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/* @source enskaryotype *******************************************************
**
** Ensembl Karyotype Band functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.52 $
** @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 "enskaryotype.h"
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== global variables ============================ */
/* ========================================================================= */
/* ========================================================================= */
/* ============================= private data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private constants =========================== */
/* ========================================================================= */
/* @conststatic karyotypebandadaptorKTablenames *******************************
**
** Array of Ensembl Karyotype Band Adaptor SQL table names
**
******************************************************************************/
static const char *const karyotypebandadaptorKTablenames[] =
{
"karyotype",
(const char *) NULL
};
/* @conststatic karyotypebandadaptorKColumnnames ******************************
**
** Array of Ensembl Karyotype Band Adaptor SQL column names
**
******************************************************************************/
static const char *const karyotypebandadaptorKColumnnames[] =
{
"karyotype.karyotype_id",
"karyotype.seq_region_id",
"karyotype.seq_region_start",
"karyotype.seq_region_end",
"karyotype.band",
"karyotype.stain",
(const char *) NULL
};
/* ========================================================================= */
/* =========================== private variables =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private functions =========================== */
/* ========================================================================= */
static int listKaryotypebandCompareEndAscending(
const void *item1,
const void *item2);
static int listKaryotypebandCompareEndDescending(
const void *item1,
const void *item2);
static int listKaryotypebandCompareIdentifierAscending(
const void *item1,
const void *item2);
static int listKaryotypebandCompareStartAscending(
const void *item1,
const void *item2);
static int listKaryotypebandCompareStartDescending(
const void *item1,
const void *item2);
static AjBool karyotypebandadaptorFetchAllbyStatement(
EnsPBaseadaptor ba,
const AjPStr statement,
EnsPAssemblymapper am,
EnsPSlice slice,
AjPList kblist);
/* ========================================================================= */
/* ======================= All functions by section ======================== */
/* ========================================================================= */
/* @filesection enskaryotype **************************************************
**
** @nam1rule ens Function belongs to the Ensembl library
**
******************************************************************************/
/* @datasection [EnsPKaryotypeband] Ensembl Karyotype Band ********************
**
** @nam2rule Karyotypeband Functions for manipulating
** Ensembl Karyotype Band objects
**
** @cc Bio::EnsEMBL::KaryotypeBand
** @cc CVS Revision: 1.11
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Karyotype Band by pointer.
** It is the responsibility of the user to first destroy any previous
** Karyotype Band. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPKaryotypeband]
**
** @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 kb [const EnsPKaryotypeband] Ensembl Karyotype Band
** @argrule Ini kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor
** @argrule Ini identifier [ajuint] Identifier
** @argrule Ini feature [EnsPFeature] Ensembl Feature
** @argrule Ini name [AjPStr] Name
** @argrule Ini stain [AjPStr] Stain
** @argrule Ref kb [EnsPKaryotypeband] Ensembl Karyotype Band
**
** @valrule * [EnsPKaryotypeband] Ensembl Karyotype Band or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensKaryotypebandNewCpy ***********************************************
**
** Object-based constructor function, which returns an independent object.
**
** @param [r] kb [const EnsPKaryotypeband] Ensembl Karyotype Band
**
** @return [EnsPKaryotypeband] Ensembl Karyotype Band or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPKaryotypeband ensKaryotypebandNewCpy(const EnsPKaryotypeband kb)
{
EnsPKaryotypeband pthis = NULL;
if (!kb)
return NULL;
AJNEW0(pthis);
pthis->Use = 1U;
pthis->Identifier = kb->Identifier;
pthis->Adaptor = kb->Adaptor;
pthis->Feature = ensFeatureNewRef(kb->Feature);
if (kb->Name)
pthis->Name = ajStrNewRef(kb->Name);
if (kb->Stain)
pthis->Stain = ajStrNewRef(kb->Stain);
return pthis;
}
/* @func ensKaryotypebandNewIni ***********************************************
**
** Constructor for an Ensembl Karyotype Band with initial values.
**
** @cc Bio::EnsEMBL::Karyotypeband::new
** @param [u] kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor
** @param [r] identifier [ajuint] Identifier
** @cc Bio::EnsEMBL::Feature::new
** @param [u] feature [EnsPFeature] Ensembl Feature
** @param [u] name [AjPStr] Name
** @param [u] stain [AjPStr] Stain
**
** @return [EnsPKaryotypeband] Ensembl Karyotype Band or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPKaryotypeband ensKaryotypebandNewIni(EnsPKaryotypebandadaptor kba,
ajuint identifier,
EnsPFeature feature,
AjPStr name,
AjPStr stain)
{
EnsPKaryotypeband kb = NULL;
if (!feature)
return NULL;
AJNEW0(kb);
kb->Use = 1U;
kb->Identifier = identifier;
kb->Adaptor = kba;
kb->Feature = ensFeatureNewRef(feature);
if (name)
kb->Name = ajStrNewRef(name);
if (stain)
kb->Stain = ajStrNewRef(stain);
return kb;
