
AjPList mss)
{
AjBool result = AJFALSE;
AjPStr statement = NULL;
EnsPDatabaseadaptor dba = NULL;
if (!msa)
return ajFalse;
if (!markerid)
return ajFalse;
if (!mss)
return ajFalse;
dba = ensMarkersynonymadaptorGetDatabaseadaptor(msa);
statement = ajFmtStr(
"SELECT "
"marker_synonym.marker_synonym_id, "
"marker_synonym.source, "
"marker_synonym.name "
"FROM "
"marker_synonym "
"WHERE "
"marker_synonym.marker_id = %u",
markerid);
result = markersynonymadaptorFetchAllbyStatement(dba, statement, mss);
ajStrDel(&statement);
return result;
}
/* @func ensMarkersynonymadaptorFetchByIdentifier *****************************
**
** Fetch an Ensembl Marker Synonym via its SQL database-internal identifier.
**
** The caller is responsible for deleting the Ensembl Marker Synonym.
**
** @param [u] msa [EnsPMarkersynonymadaptor] Ensembl Marker Synonym Adaptor
** @param [r] identifier [ajuint] SQL database-internal identifier
** @param [wP] Pms [EnsPMarkersynonym*] Ensembl Marker Synonym address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkersynonymadaptorFetchByIdentifier(
EnsPMarkersynonymadaptor msa,
ajuint identifier,
EnsPMarkersynonym *Pms)
{
AjBool result = AJFALSE;
AjPList mss = NULL;
AjPStr statement = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPMarkersynonym ms = NULL;
if (!dba)
return ajFalse;
if (!identifier)
return ajFalse;
if (!Pms)
return ajFalse;
*Pms = NULL;
dba = ensMarkersynonymadaptorGetDatabaseadaptor(msa);
statement = ajFmtStr(
"SELECT "
"marker_synonym.marker_synonym_id, "
"marker_synonym.source, "
"marker_synonym.name "
"FROM "
"marker_synonym "
"WHERE "
"marker_synonym.marker_synonym_id = %u",
identifier);
mss = ajListNew();
result = markersynonymadaptorFetchAllbyStatement(dba, statement, mss);
if (ajListGetLength(mss) > 1)
ajWarn("ensMarkersynonymadaptorFetchByIdentifier got more than one "
"Ensembl Marker Synonym for identifier %u.\n",
identifier);
ajListPop(mss, (void **) Pms);
while (ajListPop(mss, (void **) &ms))
ensMarkersynonymDel(&ms);
ajListFree(&mss);
ajStrDel(&statement);
return result;
}
/* @datasection [EnsPMarkermaplocation] Ensembl Marker Map Location ***********
**
** @nam2rule Markermaplocation Functions for manipulating
** Ensembl Marker Map Location objects
**
** @cc Bio::EnsEMBL::Map::MapLocation
** @cc CVS Revision: 1.8
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Marker Map Location by pointer.
** It is the responsibility of the user to first destroy any previous
** Marker Map Location. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPMarkermaplocation]
**
** @nam3rule New Constructor
** @nam4rule Cpy Constructor with existing object
** @nam4rule Ini Constructor with initial values
** @nam4rule Ref Constructor by incrementing the reference counter
**
** @argrule Cpy mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
** @argrule Ini ms [EnsPMarkersynonym] Ensembl Marker Synonym
** @argrule Ini mapname [AjPStr] Map name
** @argrule Ini chrname [AjPStr] Chromosome name
** @argrule Ini position [AjPStr] Position
** @argrule Ini lodscore [float] LOD score
** @argrule Ref mml [EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @valrule * [EnsPMarkermaplocation] Ensembl Marker Map Location or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensMarkermaplocationNewCpy *******************************************
**
** Object-based constructor function, which returns an independent object.
**
** @param [r] mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @return [EnsPMarkermaplocation] Ensembl Marker Map Location or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPMarkermaplocation ensMarkermaplocationNewCpy(
const EnsPMarkermaplocation mml)
{
EnsPMarkermaplocation pthis = NULL;
if (!mml)
return NULL;
AJNEW0(pthis);
pthis->Markersynonym = ensMarkersynonymNewRef(mml->Markersynonym);
if (mml->Mapname)
pthis->Mapname = ajStrNewRef(mml->Mapname);
if (mml->Chromosomename)
pthis->Chromosomename = ajStrNewRef(mml->Chromosomename);
if (mml->Position)
pthis->Position = ajStrNewRef(mml->Position);
pthis->Lodscore = mml->Lodscore;
pthis->Use = 1U;
return pthis;
}
/* @func ensMarkermaplocationNewIni *******************************************
**
** Constructor for an Ensembl Marker Map Location with initial values.
**
** @cc Bio::EnsEMBL::Map::MapLocation::new
** @param [u] ms [EnsPMarkersynonym] Ensembl Marker Synonym
** @param [u] mapname [AjPStr] Map name
** @param [u] chrname [AjPStr] Chromosome name
** @param [u] position [AjPStr] Position
** @param [r] lodscore [float] LOD score
**
** @return [EnsPMarkermaplocation] Ensembl Marker Map Location or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPMarkermaplocation ensMarkermaplocationNewIni(EnsPMarkersynonym ms,
AjPStr mapname,
AjPStr chrname,
AjPStr position,
float lodscore)
{
EnsPMarkermaplocation mml = NULL;
AJNEW0(mml);
mml->Markersynonym = ensMarkersynonymNewRef(ms);
if (mapname)
mml->Mapname = ajStrNewRef(mapname);
if (chrname)
mml->Chromosomename = ajStrNewRef(chrname);
if (position)
mml->Position = ajStrNewRef(position);
mml->Lodscore = lodscore;
mml->Use = 1U;
return mml;
}
/* @func ensMarkermaplocationNewRef *******************************************
**
** Ensembl Object referencing function, which returns a pointer to the
** Ensembl Object passed in and increases its reference count.
**
** @param [u] mml [EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @return [EnsPMarkermaplocation] Ensembl Marker Map Location or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPMarkermaplocation ensMarkermaplocationNewRef(EnsPMarkermaplocation mml)
{
if (!mml)
return NULL;
mml->Use++;
return mml;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Marker Map Location object.
**
** @fdata [EnsPMarkermaplocation]
**
** @nam3rule Del Destroy (free) an Ensembl Marker Map Location
**
** @argrule * Pmml [EnsPMarkermaplocation*] Ensembl Marker Map Location address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensMarkermaplocationDel **********************************************
**
** Default destructor for an Ensembl Marker Map Location.
**
** @param [d] Pmml [EnsPMarkermaplocation*] Ensembl Marker Map Location address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensMarkermaplocationDel(EnsPMarkermaplocation *Pmml)
{
EnsPMarkermaplocation pthis = NULL;
if (!Pmml)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensMarkermaplocationDel"))
{
ajDebug("ensMarkermaplocationDel\n"
" *Pmml %p\n",
*Pmml);
ensMarkermaplocationTrace(*Pmml, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Pmml) || --pthis->Use)
{
*Pmml = NULL;
return;
}
ensMarkersynonymDel(&pthis->Markersynonym);
ajStrDel(&pthis->Mapname);
ajStrDel(&pthis->Chromosomename);
ajStrDel(&pthis->Position);
ajMemFree((void **) Pmml);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Marker Map Location object.
**
** @fdata [EnsPMarkermaplocation]
**
** @nam3rule Get Return Marker Map Location attribute(s)
** @nam4rule Chromosomename Return the chromosome name
** @nam4rule Lodscore Return the LOD score
** @nam4rule Mapname Return the map name
** @nam4rule Markersynonym Return the Ensembl Marker Synonym
** @nam4rule Position Return the position
**
** @argrule * mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @valrule Chromosomename [AjPStr] Chromosome name or NULL
** @valrule Lodscore [float] LOD score or 0.0F
** @valrule Mapname [AjPStr] Map name or NULL
** @valrule Markersynonym [EnsPMarkersynonym] Ensembl Marker Synonym or NULL
** @valrule Position [AjPStr] Position or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensMarkermaplocationGetChromosomename ********************************
**
** Get the chromosome name member of an Ensembl Marker Map Location.
**
** @cc Bio::EnsEMBL::Map::MapLocation::chromosome_name
** @param [r] mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @return [AjPStr] Chromosome name or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjPStr ensMarkermaplocationGetChromosomename(const EnsPMarkermaplocation mml)
{
return (mml) ? mml->Chromosomename : NULL;
}
/* @func ensMarkermaplocationGetLodscore **************************************
**
** Get the LOD score member of an Ensembl Marker Map Location.
**
** @cc Bio::EnsEMBL::Map::MapLocation::lod_score
** @param [r] mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @return [float] LOD score or 0.0F
**
** @release 6.4.0
** @@
******************************************************************************/
float ensMarkermaplocationGetLodscore(const EnsPMarkermaplocation mml)
{
return (mml) ? mml->Lodscore : 0.0F;
}
/* @func ensMarkermaplocationGetMapname ***************************************
**
** Get the map name member of an Ensembl Marker Map Location.
**
** @cc Bio::EnsEMBL::Map::MapLocation::map_name
** @param [r] mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @return [AjPStr] Map name or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjPStr ensMarkermaplocationGetMapname(const EnsPMarkermaplocation mml)
{
return (mml) ? mml->Mapname : NULL;
}
/* @func ensMarkermaplocationGetMarkersynonym *********************************
**
** Get the Ensembl Marker Synonym member of an Ensembl Marker Map Location.
**
** @cc Bio::EnsEMBL::Map::MapLocation::name
** @param [r] mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @return [EnsPMarkersynonym] Ensembl Marker Synonym or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPMarkersynonym ensMarkermaplocationGetMarkersynonym(
const EnsPMarkermaplocation mml)
{
return (mml) ? mml->Markersynonym : NULL;
}
/* @func ensMarkermaplocationGetPosition **************************************
**
** Get the position member of an Ensembl Marker Map Location.
**
** @cc Bio::EnsEMBL::Map::MapLocation::position
** @param [r] mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @return [AjPStr] Position or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
AjPStr ensMarkermaplocationGetPosition(const EnsPMarkermaplocation mml)
{
return (mml) ? mml->Position : NULL;
}
/* @section member assignment *************************************************
**
** Functions for assigning members of an Ensembl Marker Map Location object.
**
** @fdata [EnsPMarkermaplocation]
**
** @nam3rule Set Set one member of an Ensembl Marker Map Location
** @nam4rule Chromosomename Set the chromosome name
** @nam4rule Lodscore Set the LOD score
** @nam4rule Mapname Set the map name
** @nam4rule Markersynonym Set the Ensembl Marker Synonym
** @nam4rule Position Set the position
**
** @argrule * mml [EnsPMarkermaplocation] Ensembl Marker Map Location
** @argrule Chromosomename chrname [AjPStr] Chromosome name
** @argrule Lodscore lodscore [float] LOD score
** @argrule Mapname mapname [AjPStr] Map name
** @argrule Markersynonym ms [EnsPMarkersynonym] Ensembl Marker Synonym
** @argrule Position position [AjPStr] Position
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory modify
******************************************************************************/
/* @func ensMarkermaplocationSetChromosomename ********************************
**
** Set the chromosome name member of an Ensembl Marker Map Location.
**
** @cc Bio::EnsEMBL::Map::MapLocation::chromosome_name
** @param [u] mml [EnsPMarkermaplocation] Ensembl Marker Map Location
** @param [u] chrname [AjPStr] Chromosome name
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkermaplocationSetChromosomename(EnsPMarkermaplocation mml,
AjPStr chrname)
{
if (!mml)
return ajFalse;
ajStrDel(&mml->Chromosomename);
mml->Chromosomename = ajStrNewRef(chrname);
return ajTrue;
}
/* @func ensMarkermaplocationSetLodscore **************************************
**
** Set the LOD score member of an Ensembl Marker Map Location.
**
** @cc Bio::EnsEMBL::Map::MapLocation::lod_score
** @param [u] mml [EnsPMarkermaplocation] Ensembl Marker Map Location
** @param [r] lodscore [float] LOD score
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkermaplocationSetLodscore(EnsPMarkermaplocation mml,
float lodscore)
{
if (!mml)
return ajFalse;
mml->Lodscore = lodscore;
return ajTrue;
}
/* @func ensMarkermaplocationSetMapname ***************************************
**
** Set the map name member of an Ensembl Marker Map Location.
**
** @cc Bio::EnsEMBL::Map::MapLocation::map_name
** @param [u] mml [EnsPMarkermaplocation] Ensembl Marker Map Location
** @param [u] mapname [AjPStr] Map name
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkermaplocationSetMapname(EnsPMarkermaplocation mml,
AjPStr mapname)
{
if (!mml)
return ajFalse;
ajStrDel(&mml->Mapname);
mml->Mapname = ajStrNewRef(mapname);
return ajTrue;
}
/* @func ensMarkermaplocationSetMarkersynonym *********************************
**
** Set the Ensembl Marker Synonym member of an Ensembl Marker Map Location.
**
** @cc Bio::EnsEMBL::Map::MapLocation::name
** @param [u] mml [EnsPMarkermaplocation] Ensembl Marker Map Location
** @param [u] ms [EnsPMarkersynonym] Ensembl Marker Synonym
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkermaplocationSetMarkersynonym(EnsPMarkermaplocation mml,
EnsPMarkersynonym ms)
{
if (!mml)
return ajFalse;
ensMarkersynonymDel(&mml->Markersynonym);
mml->Markersynonym = ensMarkersynonymNewRef(ms);
return ajTrue;
}
/* @func ensMarkermaplocationSetPosition **************************************
**
** Set the position member of an Ensembl Marker Map Location.
**
** @cc Bio::EnsEMBL::Map::MapLocation::position
** @param [u] mml [EnsPMarkermaplocation] Ensembl Marker Map Location
** @param [u] position [AjPStr] Position
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkermaplocationSetPosition(EnsPMarkermaplocation mml,
AjPStr position)
{
if (!mml)
return ajFalse;
ajStrDel(&mml->Position);
mml->Position = ajStrNewRef(position);
return ajTrue;
