emboss-lib 6.6.0+dfsg-6 / usr / lib / emboss / include / ajdmx.h

/* @include ajdmx *************************************************************
**
** AJAX objects for some of the DOMAINATRIX EMBASSY applications.
** Scophit and Scopalg objects.
**
** @author: Copyright (C) 2004 Ranjeeva Ranasinghe (rranasin@hgmp.mrc.ac.uk)
** @author: Copyright (C) 2004 Jon Ison (jison@hgmp.mrc.ac.uk)
** @version $Revision: 1.23 $
** @modified $Date: 2012/04/12 20:36:03 $ 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.
**
******************************************************************************/

#ifndef AJDMX_H
#define AJDMX_H

/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */

#include "ajdefine.h"
#include "ajstr.h"
#include "ajlist.h"
#include "ajfile.h"
#include "ajpdb.h"
#include "ajdomain.h"

AJ_BEGIN_DECLS




/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */




/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */




/* @data AjPScophit ***********************************************************
**
** AJAX SCOP Hit object
**
** Holds data associated with a protein / domain sequence. Includes SCOP
** classification records.
**
** AjPScophit is implemented as a pointer to a C data structure.
**
** @alias AjSScophit
** @alias AjOScophit
**
** @attr Class [AjPStr] Class name
** @attr Architecture [AjPStr] CATH classification.
** @attr Topology [AjPStr] CATH classification.
** @attr Fold [AjPStr] Fold name
** @attr Superfamily [AjPStr] Superfamily name
** @attr Family [AjPStr] Family name
** @attr Type [AjEDomainType] AJAX Domain Type enumeration
** @attr Sunid_Family [ajuint] Domain identifier of node (e.g. family or
** superfamily) represented.
** @attr Seq [AjPStr] Sequence as string
** @attr Start [ajuint] Start of sequence or signature alignment
**       relative to full length swissprot sequence
** @attr End [ajuint] End of sequence or signature alignment relative
**       to full length swissprot sequence
** @attr Acc [AjPStr] Accession number of sequence entry
** @attr Spr [AjPStr] Swissprot code of sequence entry
** @attr Dom [AjPStr] SCOP or CATH database identifier code of entry.
** @attr Typeobj [AjPStr] Bibliographic information ... objective
** @attr Typesbj [AjPStr] Bibliographic information ... subjective
** @attr Model [AjPStr] String for model type (HMM, Gribskov etc)
** @attr Group [AjPStr] 'REDUNDANT' or 'NON_REDUNDANT'
** @attr Rank [ajuint] Rank order of hit
** @attr Score [float] Score of hit
** @attr Eval [float] E-value of hit
** @attr Pval [float] p-value of hit
** @attr Alg [AjPStr] Alignment, e.g. of a signature to the sequence
** @attr Target [AjBool] True if the Scophit is targeted for removal
**       from a list of Scophit objects
** @attr Target2 [AjBool] Also used for garbage collection
** @attr Priority [AjBool] True if the Scop hit is high priority
** @attr Padding [char[4]] Padding to alignment boundary
**
** @new    ajDmxScophitNew Default Scophit object constructor.
** @delete ajDmxScophitDel Default Scophit object destructor.
** @delete ajDmxScophitDelWrap Wrapper to destructor for Scophit object
**         for use with generic functions.
** @assign ajDmxScophitListCopy Reads a list of Scophit structures and
**         returns a pointer to a duplicate of the list.
** @use    ajDmxScophitCheckTarget Checks to see if the Target element of a
**         Scophit object == ajTrue.
** @modify ajDmxScophitTarget Sets the Target element of a Scophit object
**         to True.
** @modify ajDmxScophitTarget2 Sets the Target2 element of a Scophit object
**         to True.
** @modify ajDmxScophitTargetLowPriority Sets the Target element of a
**         Scophit object to True if its Priority is low.
** @use    ajDmxScophitCompSpr Function to sort Scophit object by Spr element.
** @use    ajDmxScophitCompStart Function to sort Scophit object by Spr
**         element.
** @use    ajDmxScophitCompEnd Function to sort Scophit object by End element.
** @use    ajDmxScophitCompClass Function to sort Scophit object by Class
**         element.
** @use    ajDmxScophitCompFold Function to sort Scophit object by Fold
**         element.
** @use    ajDmxScophitCompSfam Function to sort Scophit object by Superfamily
**         element.
** @use    ajDmxScophitCompFam Function to sort Scophit object by Family
**         element.
** @use    ajDmxScophitCompAcc Function to sort Scophit objects by Acc element.
** @use    ajDmxScophitCompSunid Function to sort Scophit objects by Sunid
**         element.
** @use    ajDmxScophitCompScore Function to sort Scophit objects by Score
**         element.
** @use    ajDmxScophitCompPval Function to sort Scophit objects by Pval
**         element.
** @use    ajDmxScopSeqFromSunid Writes a sequence corresponding to a Scop
**         domain given a Sunid for the domain. The sequence is taken from one
**         of a list of Scop objects that is provided.
** @output ajDmxScophitsWrite Write contents of a list of Scophits to an output
**         file.
** @output ajDmxScophitsWriteFasta Write contents of a list of Scophits to an
**         output file in extended FASTA format.
** @input  ajDmxScophitReadFasta Read a Scophit object from a file in
**         extended FASTA format.
** @assign ajDmxScophitCopy Copies the contents from one Scophit object to
**         another.
** @@
******************************************************************************/