}
/* @func ensKaryotypebandNewRef ***********************************************
**
** Ensembl Object referencing function, which returns a pointer to the
** Ensembl Object passed in and increases its reference count.
**
** @param [u] kb [EnsPKaryotypeband] Ensembl Karyotype Band
**
** @return [EnsPKaryotypeband] Ensembl Karyotype Band or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPKaryotypeband ensKaryotypebandNewRef(EnsPKaryotypeband kb)
{
if (!kb)
return NULL;
kb->Use++;
return kb;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Karyotype Band object.
**
** @fdata [EnsPKaryotypeband]
**
** @nam3rule Del Destroy (free) an Ensembl Karyotype Band
**
** @argrule * Pkb [EnsPKaryotypeband*] Ensembl Karyotype Band address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensKaryotypebandDel **************************************************
**
** Default destructor for an Ensembl Karyotype Band.
**
** @param [d] Pkb [EnsPKaryotypeband*] Ensembl Karyotype Band address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensKaryotypebandDel(EnsPKaryotypeband *Pkb)
{
EnsPKaryotypeband pthis = NULL;
if (!Pkb)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensKaryotypebandDel"))
{
ajDebug("ensKaryotypebandDel\n"
" *Pkb %p\n",
*Pkb);
ensKaryotypebandTrace(*Pkb, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Pkb) || --pthis->Use)
{
*Pkb = NULL;
return;
}
ensFeatureDel(&pthis->Feature);
ajStrDel(&pthis->Name);
ajStrDel(&pthis->Stain);
ajMemFree((void **) Pkb);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Karyotype Band object.
**
** @fdata [EnsPKaryotypeband]
**
** @nam3rule Get Return Karyotype Band attribute(s)
** @nam4rule Adaptor Return the Ensembl Karyotype Band Adaptor
** @nam4rule Feature Return the Ensembl Feature
** @nam4rule Identifier Return the SQL database-internal identifier
** @nam4rule Name Return the name
** @nam4rule Stain Return the stain
**
** @argrule * kb [const EnsPKaryotypeband] Karyotype Band
**
** @valrule Adaptor [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor
** or NULL
** @valrule Feature [EnsPFeature] Ensembl Feature or NULL
** @valrule Identifier [ajuint] SQL database-internal identifier or 0U
** @valrule Name [AjPStr] Name or NULL
** @valrule Stain [AjPStr] Stain or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensKaryotypebandGetAdaptor *******************************************
**
** Get the Ensembl Karyotype Band Adaptor member of an Ensembl Karyotype Band.
**
** @param [r] kb [const EnsPKaryotypeband] Ensembl Karyotype Band
**
** @return [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPKaryotypebandadaptor ensKaryotypebandGetAdaptor(
const EnsPKaryotypeband kb)
{
return (kb) ? kb->Adaptor : NULL;
}
/* @func ensKaryotypebandGetFeature *******************************************
**
** Get the Ensembl Feature member of an Ensembl Karyotype Band.
**
** @param [r] kb [const EnsPKaryotypeband] Ensembl Karyotype Band
**
** @return [EnsPFeature] Ensembl Feature or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPFeature ensKaryotypebandGetFeature(
const EnsPKaryotypeband kb)
{
return (kb) ? kb->Feature : NULL;
}
/* @func ensKaryotypebandGetIdentifier ****************************************
**
** Get the SQL database-internal identifier member of an
** Ensembl Karyotype Band.
**
** @param [r] kb [const EnsPKaryotypeband] Ensembl Karyotype Band
**
** @return [ajuint] SQL database-internal identifier or 0U
**
** @release 6.3.0
** @@
******************************************************************************/
ajuint ensKaryotypebandGetIdentifier(
const EnsPKaryotypeband kb)
{
return (kb) ? kb->Identifier : 0U;
}
/* @func ensKaryotypebandGetName **********************************************
**
** Get the name member of an Ensembl Karyotype Band.
**
** @param [r] kb [const EnsPKaryotypeband] Ensembl Karyotype Band
**
** @return [AjPStr] Name or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
AjPStr ensKaryotypebandGetName(
const EnsPKaryotypeband kb)
{
return (kb) ? kb->Name : NULL;
