/* @include ajmatrices ********************************************************
**
** AJAX matrices functions
**
** @author Copyright (C) 2003 Alan Bleasby
** @author Copyright (C) 2003 Peter Rice
** @version $Revision: 1.25 $
** @modified Copyright (C) 2003 Jon Ison. Rewritten for string matrix labels
** @modified $Date: 2011/10/18 14:23:40 $ by $Author: rice $
** @@
**
** 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 AJMATRICES_H
#define AJMATRICES_H

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

#include "ajdefine.h"
#include "ajseq.h"

AJ_BEGIN_DECLS




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




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




/* @data AjPMatrix ************************************************************
**
** AJAX data structure for sequence comparison matrices with integer values
**
** @alias AjSMatrix
** @alias AjOMatrix
**
** @attr Size [ajint] Matrix size (size of 2D array)
** @attr SizeRow [ajint] Number of rows (if different to Size)
** @attr Name [AjPStr] Matrix name
** @attr Codes [AjPStr*] Row/column codes
** @attr CodesRow [AjPStr*] Row codes (if different to Codes)
** @attr Matrix [AjIntArray*] Matrix as 2D array
** @attr Cvt [AjPSeqCvt] Conversion table
** @@
******************************************************************************/

typedef struct AjSMatrix
{
    ajint Size;
    ajint SizeRow;
    AjPStr Name;
    AjPStr* Codes;
    AjPStr* CodesRow;
    AjIntArray* Matrix;
    AjPSeqCvt Cvt;
} AjOMatrix;

#define AjPMatrix AjOMatrix*




/* @data AjPMatrixf ***********************************************************
**
** AJAX data structure for sequence comparison matrices with floating
** point values
**
** @alias AjSMatrixf
** @alias AjOMatrixf
**
** @attr Size [ajint] Matrix size (size of 2D array)
** @attr SizeRow [ajint] Number of rows (if different to Size)
** @attr Name [AjPStr] Matrix name
** @attr Codes [AjPStr*] Row/column codes
** @attr CodesRow [AjPStr*] Row codes (if different to Codes)
** @attr Matrixf [AjFloatArray*] Matrix as 2D array
** @attr Cvt [AjPSeqCvt] Conversion table
** @@
******************************************************************************/

typedef struct AjSMatrixf
{
    ajint Size;
    ajint SizeRow;
    AjPStr Name;
    AjPStr* Codes;
    AjPStr* CodesRow;
    AjFloatArray* Matrixf;
    AjPSeqCvt Cvt;
} AjOMatrixf;

#define AjPMatrixf AjOMatrixf*




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




/*
** Prototype definitions
*/

void          ajMatrixDel(AjPMatrix *thys);
AjPStr        ajMatrixGetCodes(const AjPMatrix thys);
AjPSeqCvt     ajMatrixGetCvt(const AjPMatrix thys);
const AjPStr  ajMatrixGetLabelNum(const AjPMatrix thys, ajint i);
AjIntArray*   ajMatrixGetMatrix(const AjPMatrix thys);
const AjPStr  ajMatrixGetName(const AjPMatrix thys);
ajuint        ajMatrixGetRows(const AjPMatrix thys);
ajuint        ajMatrixGetSize(const AjPMatrix thys);
AjPMatrix     ajMatrixNew(const AjPPStr codes, ajint n,
                          const AjPStr filename);
AjPMatrix     ajMatrixNewAsym(const AjPPStr codes, ajint n,
                              const AjPPStr rcodes, ajint rn,
                              const AjPStr filename);
AjPMatrix     ajMatrixNewFile(const AjPStr filename);
AjBool        ajMatrixSeqIndex(const AjPMatrix thys, const AjPSeq seq,
                               AjPStr* numseq);

void          ajMatrixfDel(AjPMatrixf *thys);
AjPStr        ajMatrixfGetCodes(const AjPMatrixf thys);
AjPSeqCvt     ajMatrixfGetCvt(const AjPMatrixf thys);
const AjPStr  ajMatrixfGetLabelNum(const AjPMatrixf thys, ajint i);
AjFloatArray* ajMatrixfGetMatrix(const AjPMatrixf thys);
const AjPStr  ajMatrixfGetName(const AjPMatrixf thys);
ajuint        ajMatrixfGetRows(const AjPMatrixf thys);
ajuint        ajMatrixfGetSize(const AjPMatrixf thys);
AjPMatrixf    ajMatrixfNew(const AjPPStr codes, ajint n,
                           const AjPStr filename);
AjPMatrixf    ajMatrixfNewAsym(const AjPPStr codes, ajint n,
                               const AjPPStr rcodes, ajint rn,
                               const AjPStr filename);
AjPMatrixf    ajMatrixfNewFile(const AjPStr filename);
AjBool        ajMatrixfSeqIndex(const AjPMatrixf thys, const AjPSeq seq,
                                AjPStr* numseq);
void          ajMatrixExit(void);

/*
** End of prototype definitions
*/




#ifdef AJ_COMPILE_DEPRECATED_BOOK
#endif /* AJ_COMPILE_DEPRECATED_BOOK */

#ifdef AJ_COMPILE_DEPRECATED

__deprecated void          ajMatrixfChar(const AjPMatrixf thys,
                                         ajint i, AjPStr *label);
__deprecated void          ajMatrixChar(const AjPMatrix thys,
                                        ajint i, AjPStr *label);
__deprecated const AjPStr  ajMatrixfName(const AjPMatrixf thys);
__deprecated const AjPStr  ajMatrixName(const AjPMatrix thys);
__deprecated AjPSeqCvt     ajMatrixCvt(const AjPMatrix thys);
__deprecated AjPSeqCvt     ajMatrixfCvt(const AjPMatrixf thys);
__deprecated ajint         ajMatrixSize(const AjPMatrix thys);
__deprecated ajint         ajMatrixfSize(const AjPMatrixf thys);
__deprecated AjIntArray*   ajMatrixArray(const AjPMatrix thys);
__deprecated AjFloatArray* ajMatrixfArray(const AjPMatrixf thys);
__deprecated AjBool        ajMatrixRead(AjPMatrix* pthis,
                                        const AjPStr filename);
__deprecated AjBool        ajMatrixfRead(AjPMatrixf* pthis,
                                         const AjPStr filename);
__deprecated AjBool        ajMatrixSeqNum(const AjPMatrix thys,
                                          const AjPSeq seq, AjPStr* numseq);
__deprecated AjBool        ajMatrixfSeqNum(const AjPMatrixf thys,
                                           const AjPSeq seq, AjPStr* numseq);

#endif /* AJ_COMPILE_DEPRECATED */




AJ_END_DECLS

#endif /* !AJMATRICES_H */