}
/* @section debugging *********************************************************
**
** Functions for reporting of an Ensembl Marker Map Location object.
**
** @fdata [EnsPMarkermaplocation]
**
** @nam3rule Trace Report Ensembl Marker Map Location members to debug file.
**
** @argrule Trace mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
** @argrule Trace level [ajuint] Indentation level
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensMarkermaplocationTrace ********************************************
**
** Trace an Ensembl Marker Map Location.
**
** @param [r] mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
** @param [r] level [ajuint] Indentation level
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkermaplocationTrace(const EnsPMarkermaplocation mml,
ajuint level)
{
AjPStr indent = NULL;
if (!mml)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensMarkermaplocationTrace %p\n"
"%S Markersynonym %p\n"
"%S Mapname '%S'\n"
"%S Chromosomename '%S'\n"
"%S Position '%S'\n"
"%S Lodscore %f\n"
"%S Use %u\n",
indent, mml,
indent, mml->Use,
indent, mml->Markersynonym,
indent, mml->Mapname,
indent, mml->Chromosomename,
indent, mml->Lodscore);
ensMarkersynonymTrace(mml->Markersynonym, level + 1);
ajStrDel(&indent);
return ajTrue;
}
/* @section calculate *********************************************************
**
** Functions for calculating information from an
** Ensembl Marker Map Location object.
**
** @fdata [EnsPMarkermaplocation]
**
** @nam3rule Calculate Calculate Ensembl Marker Map Location information
** @nam4rule Memsize Calculate the memory size in bytes
**
** @argrule * mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @valrule Memsize [size_t] Memory size in bytes or 0
**
** @fcategory misc
******************************************************************************/
/* @func ensMarkermaplocationCalculateMemsize *********************************
**
** Calculate the memory size in bytes of an Ensembl Marker Map Location.
**
** @param [r] mml [const EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @return [size_t] Memory size in bytes or 0
**
** @release 6.4.0
** @@
******************************************************************************/
size_t ensMarkermaplocationCalculateMemsize(const EnsPMarkermaplocation mml)
{
size_t size = 0;
if (!mml)
return 0;
size += sizeof (EnsOMarkermaplocation);
size += ensMarkersynonymCalculateMemsize(mml->Markersynonym);
if (mml->Mapname)
{
size += sizeof (AjOStr);
size += ajStrGetRes(mml->Mapname);
}
if (mml->Chromosomename)
{
size += sizeof (AjOStr);
size += ajStrGetRes(mml->Chromosomename);
}
if (mml->Position)
{
size += sizeof (AjOStr);
size += ajStrGetRes(mml->Position);
}
return size;
}
/* @datasection [EnsPMarkermaplocationadaptor]
** Ensembl Marker Map Location Adaptor
**
** @nam2rule Markermaplocationadaptor Functions for manipulating
** Ensembl Marker Map Location Adaptor objects
**
******************************************************************************/
/* @funcstatic markermaplocationadaptorFetchAllbyStatement ********************
**
** Run a SQL statement against an Ensembl Database Adaptor and consolidate the
** results into an AJAX List of Ensembl Marker Map Location objects.
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @param [r] statement [const AjPStr] SQL statement
** @param [u] mmls [AjPList] AJAX List of Ensembl Marker Map Location objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
static AjBool markermaplocationadaptorFetchAllbyStatement(
EnsPDatabaseadaptor dba,
const AjPStr statement,
AjPList mmls)
{
float lodscore = 0.0F;
ajuint msid = 0U;
AjPSqlstatement sqls = NULL;
AjISqlrow sqli = NULL;
AjPSqlrow sqlr = NULL;
AjPStr msname = NULL;
AjPStr mssource = NULL;
AjPStr chrname = NULL;
AjPStr position = NULL;
AjPStr mapname = NULL;
EnsPMarkersynonym ms = NULL;
EnsPMarkermaplocation mml = NULL;
if (!dba)
return ajFalse;
if (!statement)
return ajFalse;
if (!mmls)
return ajFalse;
sqls = ensDatabaseadaptorSqlstatementNew(dba, statement);
sqli = ajSqlrowiterNew(sqls);
while (!ajSqlrowiterDone(sqli))
{
chrname = ajStrNew();
position = ajStrNew();
lodscore = 0.0F;
mapname = ajStrNew();
msid = 0;
mssource = ajStrNew();
msname = ajStrNew();
sqlr = ajSqlrowiterGet(sqli);
ajSqlcolumnToStr(sqlr, &chrname);
ajSqlcolumnToStr(sqlr, &position);
ajSqlcolumnToFloat(sqlr, &lodscore);
ajSqlcolumnToStr(sqlr, &mapname);
ajSqlcolumnToUint(sqlr, &msid);
ajSqlcolumnToStr(sqlr, &mssource);
ajSqlcolumnToStr(sqlr, &msname);
ms = ensMarkersynonymNewIni(msid, mssource, msname);
mml = ensMarkermaplocationNewIni(ms,
mapname,
chrname,
position,
lodscore);
ajListPushAppend(mmls, (void *) mml);
ensMarkersynonymDel(&ms);
ajStrDel(&chrname);
ajStrDel(&position);
ajStrDel(&mapname);
ajStrDel(&msname);
ajStrDel(&mssource);
}
ajSqlrowiterDel(&sqli);
ensDatabaseadaptorSqlstatementDel(dba, &sqls);
return ajTrue;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an
** Ensembl Marker Map Location Adaptor object.
**
** @fdata [EnsPMarkermaplocationadaptor]
**
** @nam3rule Get Return Marker Map Location Adaptor attribute(s)
** @nam4rule Databaseadaptor Return the Ensembl Database Adaptor
**
** @argrule * mmla [EnsPMarkermaplocationadaptor]
** Ensembl Marker Map Location Adaptor
**
** @valrule Databaseadaptor [EnsPDatabaseadaptor]
** Ensembl Database Adaptor or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensMarkermaplocationadaptorGetDatabaseadaptor ************************
**
** Get the Ensembl Database Adaptor member of an
** Ensembl Marker Map Location Adaptor.
**
** @param [u] mmla [EnsPMarkermaplocationadaptor]
** Ensembl Marker Map Location Adaptor
**
** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
**
** @release 6.5.0
** @@
******************************************************************************/
EnsPDatabaseadaptor ensMarkermaplocationadaptorGetDatabaseadaptor(
EnsPMarkermaplocationadaptor mmla)
{
return mmla;
}
/* @section object retrieval **************************************************
**
** Functions for fetching Ensembl Marker Map Location Adaptor objects from an
** Ensembl SQL database.
**
** @fdata [EnsPMarkermaplocationadaptor]
**
** @nam3rule Fetch Fetch Ensembl Marker Map Location object(s)
** @nam4rule All Fetch all Ensembl Marker Map Location objects
** @nam4rule Allby Fetch all Ensembl Marker Map Location objects
** matching a criterion
** @nam5rule Markeridentifier Fetch all by an Ensembl Marker identifier
** @nam4rule By Fetch one Ensembl Marker Map Location object
** matching a criterion
** @nam5rule Identifier Fetch by an SQL database-internal identifier
**
** @argrule * mmla [EnsPMarkermaplocationadaptor]
** Ensembl Marker Map Location Adaptor
** @argrule AllbyMarkeridentifier markerid [ajuint] Ensembl Marker identifier
** @argrule AllbyMarkeridentifier mmls [AjPList]
** AJAX List of Ensembl Marker Map Location objects
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensMarkermaplocationadaptorFetchAllbyMarkeridentifier ****************
**
** Fetch all Ensembl Marker Map Location objects by an
** Ensembl Marker identifier.
**
** The caller is responsible for deleting the Ensembl Marker Map Location
** objects before deleting the AJAX List.
**
** @param [u] mmla [EnsPMarkermaplocationadaptor]
** Ensembl Marker Map Location Adaptor
** @param [r] markerid [ajuint] Ensembl Marker identifier
** @param [u] mmls [AjPList] AJAX List of Ensembl Marker Map Location objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkermaplocationadaptorFetchAllbyMarkeridentifier(
EnsPMarkermaplocationadaptor mmla,
ajuint markerid,
AjPList mmls)
{
AjBool result = AJFALSE;
AjPStr statement = NULL;
EnsPDatabaseadaptor dba = NULL;
if (!mmla)
return ajFalse;
if (!markerid)
return ajFalse;
if (!mmls)
return ajFalse;
dba = ensMarkermaplocationadaptorGetDatabaseadaptor(mmla);
statement = ajFmtStr(
"SELECT "
"marker_map_location.chromosome_name, "
"marker_map_location.position, "
"marker_map_location.lod_score, "
"map.map_name, "
"marker_synonym.marker_synonym_id, "
"marker_synonym.source, "
"marker_synonym.name, "
"FROM "
"marker_map_location, "
"map, "
"marker_synonym "
"WHERE "
"marker_map_location.marker_id = %u "
"AND "
"marker_map_location.map_id = map.map_id "
"AND "
"marker_map_location.marker_synonym_id = "
"marker_synonym.marker_synonym_id",
markerid);
result = markermaplocationadaptorFetchAllbyStatement(dba, statement, mmls);
ajStrDel(&statement);
return result;
}
/* @datasection [EnsPMarker] Ensembl Marker ***********************************
**
** @nam2rule Marker Functions for manipulating Ensembl Marker objects
**
** @cc Bio::EnsEMBL::Map::Marker
** @cc CVS Revision: 1.13
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Marker by pointer.
** It is the responsibility of the user to first destroy any previous
** Markers. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPMarker]
**
** @nam3rule New Constructor
** @nam4rule Cpy Constructor with existing object
** @nam4rule Ini Constructor with initial values
** @nam4rule Ref Constructor by incrementing the reference counter
**
** @argrule Cpy marker [const EnsPMarker] Ensembl Marker
** @argrule Ini ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
** @argrule Ini identifier [ajuint] SQL database-internal identifier
** @argrule Ini display [EnsPMarkersynonym] Ensembl Marker Synonym
** @argrule Ini lprimer [AjPStr] Left primer
** @argrule Ini rprimer [AjPStr] Right primer
** @argrule Ini mss [AjPList] AJAX List of Ensembl Marker Synonym objects
** @argrule Ini mmls [AjPList] AJAX List of Ensembl Marker Map Location objects
** @argrule Ini mindistance [ajuint] Minimum primer distance
** @argrule Ini maxdistance [ajuint] Maximum primer distance
** @argrule Ini type [EnsEMarkerType] Type
** @argrule Ini priority [ajint] Priority
** @argrule Ref marker [EnsPMarker] Ensembl Marker
**
** @valrule * [EnsPMarker] Ensembl Marker or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensMarkerNewCpy ******************************************************
**
** Object-based constructor function, which returns an independent object.
**
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [EnsPMarker] Ensembl Marker or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPMarker ensMarkerNewCpy(const EnsPMarker marker)
{
AjIList iter = NULL;
EnsPMarker pthis = NULL;
EnsPMarkermaplocation mml = NULL;
EnsPMarkersynonym ms = NULL;
if (!marker)
return NULL;
AJNEW0(pthis);
pthis->Use = 1U;
pthis->Identifier = marker->Identifier;
pthis->Adaptor = marker->Adaptor;
pthis->Displaysynonym = ensMarkersynonymNewRef(marker->Displaysynonym);
if (marker->PrimerLeft)
pthis->PrimerLeft = ajStrNewRef(marker->PrimerLeft);
if (marker->PrimerRight)
pthis->PrimerRight = ajStrNewRef(marker->PrimerRight);
/* Copy the AJAX List of Ensembl Marker Synonym objects. */
if (marker->Markersynonyms && ajListGetLength(marker->Markersynonyms))
{
pthis->Markersynonyms = ajListNew();
iter = ajListIterNew(marker->Markersynonyms);
while (!ajListIterDone(iter))
{
ms = (EnsPMarkersynonym) ajListIterGet(iter);
if (ms)
ajListPushAppend(pthis->Markersynonyms,
(void *) ensMarkersynonymNewRef(ms));
}
ajListIterDel(&iter);
}
else
pthis->Markersynonyms = NULL;
/* Copy the AJAX List of Ensembl Marker Map Location objects. */
if (marker->Markermaplocations &&
ajListGetLength(marker->Markermaplocations))
{
pthis->Markermaplocations = ajListNew();
iter = ajListIterNew(marker->Markermaplocations);
while (!ajListIterDone(iter))
{
mml = (EnsPMarkermaplocation) ajListIterGet(iter);
if (mml)
ajListPushAppend(pthis->Markermaplocations,
(void *) ensMarkermaplocationNewRef(mml));
}
ajListIterDel(&iter);
}
else
pthis->Markermaplocations = NULL;
pthis->DistanceMinimum = marker->DistanceMinimum;
pthis->DistanceMaximum = marker->DistanceMaximum;
pthis->Type = marker->Type;
pthis->Priority = marker->Priority;
return pthis;