}
/* @func ensKaryotypebandGetStain *********************************************
**
** Get the stain member of an Ensembl Karyotype Band.
**
** @param [r] kb [const EnsPKaryotypeband] Ensembl Karyotype Band
**
** @return [AjPStr] Stain or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
AjPStr ensKaryotypebandGetStain(
const EnsPKaryotypeband kb)
{
return (kb) ? kb->Stain : NULL;
}
/* @section modifiers *********************************************************
**
** Functions for assigning members of an Ensembl Karyotype Band object.
**
** @fdata [EnsPKaryotypeband]
**
** @nam3rule Set Set one member of an Karyotype Band
** @nam4rule Adaptor Set the Ensembl Karyotype Band Adaptor
** @nam4rule Feature Set the Ensembl Feature
** @nam4rule Identifier Set the SQL database-internal identifier
** @nam4rule Name Set the name
** @nam4rule Stain Set the stain
**
** @argrule * kb [EnsPKaryotypeband] Ensembl Karyotype Band object
** @argrule Adaptor kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band
** Adaptor
** @argrule Feature feature [EnsPFeature] Ensembl Feature
** @argrule Identifier identifier [ajuint] Database identifier
** @argrule Name name [AjPStr] Name
** @argrule Stain stain [AjPStr] Logic name
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory modify
******************************************************************************/
/* @func ensKaryotypebandSetAdaptor *******************************************
**
** Set the Ensembl Karyotype Band Adaptor member of an Ensembl Karyotype Band.
**
** @param [u] kb [EnsPKaryotypeband] Ensembl Karyotype Band
** @param [u] kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensKaryotypebandSetAdaptor(EnsPKaryotypeband kb,
EnsPKaryotypebandadaptor kba)
{
if (!kb)
return ajFalse;
kb->Adaptor = kba;
return ajTrue;
}
/* @func ensKaryotypebandSetFeature *******************************************
**
** Set the Ensembl Feature member of an Ensembl Karyotype Band.
**
** @param [u] kb [EnsPKaryotypeband] Ensembl Karyotype Band
** @param [u] feature [EnsPFeature] Ensembl Feature
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensKaryotypebandSetFeature(EnsPKaryotypeband kb,
EnsPFeature feature)
{
if (!kb)
return ajFalse;
ensFeatureDel(&kb->Feature);
kb->Feature = ensFeatureNewRef(feature);
return ajTrue;
}
/* @func ensKaryotypebandSetIdentifier ****************************************
**
** Set the SQL database-internal identifier member of an
** Ensembl Karyotype Band.
**
** @param [u] kb [EnsPKaryotypeband] Ensembl Karyotype Band
** @param [r] identifier [ajuint] Database identifier
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensKaryotypebandSetIdentifier(EnsPKaryotypeband kb,
ajuint identifier)
{
if (!kb)
return ajFalse;
kb->Identifier = identifier;
return ajTrue;
}
/* @func ensKaryotypebandSetName **********************************************
**
** Set the name member of an Ensembl Karyotype Band.
**
** @param [u] kb [EnsPKaryotypeband] Ensembl Karyotype Band
** @param [u] name [AjPStr] Name
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensKaryotypebandSetName(EnsPKaryotypeband kb,
AjPStr name)
{
if (!kb)
return ajFalse;
ajStrDel(&kb->Name);
kb->Name = ajStrNewRef(name);
return ajTrue;
}
/* @func ensKaryotypebandSetStain *********************************************
**
** Set the stain member of an Ensembl Karyotype Band.
**
** @param [u] kb [EnsPKaryotypeband] Ensembl Karyotype Band
** @param [u] stain [AjPStr] Logic name
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensKaryotypebandSetStain(EnsPKaryotypeband kb,
AjPStr stain)
{
if (!kb)
return ajFalse;
ajStrDel(&kb->Stain);
kb->Stain = ajStrNewRef(stain);
return ajTrue;
}
/* @section debugging *********************************************************
**
** Functions for reporting of an Ensembl Karyotype Band object.
**
** @fdata [EnsPKaryotypeband]
**
** @nam3rule Trace Report Ensembl Karyotype Band members to debug file
**
** @argrule Trace kb [const EnsPKaryotypeband] Ensembl Karyotype Band
** @argrule Trace level [ajuint] Indentation level
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensKaryotypebandTrace ************************************************
