/usr/lib/emboss/include/ajmatrices.h is in emboss-lib 6.6.0+dfsg-6.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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**
** 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 */
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