}
/* @func ensMarkerNewIni ******************************************************
**
** Constructor for an Ensembl Marker with initial values.
**
** @cc Bio::EnsEMBL::Storable::new
** @param [u] ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
** @param [r] identifier [ajuint] SQL database-internal identifier
** @cc Bio::EnsEMBL::Map::Marker::new
** @param [u] display [EnsPMarkersynonym] Ensembl Marker Synonym
** @param [u] lprimer [AjPStr] Left primer
** @param [u] rprimer [AjPStr] Right primer
** @param [u] mss [AjPList] AJAX List of Ensembl Marker Synonym objects
** @param [u] mmls [AjPList] AJAX List of Ensembl Marker Map Location objects
** @param [r] mindistance [ajuint] Minimum primer distance
** @param [r] maxdistance [ajuint] Maximum primer distance
** @param [u] type [EnsEMarkerType] Type
** @param [r] priority [ajint] Priority
**
** @return [EnsPMarker] Ensembl Marker or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPMarker ensMarkerNewIni(EnsPMarkeradaptor ma,
ajuint identifier,
EnsPMarkersynonym display,
AjPStr lprimer,
AjPStr rprimer,
AjPList mss,
AjPList mmls,
ajuint mindistance,
ajuint maxdistance,
EnsEMarkerType type,
ajint priority)
{
AjIList iter = NULL;
EnsPMarker marker = NULL;
EnsPMarkermaplocation mml = NULL;
EnsPMarkersynonym ms = NULL;
AJNEW0(marker);
marker->Use = 1U;
marker->Identifier = identifier;
marker->Adaptor = ma;
marker->Displaysynonym = ensMarkersynonymNewRef(display);
if (lprimer)
marker->PrimerLeft = ajStrNewRef(lprimer);
if (rprimer)
marker->PrimerRight = ajStrNewRef(rprimer);
/* Copy the AJAX List of Ensembl Marker Synonym objects. */
if (mss && ajListGetLength(mss))
{
marker->Markersynonyms = ajListNew();
iter = ajListIterNew(mss);
while (!ajListIterDone(iter))
{
ms = (EnsPMarkersynonym) ajListIterGet(iter);
if (ms)
ajListPushAppend(marker->Markersynonyms,
(void *) ensMarkersynonymNewRef(ms));
}
ajListIterDel(&iter);
}
else
marker->Markersynonyms = NULL;
/* Copy the AJAX List of Ensembl Marker Map Location objects. */
if (mmls && ajListGetLength(mmls))
{
marker->Markermaplocations = ajListNew();
iter = ajListIterNew(mmls);
while (!ajListIterDone(iter))
{
mml = (EnsPMarkermaplocation) ajListIterGet(iter);
if (mml)
ajListPushAppend(marker->Markermaplocations,
(void *) ensMarkermaplocationNewRef(mml));
}
ajListIterDel(&iter);
}
else
marker->Markermaplocations = NULL;
marker->DistanceMinimum = mindistance;
marker->DistanceMaximum = maxdistance;
marker->Type = type;
marker->Priority = priority;
return marker;
}
/* @func ensMarkerNewRef ******************************************************
**
** Ensembl Object referencing function, which returns a pointer to the
** Ensembl Object passed in and increases its reference count.
**
** @param [u] marker [EnsPMarker] Ensembl Marker
**
** @return [EnsPMarker] Ensembl Marker or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPMarker ensMarkerNewRef(EnsPMarker marker)
{
if (!marker)
return NULL;
marker->Use++;
return marker;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Marker object.
**
** @fdata [EnsPMarker]
**
** @nam3rule Del Destroy (free) an Ensembl Marker
**
** @argrule * Pmarker [EnsPMarker*] Ensembl Marker address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensMarkerDel *********************************************************
**
** Default destructor for an Ensembl Marker.
**
** @param [d] Pmarker [EnsPMarker*] Ensembl Marker address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensMarkerDel(EnsPMarker *Pmarker)
{
EnsPMarkermaplocation mml = NULL;
EnsPMarkersynonym ms = NULL;
EnsPMarker pthis = NULL;
if (!Pmarker)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensMarkerDel"))
{
ajDebug("ensMarkerDel\n"
" *Pmarker %p\n",
*Pmarker);
ensMarkerTrace(*Pmarker, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Pmarker) || --pthis->Use)
{
*Pmarker = NULL;
return;
}
ajStrDel(&pthis->PrimerLeft);
ajStrDel(&pthis->PrimerRight);
ensMarkersynonymDel(&pthis->Displaysynonym);
while (ajListPop(pthis->Markersynonyms, (void **) &ms))
ensMarkersynonymDel(&ms);
ajListFree(&pthis->Markersynonyms);
while (ajListPop(pthis->Markermaplocations, (void **) &mml))
ensMarkermaplocationDel(&mml);
ajListFree(&pthis->Markermaplocations);
ajMemFree((void **) Pmarker);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Marker object.
**
** @fdata [EnsPMarker]
**
** @nam3rule Get Return Marker attribute(s)
** @nam4rule Adaptor Return the Ensembl Marker Adaptor
** @nam4rule Displaysynonym Return the display synonym
** @nam4rule Distance Return a distance
** @nam5rule Maximum Return the maximum distance
** @nam5rule Minimum Return the minimum distance
** @nam4rule Identifier Return the SQL database-internal identifier
** @nam4rule Primer Return a primer
** @nam5rule Left Return the left primer
** @nam5rule Right Return the right primer
** @nam4rule Priority return the priority
** @nam4rule Type Return the type
**
** @argrule * marker [const EnsPMarker] Ensembl Marker
**
** @valrule Adaptor [EnsPMarkeradaptor] Ensembl Marker Adaptor or NULL
** @valrule Displaysynonym [EnsPMarkersynonym] Ensembl Marker Synonym or NULL
** @valrule DistanceMaximum [ajuint] Maximum distance or 0U
** @valrule DistanceMinimum [ajuint] Minimum distance or 0U
** @valrule Identifier [ajuint] SQL database-internal identifier or 0U
** @valrule PrimerLeft [AjPStr] Left primer or NULL
** @valrule PrimerRight [AjPStr] Right primer or NULL
** @valrule Priority [ajint] Priority or 0
** @valrule Type [EnsEMarkerType] Type or ensEMarkerTypeNULL
**
** @fcategory use
******************************************************************************/
/* @func ensMarkerGetAdaptor **************************************************
**
** Get the Ensembl Marker Adaptor member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Storable::adaptor
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [EnsPMarkeradaptor] Ensembl Marker Adaptor or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPMarkeradaptor ensMarkerGetAdaptor(const EnsPMarker marker)
{
return (marker) ? marker->Adaptor : NULL;
}
/* @func ensMarkerGetDisplaysynonym *******************************************
**
** Get the display synonym member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::display_MarkerSynonym
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [EnsPMarkersynonym] Display Ensembl Marker Synonym or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPMarkersynonym ensMarkerGetDisplaysynonym(const EnsPMarker marker)
{
return (marker) ? marker->Displaysynonym : NULL;
}
/* @func ensMarkerGetDistanceMaximum ******************************************
**
** Get the maximum distance member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::max_primer_dist
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [ajuint] Maximum distance or 0U
**
** @release 6.4.0
** @@
******************************************************************************/
ajuint ensMarkerGetDistanceMaximum(const EnsPMarker marker)
{
return (marker) ? marker->DistanceMaximum : 0U;
}
/* @func ensMarkerGetDistanceMinimum ******************************************
**
** Get the minimum distance member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::min_primer_dist
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [ajuint] Minimum distance or 0U
**
** @release 6.4.0
** @@
******************************************************************************/
ajuint ensMarkerGetDistanceMinimum(const EnsPMarker marker)
{
return (marker) ? marker->DistanceMinimum : 0U;
}
/* @func ensMarkerGetIdentifier ***********************************************
**
** Get the SQL database-internal identifier member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Storable::dbID
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [ajuint] SQL database-internal identifier or 0U
**
** @release 6.2.0
** @@
******************************************************************************/
ajuint ensMarkerGetIdentifier(const EnsPMarker marker)
{
return (marker) ? marker->Identifier : 0U;
}
/* @func ensMarkerGetPrimerLeft ***********************************************
**
** Get the left primer member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::left_primer
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [AjPStr] Left primer or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjPStr ensMarkerGetPrimerLeft(const EnsPMarker marker)
{
return (marker) ? marker->PrimerLeft : NULL;
}
/* @func ensMarkerGetPrimerRight **********************************************
**
** Get the right primer member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::right_primer
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [AjPStr] Right primer or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjPStr ensMarkerGetPrimerRight(const EnsPMarker marker)
{
return (marker) ? marker->PrimerRight : NULL;
}
/* @func ensMarkerGetPriority *************************************************
**
** Get the priority member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::priority
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [ajint] Priority or 0
**
** @release 6.2.0
** @@
******************************************************************************/
ajint ensMarkerGetPriority(const EnsPMarker marker)
{
return (marker) ? marker->Priority : 0;
}
/* @func ensMarkerGetType *****************************************************
**
** Get the type member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::type
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [EnsEMarkerType] Type or ensEMarkerTypeNULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsEMarkerType ensMarkerGetType(const EnsPMarker marker)
{
return (marker) ? marker->Type : ensEMarkerTypeNULL;
}
/* @section load on demand ****************************************************
**
** Functions for returning members of an Ensembl Marker object,
** which may need loading from an Ensembl SQL database on demand.
**
** @fdata [EnsPMarker]
**
** @nam3rule Load Return Ensembl Marker attribute(s) loaded on demand
** @nam4rule Markermaplocations Return all Ensembl Marker Map Location objects
** @nam4rule Markersynonyms Return all Ensembl Marker Synonym objects
**
** @argrule * marker [EnsPMarker] Ensembl Marker
**
** @valrule Markermaplocations [const AjPList]
** AJAX List of Ensembl Marker Map Location objects
** @valrule Markersynonyms [const AjPList]
** AJAX List of Ensembl Marker Synonym objects
**
** @fcategory use
******************************************************************************/
/* @func ensMarkerLoadMarkermaplocations **************************************
**
** Load all Ensembl Marker Map Location objects of an Ensembl Marker.
**
** This is not a simple accessor function, it will fetch
** Ensembl Marker Map Location objects from the Ensembl Core database
** in case the AJAX List is not defined.
**
** @cc Bio::EnsEMBL::Map::Marker::get_all_MapLocations
** @param [u] marker [EnsPMarker] Ensembl Marker
**
** @return [const AjPList] AJAX List of Ensembl Marker Map Location objects
**
** @release 6.4.0
** @@
** NOTE: The Perl API uses a
** Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor::fetch_attributes method to load
** Bio::EnsEMBL::Map::MarkerSynonym and Bio::EnsEMBL::Map::MapLocation objects.
** This is not ideal as the method requires a Marker Adaptor and a Marker.
** There is no check that the MArker Adaptor and Marker refer to the same
** Ensembl Core database.
******************************************************************************/
const AjPList ensMarkerLoadMarkermaplocations(EnsPMarker marker)
{
EnsPDatabaseadaptor dba = NULL;
EnsPMarkermaplocationadaptor mmla = NULL;
if (!marker)
return NULL;
if (marker->Markermaplocations)
return marker->Markermaplocations;
dba = ensMarkeradaptorGetDatabaseadaptor(marker->Adaptor);
if (!dba)
return NULL;
mmla = ensRegistryGetMarkermaplocationadaptor(dba);
marker->Markermaplocations = ajListNew();
ensMarkermaplocationadaptorFetchAllbyMarkeridentifier(
mmla,
ensMarkerGetIdentifier(marker),
marker->Markermaplocations);
return marker->Markermaplocations;
}
/* @func ensMarkerLoadMarkersynonyms ******************************************
**
** Load all Ensembl Marker Synonym objects of an Ensembl Marker.
**
** This is not a simple accessor function, it will fetch
** Ensembl Marker Synonym objects from the Ensembl SQL database
** in case the AJAX List is not defined.
**
** @cc Bio::EnsEMBL::Map::Marker::get_all_MarkerSynonyms
** @param [u] marker [EnsPMarker] Ensembl Marker
**
** @return [const AjPList] AJAX List of Ensembl Marker Synonym objects
**
** @release 6.4.0
** @@
** NOTE: The Perl API uses a
** Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor::fetch_attributes method to load
** Bio::EnsEMBL::Map::MarkerSynonym and Bio::EnsEMBL::Map::MapLocation objects.
** This is not ideal as the method requires a Marker Adaptor and a Marker.
** There is no check that the MArker Adaptor and Marker refer to the same
** Ensembl Core database.
******************************************************************************/
const AjPList ensMarkerLoadMarkersynonyms(EnsPMarker marker)
{
EnsPDatabaseadaptor dba = NULL;
EnsPMarkersynonymadaptor msa = NULL;
if (!marker)
return NULL;
if (marker->Markersynonyms)
return marker->Markersynonyms;
dba = ensMarkeradaptorGetDatabaseadaptor(marker->Adaptor);
if (!dba)
return NULL;
msa = ensRegistryGetMarkersynonymadaptor(dba);
marker->Markersynonyms = ajListNew();
ensMarkersynonymadaptorFetchAllbyMarkeridentifier(
msa,
ensMarkerGetIdentifier(marker),
marker->Markersynonyms);
return marker->Markersynonyms;