**
** Trace an Ensembl Karyotype Band.
**
** @param [r] kb [const EnsPKaryotypeband] Ensembl Karyotype Band
** @param [r] level [ajuint] Indentation level
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensKaryotypebandTrace(const EnsPKaryotypeband kb, ajuint level)
{
AjPStr indent = NULL;
if (!kb)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensKaryotypebandTrace %p\n"
"%S Adaptor %p\n"
"%S Identifier %u\n"
"%S Feature %p\n"
"%S Name '%S'\n"
"%S Stain '%S'\n",
indent, kb,
indent, kb->Adaptor,
indent, kb->Identifier,
indent, kb->Feature,
indent, kb->Name,
indent, kb->Stain);
ensFeatureTrace(kb->Feature, 1);
ajStrDel(&indent);
return ajTrue;
}
/* @section calculate *********************************************************
**
** Functions for calculating information from an Ensembl Karyotype Band object.
**
** @fdata [EnsPKaryotypeband]
**
** @nam3rule Calculate Calculate Ensembl Karyotype Band information
** @nam4rule Memsize Calculate the memory size in bytes
**
** @argrule * kb [const EnsPKaryotypeband] Ensembl Karyotype Band
**
** @valrule Memsize [size_t] Memory size in bytes or 0
**
** @fcategory misc
******************************************************************************/
/* @func ensKaryotypebandCalculateMemsize *************************************
**
** Get the memory size in bytes of an Ensembl Karyotype Band.
**
** @param [r] kb [const EnsPKaryotypeband] Ensembl Karyotype Band
**
** @return [size_t] Memory size in bytes or 0
**
** @release 6.4.0
** @@
******************************************************************************/
size_t ensKaryotypebandCalculateMemsize(const EnsPKaryotypeband kb)
{
size_t size = 0;
if (!kb)
return 0;
size += sizeof (EnsOKaryotypeband);
size += ensFeatureCalculateMemsize(kb->Feature);
if (kb->Name)
{
size += sizeof (AjOStr);
size += ajStrGetRes(kb->Name);
}
if (kb->Stain)
{
size += sizeof (AjOStr);
size += ajStrGetRes(kb->Stain);
}
return size;
}
/* @datasection [AjPList] AJAX List *******************************************
**
** @nam2rule List Functions for manipulating AJAX List objects
**
******************************************************************************/
/* @funcstatic listKaryotypebandCompareEndAscending ***************************
**
** AJAX List of Ensembl Karyotype Band objects comparison function to sort by
** Ensembl Feature end coordinate in ascending order.
**
** @param [r] item1 [const void*] Ensembl Karyotype Band address 1
** @param [r] item2 [const void*] Ensembl Karyotype Band 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 listKaryotypebandCompareEndAscending(
const void *item1,
const void *item2)
{
EnsPKaryotypeband kb1 = *(EnsOKaryotypeband *const *) item1;
EnsPKaryotypeband kb2 = *(EnsOKaryotypeband *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listKaryotypebandCompareEndAscending"))
ajDebug("listKaryotypebandCompareEndAscending\n"
" kb1 %p\n"
" kb2 %p\n",
kb1,
kb2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (kb1 && (!kb2))
return -1;
if ((!kb1) && (!kb2))
return 0;
if ((!kb1) && kb2)
return +1;
return ensFeatureCompareEndAscending(kb1->Feature, kb2->Feature);
}
/* @funcstatic listKaryotypebandCompareEndDescending **************************
**
** AJAX List of Ensembl Karyotype Band objects comparison function to sort by
** Ensembl Feature end coordinate in descending order.
**
** @param [r] item1 [const void*] Ensembl Karyotype Band address 1
** @param [r] item2 [const void*] Ensembl Karyotype Band 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 listKaryotypebandCompareEndDescending(
const void *item1,
const void *item2)
{
EnsPKaryotypeband kb1 = *(EnsOKaryotypeband *const *) item1;
EnsPKaryotypeband kb2 = *(EnsOKaryotypeband *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listKaryotypebandCompareEndDescending"))
ajDebug("listKaryotypebandCompareEndDescending\n"
" kb1 %p\n"
" kb2 %p\n",
kb1,
kb2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (kb1 && (!kb2))
return -1;
if ((!kb1) && (!kb2))
return 0;
if ((!kb1) && kb2)
return +1;
return ensFeatureCompareEndDescending(kb1->Feature, kb2->Feature);
