/usr/lib/emboss/include/ensvariation.h is in emboss-lib 6.6.0+dfsg-6.
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**
** Ensembl Genetic Variation functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.31 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2012/08/05 11:39:02 $ 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 ENSVARIATION_H
#define ENSVARIATION_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensgvdata.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* @const EnsPGvtranscriptvariationadaptor ************************************
**
** Ensembl Genetic Variation Transcript Variation Adaptor
** Defined as an alias in EnsPGvbaseadaptor
**
** #alias EnsPGvbaseadaptor
** ##
******************************************************************************/
#define EnsPGvtranscriptvariationadaptor EnsPGvbaseadaptor
/* @enum EnsEGvconsequenceType ************************************************
**
** Ensembl Genetic Variation Consequence Type enumeration
**
** @value ensEGvconsequenceTypeNULL Null
** @value ensEGvconsequenceTypeEssentialsplicesite Essential splice site
** @value ensEGvconsequenceTypeStopgained Stop codon gained
** @value ensEGvconsequenceTypeStoplost Top codon lost
** @value ensEGvconsequenceTypeComplexindel Complex insertion or deletion
** @value ensEGvconsequenceTypeFrameshiftcoding Frameshift in coding sequence
** @value ensEGvconsequenceTypeSplicesite Splice site
** @value ensEGvconsequenceTypePartialcodon Partial codon
** @value ensEGvconsequenceTypeSynonymouscoding Synonymous
** @value ensEGvconsequenceTypeRegulatoryregion Regulatory region
** @value ensEGvconseqeunceTypeWithinmaturemirna Within a mature miRNA
** @value ensEGvconsequenceType5primeutr 5-prime untranslated region
** @value ensEGvconsequenceType3primeutr 3-prime untranslated region
** @value ensEGvconsequenceTypeUtr Untranslated region
** @value ensEGvconsequenceTypeIntronic Intronic
** @value ensEGvconsequenceTypeNmdtranscript Nonsense-mediated decay transcript
** @value ensEGvconsequenceTypeWithinnoncodinggene Non-coding gene
** @value ensEGvconsequenceTypeUpstream Upstream
** @value ensEGvconsequenceTypeDownstream Downstream
** @value ensEGvconsequenceTypeHgmdmutation HGMD Mutation
** @value ensEGvconsequenceTypeNoconsequence No consequence
** @value ensEGvconsequenceTypeIntergenic Intergenic
** @value ensEGvconsequenceType_ _
** @@
******************************************************************************/
typedef enum EnsOGvconsequenceType
{
ensEGvconsequenceTypeNULL,
ensEGvconsequenceTypeEssentialsplicesite,
ensEGvconsequenceTypeStopgained,
ensEGvconsequenceTypeStoplost,
ensEGvconsequenceTypeComplexindel,
ensEGvconsequenceTypeFrameshiftcoding,
ensEGvconsequenceTypeSplicesite,
ensEGvconsequenceTypePartialcodon,
ensEGvconsequenceTypeSynonymouscoding,
ensEGvconsequenceTypeRegulatoryregion,
ensEGvconseqeunceTypeWithinmaturemirna,
ensEGvconsequenceType5primeutr,
ensEGvconsequenceType3primeutr,
ensEGvconsequenceTypeUtr,
ensEGvconsequenceTypeIntronic,
ensEGvconsequenceTypeNmdtranscript,
ensEGvconsequenceTypeWithinnoncodinggene,
ensEGvconsequenceTypeUpstream,
ensEGvconsequenceTypeDownstream,
ensEGvconsequenceTypeHgmdmutation,
ensEGvconsequenceTypeNoconsequence,
ensEGvconsequenceTypeIntergenic,
ensEGvconsequenceType_
} EnsEGvconsequenceType;
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* @data EnsPGvconsequence ****************************************************