}
/* @section member assignment *************************************************
**
** Functions for assigning members of an Ensembl Marker object.
**
** @fdata [EnsPMarker]
**
** @nam3rule Set Set one member of an Ensembl Marker
** @nam4rule Adaptor Set the Ensembl Marker Adaptor
** @nam4rule Displaysynonym Set the display synonym
** @nam4rule Distance Set a distance
** @nam5rule Minimum Set the minimum distance
** @nam5rule Maximum Set the maximum distance
** @nam4rule Identifier Set the SQL database-internal identifier
** @nam4rule Primer Set a primer
** @nam5rule Left Set the left primer
** @nam5rule Right Set the right primer
** @nam4rule Priority Set the priority
** @nam4rule Type Set the type
**
** @argrule * marker [EnsPMarker] Ensembl Marker
** @argrule Adaptor ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
** @argrule Displaysynonym display [EnsPMarkersynonym] Display synonym
** @argrule Identifier identifier [ajuint] SQL database-internal identifier
** @argrule PrimerLeft lprimer [AjPStr] Left primer
** @argrule PrimerRight rprimer [AjPStr] Right primer
** @argrule DistanceMinimum mindistance [ajuint] Minimum distance
** @argrule DistanceMaximum maxdistance [ajuint] Maximum distance
** @argrule Priority priority [ajint] Priority
** @argrule Type type [EnsEMarkerType] Type
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory modify
******************************************************************************/
/* @func ensMarkerSetAdaptor **************************************************
**
** Set the Ensembl Marker Adaptor member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Storable::adaptor
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [u] ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerSetAdaptor(EnsPMarker marker,
EnsPMarkeradaptor ma)
{
if (!marker)
return ajFalse;
marker->Adaptor = ma;
return ajTrue;
}
/* @func ensMarkerSetDisplaysynonym *******************************************
**
** Set the display synonym member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::display_MarkerSynonym
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [u] display [EnsPMarkersynonym] Display synonym
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkerSetDisplaysynonym(EnsPMarker marker,
EnsPMarkersynonym display)
{
if (!marker)
return ajFalse;
ensMarkersynonymDel(&marker->Displaysynonym);
marker->Displaysynonym = ensMarkersynonymNewRef(display);
return ajTrue;
}
/* @func ensMarkerSetDistanceMaximum ******************************************
**
** Set the maximum distance member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::max_primer_dist
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [r] maxdistance [ajuint] Maximum distance
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkerSetDistanceMaximum(EnsPMarker marker,
ajuint maxdistance)
{
if (!marker)
return ajFalse;
marker->DistanceMaximum = maxdistance;
return ajTrue;
}
/* @func ensMarkerSetDistanceMinimum ******************************************
**
** Set the minimum distance member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::min_primer_dist
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [r] mindistance [ajuint] Minimum distance
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkerSetDistanceMinimum(EnsPMarker marker,
ajuint mindistance)
{
if (!marker)
return ajFalse;
marker->DistanceMinimum = mindistance;
return ajTrue;
}
/* @func ensMarkerSetIdentifier ***********************************************
**
** Set the SQL database-internal identifier member of an
** Ensembl Marker.
**
** @cc Bio::EnsEMBL::Storable::dbID
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [r] identifier [ajuint] SQL database-internal identifier
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerSetIdentifier(EnsPMarker marker,
ajuint identifier)
{
if (!marker)
return ajFalse;
marker->Identifier = identifier;
return ajTrue;
}
/* @func ensMarkerSetPrimerLeft ***********************************************
**
** Set the left primer member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::left_primer
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [u] lprimer [AjPStr] Left primer
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkerSetPrimerLeft(EnsPMarker marker,
AjPStr lprimer)
{
if (!marker)
return ajFalse;
ajStrDel(&marker->PrimerLeft);
if (lprimer)
marker->PrimerLeft = ajStrNewRef(lprimer);
return ajTrue;
}
/* @func ensMarkerSetPrimerRight **********************************************
**
** Set the right primer member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::right_primer
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [u] rprimer [AjPStr] Right primer
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkerSetPrimerRight(EnsPMarker marker,
AjPStr rprimer)
{
if (!marker)
return ajFalse;
ajStrDel(&marker->PrimerRight);
if (rprimer)
marker->PrimerRight = ajStrNewRef(rprimer);
return ajTrue;
}
/* @func ensMarkerSetPriority *************************************************
**
** Set the priority member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::priority
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [r] priority [ajint] Priority
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerSetPriority(EnsPMarker marker,
ajint priority)
{
if (!marker)
return ajFalse;
marker->Priority = priority;
return ajTrue;
}
/* @func ensMarkerSetType *****************************************************
**
** Set the type member of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::type
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [u] type [EnsEMarkerType] Type
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerSetType(EnsPMarker marker,
EnsEMarkerType type)
{
if (!marker)
return ajFalse;
marker->Type = type;
return ajTrue;
}
/* @section debugging *********************************************************
**
** Functions for reporting of an Ensembl Marker object.
**
** @fdata [EnsPMarker]
**
** @nam3rule Trace Report Ensembl Marker members to debug file.
**
** @argrule Trace marker [const EnsPMarker] Ensembl Marker
** @argrule Trace level [ajuint] Indentation level
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensMarkerTrace *******************************************************
**
** Trace an Ensembl Marker.
**
** @param [r] marker [const EnsPMarker] Ensembl Marker
** @param [r] level [ajuint] Indentation level
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerTrace(const EnsPMarker marker, ajuint level)
{
AjIList iter = NULL;
AjPStr indent = NULL;
EnsPMarkermaplocation mml = NULL;
EnsPMarkersynonym ms = NULL;
if (!marker)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensMarkerTrace %p\n"
"%S Use %u\n"
"%S Identifier %u\n"
"%S Adaptor %p\n"
"%S PrimerLeft '%S'\n"
"%S PrimerRight '%S'\n"
"%S Type '%S'\n"
"%S Displaysynonym %p\n"
"%S Markersynonyms %p\n"
"%S Markermaplocations %p\n"
"%S DistanceMinimum %u\n"
"%S DistanceMaximum %u\n"
"%S Priority %d\n",
indent, marker,
indent, marker->Use,
indent, marker->Identifier,
indent, marker->Adaptor,
indent, marker->PrimerLeft,
indent, marker->PrimerRight,
indent, marker->Type,
indent, marker->Displaysynonym,
indent, marker->Markersynonyms,
indent, marker->Markermaplocations,
indent, marker->DistanceMinimum,
indent, marker->DistanceMaximum,
indent, marker->Priority);
ensMarkersynonymTrace(marker->Displaysynonym, level + 1);
/* Trace the AJAX List of Ensembl Marker Synonym objects. */
iter = ajListIterNew(marker->Markersynonyms);
while (!ajListIterDone(iter))
{
ms = (EnsPMarkersynonym) ajListIterGet(iter);
ensMarkersynonymTrace(ms, level + 1);
}
ajListIterDel(&iter);
/* Trace the AJAX List of Ensembl Marker Map Location objects. */
iter = ajListIterNew(marker->Markermaplocations);
while (!ajListIterDone(iter))
{
mml = (EnsPMarkermaplocation) ajListIterGet(iter);
ensMarkermaplocationTrace(mml, level + 1);
}
ajListIterDel(&iter);
ajStrDel(&indent);
return ajTrue;
}
/* @section calculate *********************************************************
**
** Functions for calculating information from an Ensembl Marker object.
**
** @fdata [EnsPMarker]
**
** @nam3rule Calculate Calculate Ensembl Marker information
** @nam4rule Memsize Calculate the memory size in bytes
**
** @argrule * marker [const EnsPMarker] Ensembl Marker
**
** @valrule Memsize [size_t] Memory size in bytes or 0
**
** @fcategory misc
******************************************************************************/
/* @func ensMarkerCalculateMemsize ********************************************
**
** Calculate the memory size in bytes of an Ensembl Marker.
**
** @param [r] marker [const EnsPMarker] Ensembl Marker
**
** @return [size_t] Memory size in bytes or 0
**
** @release 6.4.0
** @@
******************************************************************************/
size_t ensMarkerCalculateMemsize(const EnsPMarker marker)
{
size_t size = 0;
AjIList iter = NULL;
EnsPMarkermaplocation mml = NULL;
EnsPMarkersynonym ms = NULL;
if (!marker)
return 0;
size += sizeof (EnsOMarker);
size += ensMarkersynonymCalculateMemsize(marker->Displaysynonym);
if (marker->PrimerLeft)
{
size += sizeof (AjOStr);
size += ajStrGetRes(marker->PrimerLeft);
}
if (marker->PrimerRight)
{
size += sizeof (AjOStr);
size += ajStrGetRes(marker->PrimerRight);
}
/* Summarise the AJAX List of Ensembl Marker Synonym objects. */
iter = ajListIterNew(marker->Markersynonyms);
while (!ajListIterDone(iter))
{
ms = (EnsPMarkersynonym) ajListIterGet(iter);
size += ensMarkersynonymCalculateMemsize(ms);
}
ajListIterDel(&iter);
/* Summarise the AJAX List of Ensembl Marker Map Location objects. */
iter = ajListIterNew(marker->Markermaplocations);
while (!ajListIterDone(iter))
{
mml = (EnsPMarkermaplocation) ajListIterGet(iter);
size += ensMarkermaplocationCalculateMemsize(mml);
}
ajListIterDel(&iter);
return size;
}
/* @section member addition ***************************************************
**
** Functions for adding members to an Ensembl Marker object.
**
** @fdata [EnsPMarker]
**
** @nam3rule Add Add one object to an Ensembl Marker
** @nam4rule Markermaplocation Add an Ensembl Marker Map Location
** @nam4rule Markersynonym Add an Ensembl Marker Synonym
**
** @argrule * marker [EnsPMarker] Ensembl Marker
** @argrule Markermaplocation mml [EnsPMarkermaplocation]
** Ensembl Marker Map Location
** @argrule Markersynonym ms [EnsPMarkersynonym] Ensembl Marker Synonym
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory modify
******************************************************************************/
/* @func ensMarkerAddMarkermaplocation ****************************************
**
** Add an Ensembl Marker Map Location to an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::add_MapLocations
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [u] mml [EnsPMarkermaplocation] Ensembl Marker Map Location
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerAddMarkermaplocation(EnsPMarker marker,
EnsPMarkermaplocation mml)
{
if (!marker)
return ajFalse;
if (!mml)
return ajFalse;
if (!marker->Markermaplocations)
marker->Markermaplocations = ajListNew();
ajListPushAppend(marker->Markermaplocations,
(void *) ensMarkermaplocationNewRef(mml));
return ajTrue;
}
/* @func ensMarkerAddMarkersynonym ********************************************
**
** Add an Ensembl Marker Synonym to an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::add_MarkerSynonym
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [u] ms [EnsPMarkersynonym] Ensembl Marker Synonym
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerAddMarkersynonym(EnsPMarker marker,
EnsPMarkersynonym ms)
{
if (!marker)
return ajFalse;
if (!ms)
return ajFalse;
if (!marker->Markersynonyms)
marker->Markersynonyms = ajListNew();
ajListPushAppend(marker->Markersynonyms,
(void *) ensMarkersynonymNewRef(ms));
return ajTrue;
}
/* @section member removal ****************************************************
**
** Functions for clearing members of an Ensembl Marker object.
**
** @fdata [EnsPMarker]
**
** @nam3rule Clear Clear members of an Ensembl Marker
** @nam4rule Markermaplocations Clear all Ensembl Marker Map Location objects
** @nam4rule Markersynonyms Clear all Ensembl Marker Synonym objects
**
** @argrule * marker [EnsPMarker] Ensembl Marker
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory modify
******************************************************************************/
/* @func ensMarkerClearMarkermaplocations *************************************
**
** Clear all Ensembl Marker Map Location objects of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::flush_MapLocations
** @param [u] marker [EnsPMarker] Ensembl Marker
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerClearMarkermaplocations(EnsPMarker marker)
{
EnsPMarkermaplocation mml = NULL;
if (!marker)
return ajFalse;
while (ajListPop(marker->Markermaplocations, (void **) &mml))
ensMarkermaplocationDel(&mml);
return ajTrue;
}
/* @func ensMarkerClearMarkersynonyms *****************************************
**
** Clear all Ensembl Marker Synonym objects of an Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::Marker::flush_MarkerSynonyms
** @param [u] marker [EnsPMarker] Ensembl Marker
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerClearMarkersynonyms(EnsPMarker marker)
{
EnsPMarkersynonym ms = NULL;
if (!marker)
return ajFalse;
while (ajListPop(marker->Markersynonyms, (void **) &ms))
ensMarkersynonymDel(&ms);
return ajTrue;
}
/* @datasection [EnsEMarkerType] Ensembl Marker Type **************************
**
** @nam2rule Marker Functions for manipulating
** Ensembl Marker objects
** @nam3rule MarkerType Functions for manipulating
** Ensembl Marker Type enumerations
**
******************************************************************************/
/* @section Misc **************************************************************
**
** Functions for returning an Ensembl Marker Type enumeration.
**
** @fdata [EnsEMarkerType]
**
** @nam4rule From Ensembl Marker Type query
** @nam5rule Str AJAX String object query
**
** @argrule Str type [const AjPStr] Type string
**
** @valrule * [EnsEMarkerType]
** Ensembl Marker Type enumeration or ensEMarkerTypeNULL
**
** @fcategory misc
******************************************************************************/
/* @func ensMarkerTypeFromStr *************************************************
**
** Convert an AJAX String into an Ensembl Marker Type enumeration.
**
** @param [r] type [const AjPStr] Ensembl Marker Type string
**
** @return [EnsEMarkerType]
** Ensembl Marker Type enumeration or ensEMarkerTypeNULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsEMarkerType ensMarkerTypeFromStr(const AjPStr type)
{
register EnsEMarkerType i = ensEMarkerTypeNULL;
EnsEMarkerType etype = ensEMarkerTypeNULL;
for (i = ensEMarkerTypeNULL;
markerKType[i];
i++)
if (ajStrMatchC(type, markerKType[i]))
etype = i;
if (!etype)
ajDebug("ensMarkerTypeFromStr encountered "
"unexpected string '%S'.\n", type);
return etype;