}
/* @funcstatic listKaryotypebandCompareIdentifierAscending ********************
**
** AJAX List of Ensembl Karyotype Band objects comparison function to sort by
** identifier member in ascending order.
**
** @param [r] item1 [const void*] Ensembl Karyotype Band address 1
** @param [r] item2 [const void*] Ensembl Karyotype Band 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 listKaryotypebandCompareIdentifierAscending(
const void *item1,
const void *item2)
{
EnsPKaryotypeband kb1 = *(EnsOKaryotypeband *const *) item1;
EnsPKaryotypeband kb2 = *(EnsOKaryotypeband *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listKaryotypebandCompareIdentifierAscending"))
ajDebug("listKaryotypebandCompareIdentifierAscending\n"
" kb1 %p\n"
" kb2 %p\n",
kb1,
kb2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (kb1 && (!kb2))
return -1;
if ((!kb1) && (!kb2))
return 0;
if ((!kb1) && kb2)
return +1;
if (kb1->Identifier < kb2->Identifier)
return -1;
if (kb1->Identifier > kb2->Identifier)
return +1;
return 0;
}
/* @funcstatic listKaryotypebandCompareStartAscending *************************
**
** AJAX List of Ensembl Karyotype Band objects comparison function to sort by
** Ensembl Feature start coordinate in ascending order.
**
** @param [r] item1 [const void*] Ensembl Karyotype Band address 1
** @param [r] item2 [const void*] Ensembl Karyotype Band 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 listKaryotypebandCompareStartAscending(
const void *item1,
const void *item2)
{
EnsPKaryotypeband kb1 = *(EnsOKaryotypeband *const *) item1;
EnsPKaryotypeband kb2 = *(EnsOKaryotypeband *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listKaryotypebandCompareStartAscending"))
ajDebug("listKaryotypebandCompareStartAscending\n"
" kb1 %p\n"
" kb2 %p\n",
kb1,
kb2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (kb1 && (!kb2))
return -1;
if ((!kb1) && (!kb2))
return 0;
if ((!kb1) && kb2)
return +1;
return ensFeatureCompareStartAscending(kb1->Feature, kb2->Feature);
}
/* @funcstatic listKaryotypebandCompareStartDescending ************************
**
** AJAX List of Ensembl Karyotype Band objects comparison function to sort by
** Ensembl Feature start coordinate in descending order.
**
** @param [r] item1 [const void*] Ensembl Karyotype Band address 1
** @param [r] item2 [const void*] Ensembl Karyotype Band 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 listKaryotypebandCompareStartDescending(
const void *item1,
const void *item2)
{
EnsPKaryotypeband kb1 = *(EnsOKaryotypeband *const *) item1;
EnsPKaryotypeband kb2 = *(EnsOKaryotypeband *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listKaryotypebandCompareStartDescending"))
ajDebug("listKaryotypebandCompareStartDescending\n"
" kb1 %p\n"
" kb2 %p\n",
kb1,
kb2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (kb1 && (!kb2))
return -1;
if ((!kb1) && (!kb2))
return 0;
if ((!kb1) && kb2)
return +1;
return ensFeatureCompareStartDescending(kb1->Feature, kb2->Feature);
}
/* @section list **************************************************************
**
** Functions for manipulating AJAX List objects.
**
** @fdata [AjPList]
**
** @nam3rule Karyotypeband Functions for manipulating AJAX List objects of
** Ensembl Karyotype Band 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 * kbs [AjPList] AJAX List of Ensembl Karyotype Band objects
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensListKaryotypebandSortEndAscending *********************************
**
** Sort an AJAX List of Ensembl Karyotype Band objects by their
** Ensembl Feature end coordinate in ascending order.
**
** @param [u] kbs [AjPList] AJAX List of Ensembl Karyotype Band objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListKaryotypebandSortEndAscending(AjPList kbs)
{
if (!kbs)
return ajFalse;
ajListSortTwoThree(kbs,
&listKaryotypebandCompareEndAscending,
&listKaryotypebandCompareStartAscending,
&listKaryotypebandCompareIdentifierAscending);
return ajTrue;
}
/* @func ensListKaryotypebandSortEndDescending ********************************
**
** Sort an AJAX List of Ensembl Karyotype Band objects by their
** Ensembl Feature end coordinate in descending order.
**
** @param [u] kbs [AjPList] AJAX List of Ensembl Karyotype band objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListKaryotypebandSortEndDescending(AjPList kbs)
{
if (!kbs)
return ajFalse;
ajListSortTwoThree(kbs,
&listKaryotypebandCompareEndDescending,
&listKaryotypebandCompareStartDescending,
&listKaryotypebandCompareIdentifierAscending);
return ajTrue;