typedef struct AjSScophit
{
    AjPStr Class;
    AjPStr Architecture;
    AjPStr Topology;
    AjPStr Fold;
    AjPStr Superfamily;
    AjPStr Family;
    AjEDomainType Type;
    ajuint Sunid_Family;
    AjPStr Seq;
    ajuint Start;
    ajuint End;
    AjPStr Acc;
    AjPStr Spr;
    AjPStr Dom;
    AjPStr Typeobj;
    AjPStr Typesbj;
    AjPStr Model;
    AjPStr Group;
    ajuint Rank;
    float Score;
    float Eval;
    float Pval;
    AjPStr Alg;
    AjBool Target;
    AjBool Target2;
    AjBool Priority;
    char Padding[4];
} AjOScophit, *AjXScophit;

#define AjPScophit AjOScophit*
#define AjPPScophit AjXScophit*




/* @data AjPScopalg ***********************************************************
**
** AJAX SCOP Alignment object
**
** Holds data associated with a structure alignment.
** Now adapted to hold CATH domain data also by addition of Type,
** Architecture and Topology elements.
**
** AjPScopalg is implemented as a pointer to a C data structure.
**
** @alias AjSScopalg
** @alias AjOScopalg
**
** @attr Class [AjPStr] Class name
** @attr Architecture [AjPStr] CATH classification.
** @attr Topology [AjPStr] CATH classification.
** @attr Fold [AjPStr] Fold name
** @attr Superfamily [AjPStr] Superfamily name
** @attr Family [AjPStr] Family name (SCOP only)
** @attr Sunid_Family [ajuint] SCOP sunid for family
** @attr Width [ajuint] Width (residues) of widest part of alignment
** @attr Type [AjEDomainType] AJAX Domain Type enumeration
** @attr Number [ajuint] No. of sequences in alignment
** @attr Codes [AjPStr*] Array of domain id codes of sequences
** @attr Seqs [AjPStr*] Array of sequences
** @attr Post_similar [AjPStr] Post_similar line from alignment
** @attr Positions [AjPStr] Array of integers from 'Position' line in
**                            alignment, used for manual specification of
**                            signature positions
**
**
**
** @new    ajDmxScopalgRead Read a Scopalg object from a file.
** @output ajDmxScopalgWrite Write a Scopalg object to file in clustal format
**         annotated with SCOP classification info.
** @output ajDmxScopalgWriteClustal Writes a Scopalg object to file in clustal
**         format (just the alignment without the SCOP classification
**         information).
** @output ajDmxScopalgWriteClustal2 Writes a Scopalg object to file in clustal
**         format (just the alignment without the SCOP classification
**         information).
** @output ajDmxScopalgWriteFasta Writes a Scopalg object to file in clustal
**         format (just the alignment without the SCOP classification
**         information).
** @new    ajDmxScopalgNew Scopalg object constructor.
** @delete ajDmxScopalgDel Scopalg object destructor.
** @input  ajDmxScopalgGetseqs Read a Scopalg object and writes an array of
**         AjPStr containing the sequences without gaps.
** @@
******************************************************************************/