}
/* @section Cast **************************************************************
**
** Functions for returning attributes of an
** Ensembl Marker Type enumeration.
**
** @fdata [EnsEMarkerType]
**
** @nam4rule To Return Ensembl Marker Type enumeration
** @nam5rule Char Return C character string value
**
** @argrule To type [EnsEMarkerType] Ensembl Marker Type enumeration
**
** @valrule Char [const char*] Ensembl Marker Type C-type (char *) string
**
** @fcategory cast
******************************************************************************/
/* @func ensMarkerTypeToChar **************************************************
**
** Convert an Ensembl Marker Type enumeration into a C-type (char *) string.
**
** @param [u] type [EnsEMarkerType] Ensembl Marker Type enumeration
**
** @return [const char*] Ensembl Marker Type C-type (char *) string
**
** @release 6.2.0
** @@
******************************************************************************/
const char* ensMarkerTypeToChar(EnsEMarkerType type)
{
register EnsEMarkerType i = ensEMarkerTypeNULL;
for (i = ensEMarkerTypeNULL;
markerKType[i] && (i < type);
i++);
if (!markerKType[i])
ajDebug("ensMarkerTypeToChar "
"encountered an out of boundary error on "
"Ensembl Marker Type "
"enumeration %d.\n",
type);
return markerKType[i];
}
/* @datasection [EnsPMarkeradaptor] Ensembl Marker Adaptor ********************
**
** @nam2rule Markeradaptor Functions for manipulating
** Ensembl Marker Adaptor objects
**
** @cc Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor
** @cc CVS Revision: 1.15
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @funcstatic markeradaptorFetchAllbyStatement *******************************
**
** Run a SQL statement against an Ensembl Database Adaptor and consolidate the
** results into an AJAX List of Ensembl Marker objects.
**
** @param [u] ba [EnsPBaseadaptor] Ensembl Base Adaptor
** @param [r] statement [const AjPStr] SQL statement
** @param [uN] am [EnsPAssemblymapper] Ensembl Assembly Mapper
** @param [uN] slice [EnsPSlice] Ensembl Slice
** @param [u] markers [AjPList] AJAX List of Ensembl Markers
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
** NOTE: This implementation of the Ensembl Marker Adaptor immediately selects
** all Marker Synonym objects via a LEFT JOIN clause, sets the special display
** Marker Synomym and adds all others to to the AJAX List of Marker Synonym
** objects.
** The Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor::fetch_all and
** Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor::fetch_by_dbID methods select only
** the display Marker Synonym via
** marker.display_marker_synonym = marker_synonym.marker_synonym_id.
** All other Ensembl Marker Synonym objects are loaded via the
** Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor::fetch_attributes method.
******************************************************************************/
static AjBool markeradaptorFetchAllbyStatement(
EnsPBaseadaptor ba,
const AjPStr statement,
EnsPAssemblymapper am,
EnsPSlice slice,
AjPList markers)
{
ajint priority = 0;
ajuint current = 0U;
ajuint identifier = 0U;
ajuint displaymsid = 0U;
ajuint mindistance = 0U;
ajuint maxdistance = 0U;
ajuint msid = 0U;
EnsEMarkerType etype = ensEMarkerTypeNULL;
AjPSqlstatement sqls = NULL;
AjISqlrow sqli = NULL;
AjPSqlrow sqlr = NULL;
AjPStr lprimer = NULL;
AjPStr rprimer = NULL;
AjPStr type = NULL;
AjPStr msname = NULL;
AjPStr mssource = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPMarker marker = NULL;
EnsPMarkeradaptor ma = NULL;
EnsPMarkersynonym ms = NULL;
if (ajDebugTest("markeradaptorFetchAllbyStatement"))
ajDebug("markeradaptorFetchAllbyStatement\n"
" ba %p\n"
" statement %p\n"
" am %p\n"
" slice %p\n"
" markers %p\n",
ba,
statement,
am,
slice,
markers);
if (!ba)
return ajFalse;
if (!statement)
return ajFalse;
if (!markers)
return ajFalse;
dba = ensBaseadaptorGetDatabaseadaptor(ba);
ma = ensRegistryGetMarkeradaptor(dba);
sqls = ensDatabaseadaptorSqlstatementNew(dba, statement);
sqli = ajSqlrowiterNew(sqls);
while (!ajSqlrowiterDone(sqli))
{
identifier = 0;
displaymsid = 0;
lprimer = ajStrNew();
rprimer = ajStrNew();
mindistance = 0;
maxdistance = 0;
priority = 0;
type = ajStrNew();
msid = 0;
msname = ajStrNew();
mssource = ajStrNew();
etype = ensEMarkerTypeNULL;
sqlr = ajSqlrowiterGet(sqli);
ajSqlcolumnToUint(sqlr, &identifier);
ajSqlcolumnToUint(sqlr, &displaymsid);
ajSqlcolumnToStr(sqlr, &lprimer);
ajSqlcolumnToStr(sqlr, &rprimer);
ajSqlcolumnToUint(sqlr, &mindistance);
ajSqlcolumnToUint(sqlr, &maxdistance);
ajSqlcolumnToInt(sqlr, &priority);
ajSqlcolumnToStr(sqlr, &type);
ajSqlcolumnToUint(sqlr, &msid);
ajSqlcolumnToStr(sqlr, &msname);
ajSqlcolumnToStr(sqlr, &mssource);
if (current != identifier)
{
etype = ensMarkerTypeFromStr(type);
marker = ensMarkerNewIni(ma,
identifier,
(EnsPMarkersynonym) NULL,
lprimer,
rprimer,
(AjPList) NULL,
(AjPList) NULL,
mindistance,
maxdistance,
etype,
priority);
ajListPushAppend(markers, (void *) marker);
current = identifier;
}
if (msid)
{
ms = ensMarkersynonymNewIni(msid, mssource, msname);
if (msid == displaymsid)
ensMarkerSetDisplaysynonym(marker, ms);
else
ensMarkerAddMarkersynonym(marker, ms);
ensMarkersynonymDel(&ms);
}
ajStrDel(&lprimer);
ajStrDel(&rprimer);
ajStrDel(&type);
ajStrDel(&msname);
ajStrDel(&mssource);
}
ajSqlrowiterDel(&sqli);
ensDatabaseadaptorSqlstatementDel(dba, &sqls);
return ajTrue;
}
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Marker Adaptor by pointer.
** It is the responsibility of the user to first destroy any previous
** Marker Adaptor. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPMarkeradaptor]
**
** @nam3rule New Constructor
**
** @argrule New dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @valrule * [EnsPMarkeradaptor] Ensembl Marker Adaptor or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensMarkeradaptorNew **************************************************
**
** Default constructor for an Ensembl Marker Adaptor.
**
** Ensembl Object Adaptors are singleton objects in the sense that a single
** instance of an Ensembl Object Adaptor connected to a particular database is
** sufficient to instantiate any number of Ensembl Objects from the database.
** Each Ensembl Object will have a weak reference to the Object Adaptor that
** instantiated it. Therefore, Ensembl Object Adaptors should not be
** instantiated directly, but rather obtained from the Ensembl Registry,
** which will in turn call this function if neccessary.
**
** @see ensRegistryGetDatabaseadaptor
** @see ensRegistryGetMarkeradaptor
**
** @cc Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor::new
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [EnsPMarkeradaptor] Ensembl Marker Adaptor or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPMarkeradaptor ensMarkeradaptorNew(
EnsPDatabaseadaptor dba)
{
return ensBaseadaptorNew(
dba,
markeradaptorKTablenames,
markeradaptorKColumnnames,
markeradaptorKLeftjoins,
(const char *) NULL,
(const char *) NULL,
&markeradaptorFetchAllbyStatement);
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Marker Adaptor object.
**
** @fdata [EnsPMarkeradaptor]
**
** @nam3rule Del Destroy (free) an Ensembl Marker Adaptor
**
** @argrule * Pma [EnsPMarkeradaptor*] Ensembl Marker Adaptor address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensMarkeradaptorDel **************************************************
**
** Default destructor for an Ensembl Marker Adaptor.
**
** This function also clears the internal caches.
**
** Ensembl Object Adaptors are singleton objects that are registered in the
** Ensembl Registry and weakly referenced by Ensembl Objects that have been
** instantiated by it. Therefore, Ensembl Object Adaptors should never be
** destroyed directly. Upon exit, the Ensembl Registry will call this function
** if required.
**
** @param [d] Pma [EnsPMarkeradaptor*] Ensembl Marker Adaptor address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensMarkeradaptorDel(EnsPMarkeradaptor *Pma)
{
ensBaseadaptorDel(Pma);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Marker Adaptor object.
**
** @fdata [EnsPMarkeradaptor]
**
** @nam3rule Get Return Marker Adaptor attribute(s)
** @nam4rule Baseadaptor Return the Ensembl Base Adaptor
** @nam4rule Databaseadaptor Return the Ensembl Database Adaptor
**
** @argrule * ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
**
** @valrule Baseadaptor [EnsPBaseadaptor]
** Ensembl Base Adaptor or NULL
** @valrule Databaseadaptor [EnsPDatabaseadaptor]
** Ensembl Database Adaptor or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensMarkeradaptorGetBaseadaptor ***************************************
**
** Get the Ensembl Base Adaptor member of an Ensembl Marker Adaptor.
**
** @param [u] ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
**
** @return [EnsPBaseadaptor] Ensembl Base Adaptor or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPBaseadaptor ensMarkeradaptorGetBaseadaptor(EnsPMarkeradaptor ma)
{
return ma;
}
/* @func ensMarkeradaptorGetDatabaseadaptor ***********************************
**
** Get the Ensembl Database Adaptor member of an Ensembl Marker Adaptor.
**
** @param [u] ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
**
** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPDatabaseadaptor ensMarkeradaptorGetDatabaseadaptor(EnsPMarkeradaptor ma)
{
return ensBaseadaptorGetDatabaseadaptor(
ensMarkeradaptorGetBaseadaptor(ma));
}
/* @section object retrieval **************************************************
**
** Functions for fetching Ensembl Marker objects from an
** Ensembl Core database.
**
** @fdata [EnsPMarkeradaptor]
**
** @nam3rule Fetch Fetch Ensembl Marker object(s)
** @nam4rule All Fetch all Ensembl Marker objects
** @nam4rule Allby Fetch all Ensembl Marker objects matching a criterion
** @nam5rule Synonym Fetch all by a Marker Synonym name and source
** @nam4rule By Fetch one Ensembl Marker object matching a criterion
** @nam5rule Identifier Fetch by an SQL database-internal identifier
**
** @argrule * ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
** @argrule All markers [AjPList] AJAX List of Ensembl Marker objects
** @argrule AllbySynonym name [const AjPStr] Marker Synonym name
** @argrule AllbySynonym source [const AjPStr] Marker Synonym source
** @argrule AllbySynonym markers [AjPList] AJAX List of Ensembl Marker objects
** @argrule ByIdentifier identifier [ajuint] SQL database-internal identifier
** @argrule ByIdentifier Pmarker [EnsPMarker*] Ensembl Marker address
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensMarkeradaptorFetchAll *********************************************
**
** Fetch all Ensembl Markers.
**
** The caller is responsible for deleting the Ensembl Markers before
** deleting the AJAX List.
**
** @cc Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor::fetch_all
** @param [u] ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
** @param [u] markers [AjPList] AJAX List of Ensembl Markers
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkeradaptorFetchAll(EnsPMarkeradaptor ma,
AjPList markers)
{
return ensBaseadaptorFetchAll(
ensMarkeradaptorGetBaseadaptor(ma),
markers);
}
/* @func ensMarkeradaptorFetchAllbySynonym ************************************
**
** Fetch all Ensembl Markers via a Marker Synonym name and source.
**
** The caller is responsible for deleting the Ensembl Markers before deleting
** the AJAX List.
**
** @cc Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor::fetch_all_by_synonym
** @param [u] ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
** @param [r] name [const AjPStr] Marker Synonym name
** @param [rN] source [const AjPStr] Marker Synonym source
** @param [w] markers [AjPList] AJAX List of Ensembl Marker objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkeradaptorFetchAllbySynonym(EnsPMarkeradaptor ma,
const AjPStr name,
const AjPStr source,
AjPList markers)
{
char *txtname = NULL;
char *txtsource = NULL;
ajuint identifier = 0U;
ajuint *Pidentifier = NULL;
AjBool *Pbool = NULL;
AjPSqlstatement sqls = NULL;
AjISqlrow sqli = NULL;
AjPSqlrow sqlr = NULL;
AjPStr statement = NULL;
AjPTable table = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPMarker marker = NULL;
if (!ma)
return ajFalse;
if (!name)
return ajFalse;
if (!markers)
return ajFalse;
table = ajTableuintNew(0U);
ajTableSetDestroyvalue(table, &ajMemFree);
dba = ensMarkeradaptorGetDatabaseadaptor(ma);
ensDatabaseadaptorEscapeC(dba, &txtname, name);
statement = ajFmtStr(
"SELECT "
"marker_synonym.marker_id "
"FROM "
"marker_synonym "
"WHERE "
"marker_synonym.name = '%s'",
txtname);
ajCharDel(&txtname);
if (source && ajStrGetLen(source))
{
ensDatabaseadaptorEscapeC(dba, &txtsource, source);
ajFmtPrintAppS(&statement,
" AND marker_synonym.source = '%s'",
txtsource);
ajCharDel(&txtsource);
}
sqls = ensDatabaseadaptorSqlstatementNew(dba, statement);
sqli = ajSqlrowiterNew(sqls);
/*
** TDOD: It would be good to have a FetchByIdentifiers function that
** populates an AJAX Table.
*/
while (!ajSqlrowiterDone(sqli))
{
identifier = 0U;
marker = NULL;
sqlr = ajSqlrowiterGet(sqli);
ajSqlcolumnToUint(sqlr, &identifier);
if (ajTableMatchV(table, (const void *) &identifier))
continue;
AJNEW0(Pidentifier);
*Pidentifier = identifier;
AJNEW0(Pbool);
*Pbool = ajTrue;
ajTablePut(table, (void *) Pidentifier, (void *) Pbool);
ensMarkeradaptorFetchByIdentifier(ma, identifier, &marker);
if (marker)
ajListPushAppend(markers, (void *) marker);
}
ajSqlrowiterDel(&sqli);
ensDatabaseadaptorSqlstatementDel(dba, &sqls);
ajStrDel(&statement);
ajTableDel(&table);
return ajTrue;
}
/* @func ensMarkeradaptorFetchByIdentifier ************************************
**
** Fetch an Ensembl Marker via its SQL database-internal identifier.
**
** The caller is responsible for deleting the Ensembl Marker.
**
** @cc Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor::fetch_by_dbID
** @param [u] ma [EnsPMarkeradaptor] Ensembl Marker Adaptor
** @param [r] identifier [ajuint] SQL database-internal identifier
** @param [wP] Pmarker [EnsPMarker*] Ensembl Marker address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkeradaptorFetchByIdentifier(EnsPMarkeradaptor ma,
ajuint identifier,
EnsPMarker *Pmarker)
{
return ensBaseadaptorFetchByIdentifier(
ensMarkeradaptorGetBaseadaptor(ma),
identifier,
(void **) Pmarker);
}
/* @datasection [EnsPMarkerfeature] Ensembl Marker Feature ********************
**
** @nam2rule Markerfeature Functions for manipulating
** Ensembl Marker Feature objects
**
** @cc Bio::EnsEMBL::Map::MarkerFeature
** @cc CVS Revision: 1.10
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Marker Feature by pointer.