}
/* @func ensListKaryotypebandSortIdentifierAscending **************************
**
** Sort an AJAX List of Ensembl Karyotype Band objects by their
** identifier member in ascending order.
**
** @param [u] kbs [AjPList] AJAX List of Ensembl Karyotype Band objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListKaryotypebandSortIdentifierAscending(AjPList kbs)
{
if (!kbs)
return ajFalse;
ajListSort(kbs, &listKaryotypebandCompareIdentifierAscending);
return ajTrue;
}
/* @func ensListKaryotypebandSortStartAscending *******************************
**
** Sort an AJAX List of Ensembl Karyotype Band objects by their
** Ensembl Feature start coordinate in ascending order.
**
** @param [u] kbs [AjPList] AJAX List of Ensembl Karyotype Band objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListKaryotypebandSortStartAscending(AjPList kbs)
{
if (!kbs)
return ajFalse;
ajListSortTwoThree(kbs,
&listKaryotypebandCompareStartAscending,
&listKaryotypebandCompareEndAscending,
&listKaryotypebandCompareIdentifierAscending);
return ajTrue;
}
/* @func ensListKaryotypebandSortStartDescending ******************************
**
** Sort an AJAX List of Ensembl Karyotype Band objects by their
** Ensembl Feature start coordinate in descending order.
**
** @param [u] kbs [AjPList] AJAX List of Ensembl Karyotype band objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListKaryotypebandSortStartDescending(AjPList kbs)
{
if (!kbs)
return ajFalse;
ajListSortTwoThree(kbs,
&listKaryotypebandCompareStartDescending,
&listKaryotypebandCompareEndDescending,
&listKaryotypebandCompareIdentifierAscending);
return ajTrue;
}
/* @datasection [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor *****
**
** @nam2rule Karyotypebandadaptor Functions for manipulating
** Ensembl Karyotype Band Adaptor objects
**
** @cc Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor
** @cc CVS Revision: 1.35
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @funcstatic karyotypebandadaptorFetchAllbyStatement ************************
**
** Fetch all Ensembl Karyotype Band 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] kblist [AjPList] AJAX List of Ensembl Karyotype Band objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
static AjBool karyotypebandadaptorFetchAllbyStatement(
EnsPBaseadaptor ba,
const AjPStr statement,
EnsPAssemblymapper am,
EnsPSlice slice,
AjPList kblist)
{
ajuint identifier = 0U;
ajuint srid = 0U;
ajuint srstart = 0U;
ajuint srend = 0U;
ajint srstrand = 1;
AjPStr name = NULL;
AjPStr stain = NULL;
AjPSqlstatement sqls = NULL;
AjISqlrow sqli = NULL;
AjPSqlrow sqlr = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPFeature feature = NULL;
EnsPKaryotypeband kb = NULL;
EnsPKaryotypebandadaptor kba = NULL;
if (ajDebugTest("karyotypebandadaptorFetchAllbyStatement"))
ajDebug("karyotypebandadaptorFetchAllbyStatement\n"
" ba %p\n"
" statement %p\n"
" am %p\n"
" slice %p\n"
" kblist %p\n",
ba,
statement,
am,
slice,
kblist);
if (!ba)
return ajFalse;
if (!statement)
return ajFalse;
if (!kblist)
return ajFalse;
dba = ensBaseadaptorGetDatabaseadaptor(ba);
kba = ensRegistryGetKaryotypebandadaptor(dba);
sqls = ensDatabaseadaptorSqlstatementNew(dba, statement);
sqli = ajSqlrowiterNew(sqls);
while (!ajSqlrowiterDone(sqli))
{
identifier = 0;
srid = 0;
srstart = 0;
srend = 0;
name = ajStrNew();
stain = ajStrNew();
sqlr = ajSqlrowiterGet(sqli);
ajSqlcolumnToUint(sqlr, &identifier);
ajSqlcolumnToUint(sqlr, &srid);
ajSqlcolumnToUint(sqlr, &srstart);
ajSqlcolumnToUint(sqlr, &srend);
ajSqlcolumnToStr(sqlr, &name);
ajSqlcolumnToStr(sqlr, &stain);
ensBaseadaptorRetrieveFeature(ba,
0U,
srid,
srstart,
srend,
srstrand,
am,
slice,
&feature);
if (!feature)
{
ajStrDel(&name);
ajStrDel(&stain);
continue;
}
kb = ensKaryotypebandNewIni(kba, identifier, feature, name, stain);
ajListPushAppend(kblist, (void *) kb);
ensFeatureDel(&feature);
ajStrDel(&name);
ajStrDel(&stain);
}
ajSqlrowiterDel(&sqli);
ensDatabaseadaptorSqlstatementDel(dba, &sqls);
return ajTrue;
}
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Karyotype Band Adaptor by pointer.