typedef struct AjSScopalg
{
    AjPStr Class;
    AjPStr Architecture;
    AjPStr Topology;
    AjPStr Fold;
    AjPStr Superfamily;
    AjPStr Family;
    ajuint Sunid_Family;
    ajuint Width;
    AjEDomainType Type;
    ajuint Number;
    AjPStr *Codes;
    AjPStr *Seqs;
    AjPStr Post_similar;
    AjPStr Positions;
} AjOScopalg;

#define AjPScopalg AjOScopalg*




/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */




/*
** Prototype definitions
*/

void          ajDmxDummyFunction(void);
void          ajDmxExit(void);




/* ======================================================================= */
/* ========================== Scophit object ============================= */
/* ======================================================================= */




AjPScophit    ajDmxScophitNew(void);
void          ajDmxScophitDel(AjPScophit *Pscophit);
void          ajDmxScophitDelWrap(void **Pitem);
AjPList       ajDmxScophitListCopy(const AjPList scophits);

AjBool        ajDmxScophitCheckTarget(const AjPScophit scophit);
AjBool        ajDmxScophitTarget(AjPScophit *Pscophit);
AjBool        ajDmxScophitTarget2(AjPScophit *Pscophit);
AjBool        ajDmxScophitTargetLowPriority(AjPScophit *Pscophit);

ajint         ajDmxScophitCompSpr(const void *item1, const void *item2);
ajint         ajDmxScophitCompStart(const void *item1, const void *item2);
ajint         ajDmxScophitCompEnd(const void *item1, const void *item2);
ajint         ajDmxScophitCompClass(const void *item1, const void *item2);
ajint         ajDmxScophitCompFold(const void *item1, const void *item2);
ajint         ajDmxScophitCompSfam(const void *item1, const void *item2);
ajint         ajDmxScophitCompFam(const void *item1, const void *item2);
ajint         ajDmxScophitCompAcc(const void *item1, const void *item2);
ajint         ajDmxScophitCompSunid(const void *item1, const void *item2);
ajint         ajDmxScophitCompScore(const void *item1, const void *item2);
ajint         ajDmxScophitCompPval(const void *item1, const void *item2);

AjBool        ajDmxScopSeqFromSunid(ajint identifier, AjPStr *seq,
                                    const AjPList scops);
AjBool        ajDmxScophitsWrite(AjPFile outf, const AjPList scophits);
AjBool        ajDmxScophitsWriteFasta(AjPFile outf, const AjPList scophits);
AjPScophit    ajDmxScophitReadFasta(AjPFile inf);
AjBool        ajDmxScophitCopy(AjPScophit *Pto, const AjPScophit from);




/* ======================================================================= */
/* ========================== Scopalg object ============================= */
/* ======================================================================= */




AjBool        ajDmxScopalgRead(AjPFile inf, AjPScopalg *Pscopalg);
AjBool        ajDmxScopalgWrite(const AjPScopalg scopalg, AjPFile outf);
AjBool        ajDmxScopalgWriteClustal(const AjPScopalg scopalg, AjPFile outf);
AjBool        ajDmxScopalgWriteClustal2(const AjPScopalg scopalg, AjPFile outf);
AjBool        ajDmxScopalgWriteFasta(const AjPScopalg scopalg, AjPFile outf);
AjPScopalg    ajDmxScopalgNew(ajuint n);
void          ajDmxScopalgDel(AjPScopalg *Pscopalg);
ajuint        ajDmxScopalgGetseqs(const AjPScopalg scopalg, AjPStr **array);

/*
** End of prototype definitions
*/




AJ_END_DECLS

#endif /* !AJDMX_H */