** It is the responsibility of the user to first destroy any previous
** Marker Feature. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPMarkerfeature]
**
** @nam3rule New Constructor
** @nam4rule Cpy Constructor with existing object
** @nam4rule Ini Constructor with initial values
** @nam4rule Ref Constructor by incrementing the reference counter
**
** @argrule Cpy mf [const EnsPMarkerfeature] Ensembl Marker Feature
** @argrule Ini mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
** @argrule Ini identifier [ajuint] SQL database-internal identifier
** @argrule Ini feature [EnsPFeature] Ensembl Feature
** @argrule Ini marker [EnsPMarker] Ensembl Marker
** @argrule Ini mapweight [ajint] Map weight
** @argrule Ref mf [EnsPMarkerfeature] Ensembl Marker Feature
**
** @valrule * [EnsPMarkerfeature] Ensembl Marker Feature or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensMarkerfeatureNewCpy ***********************************************
**
** Object-based constructor function, which returns an independent object.
**
** @param [r] mf [const EnsPMarkerfeature] Ensembl Marker Feature
**
** @return [EnsPMarkerfeature] Ensembl Marker Feature or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPMarkerfeature ensMarkerfeatureNewCpy(const EnsPMarkerfeature mf)
{
EnsPMarkerfeature pthis = NULL;
if (!mf)
return NULL;
AJNEW0(pthis);
pthis->Use = 1U;
pthis->Identifier = mf->Identifier;
pthis->Adaptor = mf->Adaptor;
pthis->Feature = ensFeatureNewRef(mf->Feature);
pthis->Marker = ensMarkerNewRef(mf->Marker);
pthis->Mapweight = mf->Mapweight;
return pthis;
}
/* @func ensMarkerfeatureNewIni ***********************************************
**
** Constructor for an Ensembl Marker Feature with initial values.
**
** @cc Bio::EnsEMBL::Storable::new
** @param [u] mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
** @param [r] identifier [ajuint] SQL database-internal identifier
** @cc Bio::EnsEMBL::Feature::new
** @param [u] feature [EnsPFeature] Ensembl Feature
** @cc Bio::EnsEMBL::Map::MarkerFeature::new
** @param [u] marker [EnsPMarker] Ensembl Marker
** @param [r] mapweight [ajint] Map weight
**
** @return [EnsPMarkerfeature] Ensembl Marker Feature or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPMarkerfeature ensMarkerfeatureNewIni(EnsPMarkerfeatureadaptor mfa,
ajuint identifier,
EnsPFeature feature,
EnsPMarker marker,
ajint mapweight)
{
EnsPMarkerfeature mf = NULL;
AJNEW0(mf);
mf->Use = 1U;
mf->Identifier = identifier;
mf->Adaptor = mfa;
mf->Feature = ensFeatureNewRef(feature);
mf->Marker = ensMarkerNewRef(marker);
mf->Mapweight = mapweight;
return mf;
}
/* @func ensMarkerfeatureNewRef ***********************************************
**
** Ensembl Object referencing function, which returns a pointer to the
** Ensembl Object passed in and increases its reference count.
**
** @param [u] mf [EnsPMarkerfeature] Ensembl Marker Feature
**
** @return [EnsPMarkerfeature] Ensembl Marker Feature or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPMarkerfeature ensMarkerfeatureNewRef(EnsPMarkerfeature mf)
{
if (!mf)
return NULL;
mf->Use++;
return mf;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Marker Feature object.
**
** @fdata [EnsPMarkerfeature]
**
** @nam3rule Del Destroy (free) an Ensembl Marker Feature
**
** @argrule * Pmf [EnsPMarkerfeature*] Ensembl Marker Feature address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensMarkerfeatureDel **************************************************
**
** Default destructor for an Ensembl Marker Feature.
**
** @param [d] Pmf [EnsPMarkerfeature*] Ensembl Marker Feature address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensMarkerfeatureDel(EnsPMarkerfeature *Pmf)
{
EnsPMarkerfeature pthis = NULL;
if (!Pmf)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensMarkerfeatureDel"))
{
ajDebug("ensMarkerfeatureDel\n"
" *Pmf %p\n",
*Pmf);
ensMarkerfeatureTrace(*Pmf, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Pmf) || --pthis->Use)
{
*Pmf = NULL;
return;
}
ensFeatureDel(&pthis->Feature);
ensMarkerDel(&pthis->Marker);
ajMemFree((void **) Pmf);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Marker Feature object.
**
** @fdata [EnsPMarkerfeature]
**
** @nam3rule Get Return Marker Feature attribute(s)
** @nam4rule Adaptor Return the Ensembl Marker Feature Adaptor
** @nam4rule Feature Return the Ensembl Feature
** @nam4rule Identifier Return the SQL database-internal identifier
** @nam4rule Marker Return the Ensembl Marker
** @nam4rule Mapweight return the map weight
**
** @argrule * mf [const EnsPMarkerfeature] Ensembl Marker Feature
**
** @valrule Adaptor [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
** or NULL
** @valrule Feature [EnsPFeature] Ensembl Feature or NULL
** @valrule Identifier [ajuint] SQL database-internal identifier or 0U
** @valrule Marker [EnsPMarker] Ensembl Marker or NULL
** @valrule Mapweight [ajint] Map weight or 0
**
** @fcategory use
******************************************************************************/
/* @func ensMarkerfeatureGetAdaptor *******************************************
**
** Get the Ensembl Marker Feature Adaptor member of an Ensembl Marker Feature.
**
** @cc Bio::EnsEMBL::Storable::adaptor
** @param [r] mf [const EnsPMarkerfeature] Ensembl Marker Feature
**
** @return [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPMarkerfeatureadaptor ensMarkerfeatureGetAdaptor(
const EnsPMarkerfeature mf)
{
return (mf) ? mf->Adaptor : NULL;
}
/* @func ensMarkerfeatureGetFeature *******************************************
**
** Get the Ensembl Feature member of an Ensembl Marker Feature.
**
** @param [r] mf [const EnsPMarkerfeature] Ensembl Marker Feature
**
** @return [EnsPFeature] Ensembl Feature or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPFeature ensMarkerfeatureGetFeature(const EnsPMarkerfeature mf)
{
return (mf) ? mf->Feature : NULL;
}
/* @func ensMarkerfeatureGetIdentifier ****************************************
**
** Get the SQL database-internal identifier member of an
** Ensembl Marker Feature.
**
** @cc Bio::EnsEMBL::Storable::dbID
** @param [r] mf [const EnsPMarkerfeature] Ensembl Marker Feature
**
** @return [ajuint] SQL database-internal identifier or 0U
**
** @release 6.2.0
** @@
******************************************************************************/
ajuint ensMarkerfeatureGetIdentifier(const EnsPMarkerfeature mf)
{
return (mf) ? mf->Identifier : 0U;
}
/* @func ensMarkerfeatureGetMapweight *****************************************
**
** Get the map wight member of an Ensembl Marker Feature.
**
** @cc Bio::EnsEMBL::Map::MarkerFeature::map_weight
** @param [r] mf [const EnsPMarkerfeature] Ensembl Marker Feature
**
** @return [ajint] Map weight or 0
**
** @release 6.4.0
** @@
******************************************************************************/
ajint ensMarkerfeatureGetMapweight(const EnsPMarkerfeature mf)
{
return (mf) ? mf->Mapweight : 0;
}
/* @func ensMarkerfeatureGetMarker ********************************************
**
** Get the Ensembl Marker member of an Ensembl Marker Feature.
**
** @cc Bio::EnsEMBL::Map::MarkerFeature::marker
** @param [r] mf [const EnsPMarkerfeature] Ensembl Marker Feature
**
** @return [EnsPMarker] Ensembl Marker or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPMarker ensMarkerfeatureGetMarker(const EnsPMarkerfeature mf)
{
return (mf) ? mf->Marker : NULL;
}
/* @section member assignment *************************************************
**
** Functions for assigning members of an Ensembl Marker Feature object.
**
** @fdata [EnsPMarkerfeature]
**
** @nam3rule Set Set one member of an Ensembl Marker Feature
** @nam4rule Adaptor Set the Ensembl Marker Feature Adaptor
** @nam4rule Feature Set the Ensembl Feature
** @nam4rule Identifier Set the SQL database-internal identifier
** @nam4rule Mapweight Set the map weight
** @nam4rule Marker Set the Ensembl Marker
**
** @argrule * mf [EnsPMarkerfeature] Ensembl Marker Feature
** @argrule Adaptor mfa [EnsPMarkerfeatureadaptor]
** Ensembl Marker Feature Adaptor
** @argrule Feature feature [EnsPFeature] Ensembl Feature
** @argrule Identifier identifier [ajuint] SQL database-internal identifier
** @argrule Mapweight mapweight [ajint] Map weight
** @argrule Marker marker [EnsPMarker] Ensembl Marker
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory modify
******************************************************************************/
/* @func ensMarkerfeatureSetAdaptor *******************************************
**
** Set the Ensembl Marker Feature Adaptor member of an Ensembl Marker Feature.
**
** @cc Bio::EnsEMBL::Storable::adaptor
** @param [u] mf [EnsPMarkerfeature] Ensembl Marker Feature
** @param [u] mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerfeatureSetAdaptor(EnsPMarkerfeature mf,
EnsPMarkerfeatureadaptor mfa)
{
if (!mf)
return ajFalse;
mf->Adaptor = mfa;
return ajTrue;
}
/* @func ensMarkerfeatureSetFeature *******************************************
**
** Set the Ensembl Feature member of an Ensembl Marker Feature.
**
** @param [u] mf [EnsPMarkerfeature] Ensembl Marker Feature
** @param [u] feature [EnsPFeature] Ensembl Feature
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerfeatureSetFeature(EnsPMarkerfeature mf, EnsPFeature feature)
{
if (!mf)
return ajFalse;
ensFeatureDel(&mf->Feature);
mf->Feature = ensFeatureNewRef(feature);
return ajTrue;
}
/* @func ensMarkerfeatureSetIdentifier ****************************************
**
** Set the SQL database-internal identifier member of an
** Ensembl Marker Feature.
**
** @cc Bio::EnsEMBL::Storable::dbID
** @param [u] mf [EnsPMarkerfeature] Ensembl Marker Feature
** @param [r] identifier [ajuint] SQL database-internal identifier
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerfeatureSetIdentifier(EnsPMarkerfeature mf, ajuint identifier)
{
if (!mf)
return ajFalse;
mf->Identifier = identifier;
return ajTrue;
}
/* @func ensMarkerfeatureSetMapweight *****************************************
**
** Set the map weight member of an Ensembl Marker Feature.
**
** @cc Bio::EnsEMBL::Map::MarkerFeature::map_weight
** @param [u] mf [EnsPMarkerfeature] Ensembl Marker Feature
** @param [r] mapweight [ajint] Map weight
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkerfeatureSetMapweight(EnsPMarkerfeature mf, ajint mapweight)
{
if (!mf)
return ajFalse;
mf->Mapweight = mapweight;
return ajTrue;
}
/* @func ensMarkerfeatureSetMarker ********************************************
**
** Set the Ensembl Marker member of an Ensembl Marker Feature.
**
** @cc Bio::EnsEMBL::Map::MarkerFeature::marker
** @param [u] mf [EnsPMarkerfeature] Ensembl Marker Feature
** @param [u] marker [EnsPMarker] Ensembl Marker
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerfeatureSetMarker(EnsPMarkerfeature mf, EnsPMarker marker)
{
if (!mf)
return ajFalse;
ensMarkerDel(&mf->Marker);
mf->Marker = ensMarkerNewRef(marker);
return ajTrue;
}
/* @section debugging *********************************************************
**
** Functions for reporting of an Ensembl Marker Feature object.
**
** @fdata [EnsPMarkerfeature]
**
** @nam3rule Trace Report Ensembl Marker Feature members to debug file.
**
** @argrule Trace mf [const EnsPMarkerfeature] Ensembl Marker Feature
** @argrule Trace level [ajuint] Indentation level
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensMarkerfeatureTrace ************************************************
**
** Trace an Ensembl Marker Feature.
**
** @param [r] mf [const EnsPMarkerfeature] Ensembl Marker Feature
** @param [r] level [ajuint] Indentation level
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensMarkerfeatureTrace(const EnsPMarkerfeature mf, ajuint level)
{
AjPStr indent = NULL;
if (!mf)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensMarkerfeatureTrace %p\n"
"%S Use %u\n"
"%S Identifier %u\n"
"%S Adaptor %p\n"
"%S Feature %p\n"
"%S Marker %p\n"
"%S Mapweight %d\n",
indent, mf,
indent, mf->Use,
indent, mf->Identifier,
indent, mf->Adaptor,
indent, mf->Feature,
indent, mf->Marker,
indent, mf->Mapweight);
ensFeatureTrace(mf->Feature, level + 1);
ensMarkerTrace(mf->Marker, level + 1);
ajStrDel(&indent);
return ajTrue;