** It is the responsibility of the user to first destroy any previous
** Karyotype Band Adaptor. The target pointer does not need to be
** initialised to NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPKaryotypebandadaptor]
**
** @nam3rule New Constructor
**
** @argrule New dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @valrule * [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensKaryotypebandadaptorNew *******************************************
**
** Default constructor for an Ensembl Karyotype Band 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 ensRegistryGetKaryotypebandadaptor
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPKaryotypebandadaptor ensKaryotypebandadaptorNew(
EnsPDatabaseadaptor dba)
{
return ensFeatureadaptorNew(
dba,
karyotypebandadaptorKTablenames,
karyotypebandadaptorKColumnnames,
(const EnsPBaseadaptorLeftjoin) NULL,
(const char *) NULL,
(const char *) NULL,
&karyotypebandadaptorFetchAllbyStatement,
(void *(*)(const void *)) NULL,
(void *(*)(void *)) &ensKaryotypebandNewRef,
(AjBool (*)(const void *)) NULL,
(void (*)(void **)) &ensKaryotypebandDel,
(size_t (*)(const void *)) &ensKaryotypebandCalculateMemsize,
(EnsPFeature (*)(const void *)) &ensKaryotypebandGetFeature,
"Karyotype Band");
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Karyotype Band Adaptor object.
**
** @fdata [EnsPKaryotypebandadaptor]
**
** @nam3rule Del Destroy (free) an Ensembl Karyotype Band Adaptor
**
** @argrule * Pkba [EnsPKaryotypebandadaptor*]
** Ensembl Karyotype Band Adaptor address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensKaryotypebandadaptorDel *******************************************
**
** Default destructor for an Ensembl Karyotype Band 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] Pkba [EnsPKaryotypebandadaptor*]
** Ensembl Karyotype Band Adaptor address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensKaryotypebandadaptorDel(EnsPKaryotypebandadaptor *Pkba)
{
ensFeatureadaptorDel(Pkba);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an
** Ensembl Karyotype Band Adaptor object.
**
** @fdata [EnsPKaryotypebandadaptor]
**
** @nam3rule Get Return Ensembl Karyotype Band 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 * kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band 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 ensKaryotypebandadaptorGetBaseadaptor ********************************
**
** Get the Ensembl Base Adaptor member of an
** Ensembl Karyotype Band Adaptor.
**
** @param [u] kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor
**
** @return [EnsPBaseadaptor] Ensembl Base Adaptor or NULL
**
** @release 6.5.0
** @@
******************************************************************************/
EnsPBaseadaptor ensKaryotypebandadaptorGetBaseadaptor(
EnsPKaryotypebandadaptor kba)
{
return ensFeatureadaptorGetBaseadaptor(
ensKaryotypebandadaptorGetFeatureadaptor(kba));
}
/* @func ensKaryotypebandadaptorGetDatabaseadaptor ****************************
**
** Get the Ensembl Database Adaptor member of an
** Ensembl Karyotype Band Adaptor.
**
** @param [u] kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor
**
** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPDatabaseadaptor ensKaryotypebandadaptorGetDatabaseadaptor(
EnsPKaryotypebandadaptor kba)
{
return ensFeatureadaptorGetDatabaseadaptor(
ensKaryotypebandadaptorGetFeatureadaptor(kba));
}
/* @func ensKaryotypebandadaptorGetFeatureadaptor *****************************
**
** Get the Ensembl Feature Adaptor member of an
** Ensembl Karyotype Band Adaptor.
**
** @param [u] kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor
**
** @return [EnsPFeatureadaptor] Ensembl Feature or NULL
**
** @release 6.5.0
** @@
******************************************************************************/
EnsPFeatureadaptor ensKaryotypebandadaptorGetFeatureadaptor(
EnsPKaryotypebandadaptor kba)
{
return kba;
