/usr/lib/emboss/include/embdmx.h is in emboss-lib 6.3.1-6ubuntu3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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**
** @source embdmx.h
**
** @source Algorithms for some of the DOMAINATRIX EMBASSY applications.
** For Scophit and Scopalign objects defined in ajxyz.h
** The functionality will eventually be subsumed by other AJAX and NUCLEUS
** libraries.
**
** @author: Copyright (C) 2004 Ranjeeva Ranasinghe (rranasin@hgmp.mrc.ac.uk)
** @author: Copyright (C) 2004 Jon Ison (jison@hgmp.mrc.ac.uk)
** @version 1.0
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Library General Public
** License as published by the Free Software Foundation; either
** version 2 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
** Library General Public License for more details.
**
** You should have received a copy of the GNU Library General Public
** License along with this library; if not, write to the
** Free Software Foundation, Inc., 59 Temple Place - Suite 330,
** Boston, MA 02111-1307, USA.
****************************************************************************/
#ifdef __cplusplus
extern "C"
{
#endif
#ifndef embdmx_h
#define embdmx_h
/* @data EmbPDmxNrseq *********************************************************
**
** NUCLEUS data structure for non-redundant sequence testing
**
** @attr Seq [AjPSeq] Sequence to be tested for redundancy
** @attr Garbage [AjBool] True if sequence is to be ignored
** @attr Padding [char[4]] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EmbSDmxNrseq {
AjPSeq Seq;
AjBool Garbage;
char Padding[4];
} EmbODmxNrseq;
#define EmbPDmxNrseq EmbODmxNrseq*
/*****************************************************************************/
/* These functions are NOT YET DOCUMENTED in the appropriate data structures */
/*****************************************************************************/
/*
** Prototype definitions
*/
void embDmxNrseqDel(EmbPDmxNrseq* Pnrseq);
EmbPDmxNrseq embDmxNrseqNew(const AjPSeq seq);
AjPList embDmxScophitReadAllFasta(AjPFile in);
AjBool embDmxHitlistToScophits(const AjPList in,
AjPList out);
AjBool embDmxScophitsToHitlist(const AjPList in,
EmbPHitlist *out,
AjIList *iter);
AjBool embDmxScophitToHit(EmbPHit *to,
const AjPScophit from);
AjBool embDmxScophitsAccToHitlist(const AjPList in,
EmbPHitlist *out,
AjIList *iter);
AjBool embDmxHitsWrite(AjPFile outf,
EmbPHitlist hits,
ajint maxhits);
AjBool embDmxScopToScophit(const AjPScop source,
AjPScophit* target);
AjBool embDmxScopalgToScop(const AjPScopalg align,
AjPScop const *scop_arr,
ajint scop_dim,
AjPList* list);
AjBool embDmxScophitsOverlap(const AjPScophit h1,
const AjPScophit h2,
ajuint n);
AjBool embDmxScophitsOverlapAcc(const AjPScophit h1,
const AjPScophit h2,
ajuint n);
AjPScophit embDmxScophitMerge(const AjPScophit hit1,
const AjPScophit hit2);
AjBool embDmxScophitMergeInsertThis(const AjPList list,
AjPScophit hit1,
AjPScophit hit2,
AjIList iter);
AjBool embDmxScophitMergeInsertThisTarget(const AjPList list,
AjPScophit hit1,
AjPScophit hit2,
AjIList iter);
AjBool embDmxScophitMergeInsertThisTargetBoth(const AjPList list,
AjPScophit hit1,
AjPScophit hit2,
AjIList iter);
AjBool embDmxScophitMergeInsertOther(AjPList list,
AjPScophit hit1,
AjPScophit hit2);
AjBool embDmxScophitMergeInsertOtherTargetBoth(AjPList list,
AjPScophit hit1,
AjPScophit hit2);
AjBool embDmxScophitMergeInsertOtherTarget(AjPList list,
AjPScophit hit1,
AjPScophit hit2);
AjBool embDmxSeqNR(const AjPList input,
AjPUint *keep,
ajint *nset,
const AjPMatrixf matrix,
float gapopen,
float gapextend,
float thresh,
AjBool CheckGarbage);
AjBool embDmxSeqNRRange(const AjPList input,
AjPUint *keep,
ajint *nset,
const AjPMatrixf matrix,
float gapopen,
float gapextend,
float thresh1,
float thresh2,
AjBool CheckGarbage);
AjBool embDmxSeqCompall(const AjPList input,
AjPFloat2d *scores,
const AjPMatrixf matrix,
float gapopen,
float gapextend);
/*
** End of prototype definitions
*/
#endif
#ifdef __cplusplus
}
#endif
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