}
/* @section calculate *********************************************************
**
** Functions for calculating information from an Ensembl Marker Feature object.
**
** @fdata [EnsPMarkerfeature]
**
** @nam3rule Calculate Calculate Ensembl Marker Feature information
** @nam4rule Memsize Calculate the memory size in bytes
**
** @argrule * mf [const EnsPMarkerfeature] Ensembl Marker Feature
**
** @valrule Memsize [size_t] Memory size in bytes or 0
**
** @fcategory misc
******************************************************************************/
/* @func ensMarkerfeatureCalculateMemsize *************************************
**
** Calculate the memory size in bytes of an Ensembl Marker Feature.
**
** @param [r] mf [const EnsPMarkerfeature] Ensembl Marker Feature
**
** @return [size_t] Memory size in bytes or 0
**
** @release 6.4.0
** @@
******************************************************************************/
size_t ensMarkerfeatureCalculateMemsize(const EnsPMarkerfeature mf)
{
size_t size = 0;
if (!mf)
return 0;
size += sizeof (EnsOMarkerfeature);
size += ensFeatureCalculateMemsize(mf->Feature);
size += ensMarkerCalculateMemsize(mf->Marker);
return size;
}
/* @datasection [AjPList] AJAX List *******************************************
**
** @nam2rule List Functions for manipulating AJAX List objects
**
******************************************************************************/
/* @funcstatic listMarkerfeatureCompareEndAscending ***************************
**
** AJAX List of Ensembl Marker Feature objects comparison function to sort by
** Ensembl Feature end member in ascending order.
**
** @param [r] item1 [const void*] Ensembl Marker Feature address 1
** @param [r] item2 [const void*] Ensembl Marker Feature address 2
** @see ajListSort
**
** @return [int] The comparison function returns an integer less than,
** equal to, or greater than zero if the first argument is
** considered to be respectively less than, equal to, or
** greater than the second.
**
** @release 6.4.0
** @@
******************************************************************************/
static int listMarkerfeatureCompareEndAscending(
const void *item1,
const void *item2)
{
EnsPMarkerfeature mf1 = *(EnsOMarkerfeature *const *) item1;
EnsPMarkerfeature mf2 = *(EnsOMarkerfeature *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listMarkerfeatureCompareEndAscending"))
ajDebug("listMarkerfeatureCompareEndAscending\n"
" mf1 %p\n"
" mf2 %p\n",
mf1,
mf2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (mf1 && (!mf2))
return -1;
if ((!mf1) && (!mf2))
return 0;
if ((!mf1) && mf2)
return +1;
return ensFeatureCompareEndAscending(mf1->Feature, mf2->Feature);
}
/* @funcstatic listMarkerfeatureCompareEndDescending ************************
**
** AJAX List of Ensembl Marker Feature objects comparison function to sort by
** Ensembl Feature end member in descending order.
**
** @param [r] item1 [const void*] Ensembl Marker Feature address 1
** @param [r] item2 [const void*] Ensembl Marker Feature address 2
** @see ajListSort
**
** @return [int] The comparison function returns an integer less than,
** equal to, or greater than zero if the first argument is
** considered to be respectively less than, equal to, or
** greater than the second.
**
** @release 6.4.0
** @@
******************************************************************************/
static int listMarkerfeatureCompareEndDescending(
const void *item1,
const void *item2)
{
EnsPMarkerfeature mf1 = *(EnsOMarkerfeature *const *) item1;
EnsPMarkerfeature mf2 = *(EnsOMarkerfeature *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listMarkerfeatureCompareEndDescending"))
ajDebug("listMarkerfeatureCompareEndDescending\n"
" mf1 %p\n"
" mf2 %p\n",
mf1,
mf2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (mf1 && (!mf2))
return -1;
if ((!mf1) && (!mf2))
return 0;
if ((!mf1) && mf2)
return +1;
return ensFeatureCompareEndDescending(mf1->Feature, mf2->Feature);
}
/* @funcstatic listMarkerfeatureCompareIdentifierAscending ********************
**
** AJAX List of Ensembl Marker Feature objects comparison function to sort by
** identifier member in ascending order.
**
** @param [r] item1 [const void*] Ensembl Marker Feature address 1
** @param [r] item2 [const void*] Ensembl Marker Feature address 2
** @see ajListSort
**
** @return [int] The comparison function returns an integer less than,
** equal to, or greater than zero if the first argument is
** considered to be respectively less than, equal to, or
** greater than the second.
**
** @release 6.4.0
** @@
******************************************************************************/
static int listMarkerfeatureCompareIdentifierAscending(
const void *item1,
const void *item2)
{
EnsPMarkerfeature mf1 = *(EnsOMarkerfeature *const *) item1;
EnsPMarkerfeature mf2 = *(EnsOMarkerfeature *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listMarkerfeatureCompareIdentifierAscending"))
ajDebug("listMarkerfeatureCompareIdentifierAscending\n"
" mf1 %p\n"
" mf2 %p\n",
mf1,
mf2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (mf1 && (!mf2))
return -1;
if ((!mf1) && (!mf2))
return 0;
if ((!mf1) && mf2)
return +1;
if (mf1->Identifier < mf2->Identifier)
return -1;
if (mf1->Identifier > mf2->Identifier)
return +1;
return 0;
}
/* @funcstatic listMarkerfeatureCompareStartAscending *************************
**
** AJAX List of Ensembl Marker Feature objects comparison function to sort by
** Ensembl Feature start member in ascending order.
**
** @param [r] item1 [const void*] Ensembl Marker Feature address 1
** @param [r] item2 [const void*] Ensembl Marker Feature address 2
** @see ajListSort
**
** @return [int] The comparison function returns an integer less than,
** equal to, or greater than zero if the first argument is
** considered to be respectively less than, equal to, or
** greater than the second.
**
** @release 6.4.0
** @@
******************************************************************************/
static int listMarkerfeatureCompareStartAscending(
const void *item1,
const void *item2)
{
EnsPMarkerfeature mf1 = *(EnsOMarkerfeature *const *) item1;
EnsPMarkerfeature mf2 = *(EnsOMarkerfeature *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listMarkerfeatureCompareStartAscending"))
ajDebug("listMarkerfeatureCompareStartAscending\n"
" mf1 %p\n"
" mf2 %p\n",
mf1,
mf2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (mf1 && (!mf2))
return -1;
if ((!mf1) && (!mf2))
return 0;
if ((!mf1) && mf2)
return +1;
return ensFeatureCompareStartAscending(mf1->Feature, mf2->Feature);
}
/* @funcstatic listMarkerfeatureCompareStartDescending ************************
**
** AJAX List of Ensembl Marker Feature objects comparison function to sort by
** Ensembl Feature start member in descending order.
**
** @param [r] item1 [const void*] Ensembl Marker Feature address 1
** @param [r] item2 [const void*] Ensembl Marker Feature address 2
** @see ajListSort
**
** @return [int] The comparison function returns an integer less than,
** equal to, or greater than zero if the first argument is
** considered to be respectively less than, equal to, or
** greater than the second.
**
** @release 6.4.0
** @@
******************************************************************************/
static int listMarkerfeatureCompareStartDescending(
const void *item1,
const void *item2)
{
EnsPMarkerfeature mf1 = *(EnsOMarkerfeature *const *) item1;
EnsPMarkerfeature mf2 = *(EnsOMarkerfeature *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listMarkerfeatureCompareStartDescending"))
ajDebug("listMarkerfeatureCompareStartDescending\n"
" mf1 %p\n"
" mf2 %p\n",
mf1,
mf2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (mf1 && (!mf2))
return -1;
if ((!mf1) && (!mf2))
return 0;
if ((!mf1) && mf2)
return +1;
return ensFeatureCompareStartDescending(mf1->Feature, mf2->Feature);
}
/* @section list **************************************************************
**
** Functions for manipulating AJAX List objects.
**
** @fdata [AjPList]
**
** @nam3rule Markerfeature Functions for manipulating AJAX List objects of
** Ensembl Marker Feature objects
** @nam4rule Sort Sort functions
** @nam5rule End Sort by Ensembl Feature end member
** @nam5rule Identifier Sort by identifier member
** @nam5rule Start Sort by Ensembl Feature start member
** @nam6rule Ascending Sort in ascending order
** @nam6rule Descending Sort in descending order
**
** @argrule Ascending mfs [AjPList]
** AJAX List of Ensembl Marker Feature objects
** @argrule Descending mfs [AjPList]
** AJAX List of Ensembl Marker Feature objects
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensListMarkerfeatureSortEndAscending *********************************
**
** Sort an AJAX List of Ensembl Marker Feature objects by their
** Ensembl Feature end member in ascending order.
**
** @param [u] mfs [AjPList] AJAX List of Ensembl Marker Feature objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListMarkerfeatureSortEndAscending(AjPList mfs)
{
if (!mfs)
return ajFalse;
ajListSortTwoThree(mfs,
&listMarkerfeatureCompareEndAscending,
&listMarkerfeatureCompareStartAscending,
&listMarkerfeatureCompareIdentifierAscending);
return ajTrue;
}
/* @func ensListMarkerfeatureSortEndDescending ********************************
**
** Sort an AJAX List of Ensembl Marker Feature objects by their
** Ensembl Feature end member in descending order.
**
** @param [u] mfs [AjPList] AJAX List of Ensembl Marker Feature objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListMarkerfeatureSortEndDescending(AjPList mfs)
{
if (!mfs)
return ajFalse;
ajListSortTwoThree(mfs,
&listMarkerfeatureCompareEndDescending,
&listMarkerfeatureCompareStartDescending,
&listMarkerfeatureCompareIdentifierAscending);
return ajTrue;
}
/* @func ensListMarkerfeatureSortIdentifierAscending **************************
**
** Sort an AJAX List of Ensembl Marker Feature objects by their
** identifier member in ascending order.
**
** @param [u] mfs [AjPList] AJAX List of Ensembl Marker Feature objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListMarkerfeatureSortIdentifierAscending(AjPList mfs)
{
if (!mfs)
return ajFalse;
ajListSort(mfs, &listMarkerfeatureCompareIdentifierAscending);
return ajTrue;
}
/* @func ensListMarkerfeatureSortStartAscending *******************************
**
** Sort an AJAX List of Ensembl Marker Feature objects by their
** Ensembl Feature start member in ascending order.
**
** @param [u] mfs [AjPList] AJAX List of Ensembl Marker Feature objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListMarkerfeatureSortStartAscending(AjPList mfs)
{
if (!mfs)
return ajFalse;
ajListSortTwoThree(mfs,
&listMarkerfeatureCompareStartAscending,
&listMarkerfeatureCompareEndAscending,
&listMarkerfeatureCompareIdentifierAscending);
return ajTrue;
}
/* @func ensListMarkerfeatureSortStartDescending ******************************
**
** Sort an AJAX List of Ensembl Marker Feature objects by their
** Ensembl Feature start member in descending order.
**
** @param [u] mfs [AjPList] AJAX List of Ensembl Marker Feature objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListMarkerfeatureSortStartDescending(AjPList mfs)
{
if (!mfs)
return ajFalse;
ajListSortTwoThree(mfs,
&listMarkerfeatureCompareStartDescending,
&listMarkerfeatureCompareEndDescending,
&listMarkerfeatureCompareIdentifierAscending);
return ajTrue;
}
/* @datasection [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor *****
**
** @nam2rule Markerfeatureadaptor Functions for manipulating
** Ensembl Marker Feature Adaptor objects
**
** @cc Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor
** @cc CVS Revision: 1.17
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @funcstatic markerfeatureadaptorFetchAllbyStatement ************************