}
/* @section canonical object retrieval ****************************************
**
** Functions for fetching Ensembl Karyotype Band objects from an
** Ensembl SQL database.
**
** @fdata [EnsPKaryotypebandadaptor]
**
** @nam3rule Fetch Fetch Ensembl Karyotype Band object(s)
** @nam4rule All Fetch all Ensembl Karyotype Band objects
** @nam4rule Allby Fetch all Ensembl Karyotype Band objects matching a
** criterion
** @nam5rule Chromosomeband Fetch all by a chromosome band
** @nam5rule Chromosomename Fetch all by a chromosome name
** @nam5rule Slice Fetch all by an Ensembl Slice
** @nam4rule By Fetch one Ensembl Karyotype Band object matching a criterion
** @nam5rule Identifier Fetch by SQL database-internal identifier
**
** @argrule * kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor
** @argrule All kbs [AjPList] AJAX List of Ensembl Karyotype Band objects
** @argrule AllbySlice slice [EnsPSlice] Ensembl Slice
** @argrule AllbySlice constraint [const AjPStr] SQL constraint
** @argrule AllbySlice kbs [AjPList] AJAX List of Ensembl Karyotype Band
** objects
** @argrule AllbyChromosomeband name [const AjPStr] Chromosome name
** @argrule AllbyChromosomeband band [const AjPStr] Karyotype Band name
** @argrule AllbyChromosomeband kblist [AjPList] AJAX List of Ensembl
** Karyotype Band objects
** @argrule AllbyChromosomename name [const AjPStr] Chromosome name
** @argrule AllbyChromosomename kblist [AjPList] AJAX List of Ensembl
** Karyotype Band objects
** @argrule ByIdentifier identifier [ajuint] SQL database-internal identifier
** @argrule ByIdentifier Pkb [EnsPKaryotypeband*] Ensembl Karyotype Band
** address
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensKaryotypebandadaptorFetchAllbyChromosomeband **********************
**
** Fetch all Ensembl Karyotype Band objects via a chromosome and band name.
**
** This function uses fuzzy matching of the band name.
** For example the bands 'q23.1' and 'q23.4' could be matched by 'q23'.
**
** @cc Bio::EnsEMBL::DBSQL::Karyotypebandadaptor::fetch_all_by_chr_band
** @param [u] kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor
** @param [r] name [const AjPStr] Chromosome name
** @param [r] band [const AjPStr] Karyotype Band name
** @param [u] kblist [AjPList] AJAX List of Ensembl Karyotype Band objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensKaryotypebandadaptorFetchAllbyChromosomeband(
EnsPKaryotypebandadaptor kba,
const AjPStr name,
const AjPStr band,
AjPList kblist)
{
char *txtband = NULL;
AjBool result = AJFALSE;
AjPStr constraint = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPSlice slice = NULL;
if (!kba)
return ajFalse;
if (!name)
return ajFalse;
if (!band)
return ajFalse;
if (!kblist)
return ajFalse;
dba = ensKaryotypebandadaptorGetDatabaseadaptor(kba);
ensSliceadaptorFetchBySeqregionName(
ensRegistryGetSliceadaptor(dba),
(const AjPStr) NULL,
(const AjPStr) NULL,
name,
&slice);
if (!slice)
{
ajDebug("ensKaryotypebandadaptorFetchAllbyChromosomeband could not "
"fetch an Ensembl Slice for chromosome name '%S'.\n", name);
return ajFalse;
}
ensDatabaseadaptorEscapeC(dba, &txtband, band);
constraint = ajFmtStr("karyotype.band LIKE '%s%%'", txtband);
ajCharDel(&txtband);
result = ensFeatureadaptorFetchAllbySlice(
ensKaryotypebandadaptorGetFeatureadaptor(kba),
slice,
constraint,
(const AjPStr) NULL,
kblist);
ajStrDel(&constraint);
ensSliceDel(&slice);
return result;
}
/* @func ensKaryotypebandadaptorFetchAllbyChromosomename **********************
**
** Fetch all Ensembl Karyotype Band objects via a chromosome name.
**
** @cc Bio::EnsEMBL::DBSQL::Karyotypebandadaptor::fetch_all_by_chr_name
** @param [u] kba [EnsPKaryotypebandadaptor] Ensembl Karyotype Band Adaptor
** @param [r] name [const AjPStr] Chromosome name
** @param [u] kblist [AjPList] AJAX List of Ensembl Karyotype Band objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensKaryotypebandadaptorFetchAllbyChromosomename(
EnsPKaryotypebandadaptor kba,
const AjPStr name,
AjPList kblist)
{
AjBool result = AJFALSE;
EnsPDatabaseadaptor dba = NULL;
EnsPSlice slice = NULL;
if (!kba)
return ajFalse;
if (!name)
return ajFalse;
if (!kblist)
return ajFalse;
dba = ensKaryotypebandadaptorGetDatabaseadaptor(kba);
ensSliceadaptorFetchBySeqregionName(
ensRegistryGetSliceadaptor(dba),
(const AjPStr) NULL,
(const AjPStr) NULL,
name,
&slice);
if (!slice)
{
ajDebug("ensKaryotypebandadaptorFetchAllbyChromosomename could not "
"fetch an Ensembl Slice for chromosome name '%S'.\n", name);
return ajFalse;
}
result = ensFeatureadaptorFetchAllbySlice(
ensKaryotypebandadaptorGetFeatureadaptor(kba),
slice,
(const AjPStr) NULL,
(const AjPStr) NULL,
kblist);
ensSliceDel(&slice);
return result;
}
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