**
** Fetch all Ensembl Marker Feature objects via an SQL statement.
**
** @param [u] ba [EnsPBaseadaptor] Ensembl Base Adaptor
** @param [r] statement [const AjPStr] SQL statement
** @param [uN] am [EnsPAssemblymapper] Ensembl Assembly Mapper
** @param [uN] slice [EnsPSlice] Ensembl Slice
** @param [u] mfs [AjPList] AJAX List of Ensembl Marker Feature objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
static AjBool markerfeatureadaptorFetchAllbyStatement(
EnsPBaseadaptor ba,
const AjPStr statement,
EnsPAssemblymapper am,
EnsPSlice slice,
AjPList mfs)
{
ajint mapweight = 0;
ajint priority = 0;
ajuint srid = 0U;
ajuint srstart = 0U;
ajuint srend = 0U;
ajint srstrand = 1;
ajuint identifier = 0U;
ajuint analysisid = 0U;
ajuint markerid = 0U;
ajuint mindistance = 0U;
ajuint maxdistance = 0U;
ajuint msid = 0U;
ajuint *Pidentifier = NULL;
AjPSqlstatement sqls = NULL;
AjISqlrow sqli = NULL;
AjPSqlrow sqlr = NULL;
AjPStr lprimer = NULL;
AjPStr rprimer = NULL;
AjPStr type = NULL;
AjPStr msname = NULL;
AjPStr mssource = NULL;
AjPTable markers = NULL;
EnsEMarkerType etype = ensEMarkerTypeNULL;
EnsPDatabaseadaptor dba = NULL;
EnsPFeature feature = NULL;
EnsPMarker marker = NULL;
EnsPMarkeradaptor ma = NULL;
EnsPMarkerfeature mf = NULL;
EnsPMarkerfeatureadaptor mfa = NULL;
EnsPMarkersynonym ms = NULL;
if (ajDebugTest("markerfeatureadaptorFetchAllbyStatement"))
ajDebug("markerfeatureadaptorFetchAllbyStatement\n"
" ba %p\n"
" statement %p\n"
" am %p\n"
" slice %p\n"
" mfs %p\n",
ba,
statement,
am,
slice,
mfs);
if (!ba)
return ajFalse;
if (!statement)
return ajFalse;
if (!mfs)
return ajFalse;
dba = ensBaseadaptorGetDatabaseadaptor(ba);
ma = ensRegistryGetMarkeradaptor(dba);
mfa = ensRegistryGetMarkerfeatureadaptor(dba);
markers = ajTableuintNew(0U);
ajTableSetDestroyvalue(markers, (void (*)(void **)) &ensMarkerDel);
sqls = ensDatabaseadaptorSqlstatementNew(dba, statement);
sqli = ajSqlrowiterNew(sqls);
while (!ajSqlrowiterDone(sqli))
{
identifier = 0U;
srid = 0U;
srstart = 0;
srend = 0;
analysisid = 0U;
mapweight = 0;
markerid = 0U;
lprimer = ajStrNew();
rprimer = ajStrNew();
mindistance = 0U;
maxdistance = 0U;
priority = 0;
type = ajStrNew();
msid = 0U;
msname = ajStrNew();
mssource = ajStrNew();
etype = ensEMarkerTypeNULL;
sqlr = ajSqlrowiterGet(sqli);
ajSqlcolumnToUint(sqlr, &identifier);
ajSqlcolumnToUint(sqlr, &srid);
ajSqlcolumnToUint(sqlr, &srstart);
ajSqlcolumnToUint(sqlr, &srend);
ajSqlcolumnToUint(sqlr, &analysisid);
ajSqlcolumnToInt(sqlr, &mapweight);
ajSqlcolumnToUint(sqlr, &markerid);
ajSqlcolumnToStr(sqlr, &lprimer);
ajSqlcolumnToStr(sqlr, &rprimer);
ajSqlcolumnToUint(sqlr, &mindistance);
ajSqlcolumnToUint(sqlr, &maxdistance);
ajSqlcolumnToInt(sqlr, &priority);
ajSqlcolumnToStr(sqlr, &type);
ajSqlcolumnToUint(sqlr, &msid);
ajSqlcolumnToStr(sqlr, &msname);
ajSqlcolumnToStr(sqlr, &mssource);
ensBaseadaptorRetrieveFeature(ba,
analysisid,
srid,
srstart,
srend,
srstrand,
am,
slice,
&feature);
if (!feature)
{
ajStrDel(&lprimer);
ajStrDel(&rprimer);
ajStrDel(&type);
ajStrDel(&msname);
ajStrDel(&mssource);
continue;
}
marker = (EnsPMarker) ajTableFetchmodV(markers,
(const void *) &markerid);
if (!marker)
{
if (msid)
ms = ensMarkersynonymNewIni(msid, mssource, msname);
AJNEW0(Pidentifier);
*Pidentifier = markerid;
etype = ensMarkerTypeFromStr(type);
marker = ensMarkerNewIni(ma,
markerid,
ms,
lprimer,
rprimer,
(AjPList) NULL,
(AjPList) NULL,
mindistance,
maxdistance,
etype,
priority);
ajTablePut(markers, (void *) Pidentifier, (void *) marker);
ensMarkersynonymDel(&ms);
}
mf = ensMarkerfeatureNewIni(mfa,
identifier,
feature,
marker,
mapweight);
ajListPushAppend(mfs, (void *) mf);
ensFeatureDel(&feature);
ajStrDel(&lprimer);
ajStrDel(&rprimer);
ajStrDel(&type);
ajStrDel(&msname);
ajStrDel(&mssource);
}
ajSqlrowiterDel(&sqli);
ensDatabaseadaptorSqlstatementDel(dba, &sqls);
ajTableDel(&markers);
return ajTrue;
}
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Marker Feature Adaptor by pointer.
** It is the responsibility of the user to first destroy any previous
** Marker Feature Adaptor. The target pointer does not need to be initialised
** to NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPMarkerfeatureadaptor]
**
** @nam3rule New Constructor
**
** @argrule New dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @valrule * [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensMarkerfeatureadaptorNew *******************************************
**
** Default constructor for an Ensembl Marker Feature Adaptor.
**
** Ensembl Object Adaptors are singleton objects in the sense that a single
** instance of an Ensembl Object Adaptor connected to a particular database is
** sufficient to instantiate any number of Ensembl Objects from the database.
** Each Ensembl Object will have a weak reference to the Object Adaptor that
** instantiated it. Therefore, Ensembl Object Adaptors should not be
** instantiated directly, but rather obtained from the Ensembl Registry,
** which will in turn call this function if neccessary.
**
** @see ensRegistryGetDatabaseadaptor
** @see ensRegistryGetMarkerfeatureadaptor
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPMarkerfeatureadaptor ensMarkerfeatureadaptorNew(
EnsPDatabaseadaptor dba)
{
return ensFeatureadaptorNew(
dba,
markerfeatureadaptorKTablenames,
markerfeatureadaptorKColumnnames,
markerfeatureadaptorKLeftjoins,
markerfeatureadaptorKDefaultcondition,
(const char *) NULL,
&markerfeatureadaptorFetchAllbyStatement,
(void *(*)(const void *)) NULL,
(void *(*)(void *)) &ensMarkerfeatureNewRef,
(AjBool (*)(const void *)) NULL,
(void (*)(void **)) &ensMarkerfeatureDel,
(size_t (*)(const void *)) &ensMarkerfeatureCalculateMemsize,
(EnsPFeature (*)(const void *)) &ensMarkerfeatureGetFeature,
"Marker Feature");
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Marker Feature Adaptor object.
**
** @fdata [EnsPMarkerfeatureadaptor]
**
** @nam3rule Del Destroy (free) an Ensembl Marker Feature Adaptor
**
** @argrule * Pmfa [EnsPMarkerfeatureadaptor*]
** Ensembl Marker Feature Adaptor address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensMarkerfeatureadaptorDel *******************************************
**
** Default destructor for an Ensembl Marker Feature Adaptor.
**
** Ensembl Object Adaptors are singleton objects that are registered in the
** Ensembl Registry and weakly referenced by Ensembl Objects that have been
** instantiated by it. Therefore, Ensembl Object Adaptors should never be
** destroyed directly. Upon exit, the Ensembl Registry will call this function
** if required.
**
** @param [d] Pmfa [EnsPMarkerfeatureadaptor*]
** Ensembl Marker Feature Adaptor address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensMarkerfeatureadaptorDel(EnsPMarkerfeatureadaptor *Pmfa)
{
ensFeatureadaptorDel(Pmfa);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Marker Feature Adaptor
** object.
**
** @fdata [EnsPMarkerfeatureadaptor]
**
** @nam3rule Get Return Marker Feature Adaptor attribute(s)
** @nam4rule Baseadaptor Return the Ensembl Base Adaptor
** @nam4rule Databaseadaptor Return the Ensembl Database Adaptor
** @nam4rule Featureadaptor Return the Ensembl Feature Adaptor
**
** @argrule * mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
**
** @valrule Baseadaptor [EnsPBaseadaptor]
** Ensembl Base Adaptor or NULL
** @valrule Databaseadaptor [EnsPDatabaseadaptor]
** Ensembl Database Adaptor or NULL
** @valrule Featureadaptor [EnsPFeatureadaptor]
** Ensembl Feature Adaptor or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensMarkerfeatureadaptorGetBaseadaptor ********************************
**
** Get the Ensembl Base Adaptor member of an
** Ensembl Marker Feature Adaptor.
**
** @param [u] mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
**
** @return [EnsPBaseadaptor] Ensembl Base Adaptor or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPBaseadaptor ensMarkerfeatureadaptorGetBaseadaptor(
EnsPMarkerfeatureadaptor mfa)
{
return ensFeatureadaptorGetBaseadaptor(
ensMarkerfeatureadaptorGetFeatureadaptor(mfa));
}
/* @func ensMarkerfeatureadaptorGetDatabaseadaptor ****************************
**
** Get the Ensembl Database Adaptor member of an
** Ensembl Marker Feature Adaptor.
**
** @param [u] mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
**
** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPDatabaseadaptor ensMarkerfeatureadaptorGetDatabaseadaptor(
EnsPMarkerfeatureadaptor mfa)
{
return ensFeatureadaptorGetDatabaseadaptor(
ensMarkerfeatureadaptorGetFeatureadaptor(mfa));
}
/* @func ensMarkerfeatureadaptorGetFeatureadaptor *****************************
**
** Get the Ensembl Feature Adaptor member of an
** Ensembl Marker Feature Adaptor.
**
** @param [u] mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
**
** @return [EnsPFeatureadaptor] Ensembl Feature Adaptor or NULL
**
** @release 6.5.0
** @@
******************************************************************************/
EnsPFeatureadaptor ensMarkerfeatureadaptorGetFeatureadaptor(
EnsPMarkerfeatureadaptor mfa)
{
return mfa;
}
/* @section object retrieval **************************************************
**
** Functions for fetching Ensembl Marker Feature objects from an
** Ensembl SQL database.
**
** @fdata [EnsPMarkerfeatureadaptor]
**
** @nam3rule Fetch Fetch Ensembl Marker Feature object(s)
** @nam4rule All Fetch all Ensembl Marker Feature objects
** @nam4rule Allby Fetch all Ensembl Marker Feature objects
** matching a criterion
** @nam5rule Marker Fetch all by an Ensembl Marker
** @nam5rule Slice Fetch all by an Ensembl Slice
** @nam5rule Slicemarkername Fetch all by an Ensembl Slice and
** Ensembl Marker name
** @nam4rule By Fetch one Ensembl Marker Feature object
** matching a criterion
**
** @argrule * mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
** @argrule All mfs [AjPList] AJAX List of Ensembl Marker Feature objects
** @argrule AllbyMarker marker [const EnsPMarker] Ensembl Marker
** @argrule AllbyMarker mfs [AjPList]
** AJAX List of Ensembl Marker Feature objects
** @argrule AllbySlice slice [EnsPSlice] Ensembl Slice
** @argrule AllbySlice priority [ajint] Priority
** @argrule AllbySlice mapweight [ajuint] Map weight
** @argrule AllbySlice anname [const AjPStr] Ensembl Analysis name
** @argrule AllbySlice mfs [AjPList]
** AJAX List of Ensembl Marker Feature objects
** @argrule AllbySlicemarkername slice [EnsPSlice] Ensembl Slice
** @argrule AllbySlicemarkername name [const AjPStr] Ensembl Marker name
** @argrule AllbySlicemarkername mfs [AjPList]
** AJAX List of Ensembl Marker Feature objects
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensMarkerfeatureadaptorFetchAllbyMarker ******************************
**
** Fetch all Ensembl Marker Feature objects by an Ensembl Marker.
**
** The caller is responsible for deleting the Ensembl Markers Feature objects
** before deleting the AJAX List.
**
** @cc Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor::fetch_all_by_Marker
** @param [u] mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
** @param [r] marker [const EnsPMarker] Ensembl Marker
** @param [u] mfs [AjPList] AJAX List of Ensembl Marker Feature objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkerfeatureadaptorFetchAllbyMarker(
EnsPMarkerfeatureadaptor mfa,
const EnsPMarker marker,
AjPList mfs)
{
AjBool result = AJFALSE;
AjPStr constraint = NULL;
if (!mfa)
return ajFalse;
if (!marker)
return ajFalse;
if (!mfs)
return ajFalse;
constraint = ajFmtStr("marker.marker_id = %u", marker->Identifier);
result = ensBaseadaptorFetchAllbyConstraint(
ensMarkerfeatureadaptorGetBaseadaptor(mfa),
constraint,
(EnsPAssemblymapper) NULL,
(EnsPSlice) NULL,
mfs);
ajStrDel(&constraint);
return result;
}
/* @func ensMarkerfeatureadaptorFetchAllbySlice *******************************
**
** Fetch all Ensembl Marker Feature objects by an Ensembl Slice.
**
** The caller is responsible for deleting the Ensembl Markers Feature objects
** before deleting the AJAX List.
**
** @cc Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor::
** fetch_all_by_Slice_and_priority
** @param [u] mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [r] priority [ajint] Priority
** @param [r] mapweight [ajuint] Map weight
** @param [r] anname [const AjPStr] Ensembl Analysis name
** @param [u] mfs [AjPList] AJAX List of Ensembl Marker Feature objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkerfeatureadaptorFetchAllbySlice(
EnsPMarkerfeatureadaptor mfa,
EnsPSlice slice,
ajint priority,
ajuint mapweight,
const AjPStr anname,
AjPList mfs)
{
AjBool result = AJFALSE;
AjPStr constraint = NULL;
if (!mfa)
return ajFalse;
if (!slice)
return ajFalse;
if (!mfs)
return ajFalse;
if (priority)
constraint = ajFmtStr("marker.priority > %d", priority);
if (mapweight)
{
if (constraint)
ajFmtPrintAppS(&constraint,
" AND marker_feature.map_weight < %u",
mapweight);
else
constraint = ajFmtStr("marker_feature.map_weight < %u", mapweight);
}
result = ensFeatureadaptorFetchAllbySlice(
ensMarkerfeatureadaptorGetFeatureadaptor(mfa),
slice,
constraint,
anname,
mfs);
ajStrDel(&constraint);
return result;
}
/* @func ensMarkerfeatureadaptorFetchAllbySlicemarkername *********************
**
** Fetch all Ensembl Marker Feature objects by an Ensembl Slice and
** Ensembl Marker name.
**
** The caller is responsible for deleting the Ensembl Markers Feature objects
** before deleting the AJAX List.
**
** @cc Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor::
** fetch_all_by_Slice_and_MarkerName
** @param [u] mfa [EnsPMarkerfeatureadaptor] Ensembl Marker Feature Adaptor
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [r] name [const AjPStr] Ensembl Marker name
** @param [u] mfs [AjPList] AJAX List of Ensembl Marker Feature objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensMarkerfeatureadaptorFetchAllbySlicemarkername(
EnsPMarkerfeatureadaptor mfa,
EnsPSlice slice,
const AjPStr name,
AjPList mfs)
{
char *txtname = NULL;
AjBool result = AJFALSE;
AjPStr constraint = NULL;
if (!mfa)
return ajFalse;
if (!slice)
return ajFalse;
if (!name)
return ajFalse;
if (!mfs)
return ajFalse;
ensFeatureadaptorEscapeC(mfa, &txtname, name);
constraint = ajFmtStr("marker_synonym.name = '%s'", txtname);
ajCharDel(&txtname);
result = ensFeatureadaptorFetchAllbySlice(
ensMarkerfeatureadaptorGetFeatureadaptor(mfa),
slice,
constraint,
(AjPStr) NULL,
mfs);
ajStrDel(&constraint);
return result;
}
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