**
** Ensembl Genetic Variation Consequence.
**
** @alias EnsSGvconsequence
** @alias EnsOGvconsequence
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Variation::ConsequenceType
** @attr Transcriptidentifier [ajuint] Ensembl Transcript identifier
** @attr Gvvariationfeatureidentifier [ajuint] Ensembl Genetic Variation
** Variation Feature identifier
** @attr Start [ajuint] Start
** @attr End [ajuint] End
** @attr Strand [ajuint] Strand
** @attr Alleles [AjPList] AJAX List of AJAX String objects
** @attr Types [AjPList] AJAX List of AJAX String objects
** @@
******************************************************************************/
typedef struct EnsSGvconsequence
{
ajuint Use;
ajuint Transcriptidentifier;
ajuint Gvvariationfeatureidentifier;
ajuint Start;
ajuint End;
ajuint Strand;
AjPList Alleles;
AjPList Types;
} EnsOGvconsequence;
#define EnsPGvconsequence EnsOGvconsequence*
/* @data EnsPGvtranscriptvariation ********************************************
**
** Ensembl Genetic Variation Transcript Variation.
**
** @alias EnsSGvtranscriptvariation
** @alias EnsOGvtranscriptvariation
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] SQL database-internal identifier
** @attr Adaptor [EnsPGvtranscriptvariationadaptor]
** Ensembl Genetic Variation Transcript Variation Adaptor
** @cc Bio::EnsEMBL::Variation::TranscriptVariation
** @attr Gvvariationfeature [EnsPGvvariationfeature]
** Ensembl Genetic Variation Variation Feature
** @attr TranscriptObject [EnsPTranscript] Ensembl Transcript
** @attr TranslationAllele [AjPStr] Ensembl Translation allele
** @attr TranscriptStart [ajuint] Transcript start
** @attr TranscriptEnd [ajuint] Transcript end
** @attr CodingStart [ajuint] Coding start
** @attr CodingEnd [ajuint] Coding end
** @attr TranslationStart [ajuint] Translation start
** @attr TranslationEnd [ajuint] Translation end
** @attr GvconsequenceTypes [ajuint] Ensembl Genetic Variation Consequence Type
** bit field
** @attr Padding [ajuint] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EnsSGvtranscriptvariation
{
ajuint Use;
ajuint Identifier;
EnsPGvtranscriptvariationadaptor Adaptor;
EnsPGvvariationfeature Gvvariationfeature;
EnsPTranscript TranscriptObject;
AjPStr TranslationAllele;
ajuint TranscriptStart;
ajuint TranscriptEnd;
ajuint CodingStart;
ajuint CodingEnd;
ajuint TranslationStart;
ajuint TranslationEnd;
ajuint GvconsequenceTypes;
ajuint Padding;
} EnsOGvtranscriptvariation;
#define EnsPGvtranscriptvariation EnsOGvtranscriptvariation*
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
/* Ensembl Genetic Variation Consequence */
EnsPGvconsequence ensGvconsequenceNewCpy(const EnsPGvconsequence gvc);
EnsPGvconsequence ensGvconsequenceNewIni(ajuint transcriptid,
ajuint gvvfid,
ajint start,
ajint end,
ajint strand);
EnsPGvconsequence ensGvconsequenceNewRef(EnsPGvconsequence gvc);
void ensGvconsequenceDel(EnsPGvconsequence *Pgvc);
ajint ensGvconsequenceGetEnd(
const EnsPGvconsequence gvc);
ajuint ensGvconsequenceGetGvvariationfeatureidentifier(
const EnsPGvconsequence gvc);
ajint ensGvconsequenceGetStart(
const EnsPGvconsequence gvc);
ajint ensGvconsequenceGetStrand(
const EnsPGvconsequence gvc);
ajuint ensGvconsequenceGetTranscriptidentifier(
const EnsPGvconsequence gvc);
AjBool ensGvconsequenceSetEnd(EnsPGvconsequence gvc,
ajint end);
AjBool ensGvconsequenceSetGvvariationfeatureidentifier(EnsPGvconsequence gvc,
ajuint gvvfid);
AjBool ensGvconsequenceSetStart(EnsPGvconsequence gvc,
ajint start);
AjBool ensGvconsequenceSetStrand(EnsPGvconsequence gvc,
ajint strand);
AjBool ensGvconsequenceSetTranscriptidentifier(EnsPGvconsequence gvc,
ajuint transcriptid);
AjBool ensGvconsequenceTrace(const EnsPGvconsequence gvc,
ajuint level);
size_t ensGvconsequenceCalculateMemsize(const EnsPGvconsequence gvc);
/* Ensembl Genetic Variation Consequence Type */
EnsEGvconsequenceType ensGvconsequenceTypeFromStr(
const AjPStr consequencetype);
const char *ensGvconsequenceTypeToChar(
EnsEGvconsequenceType gvct);
ajuint ensGvconsequenceTypesFromSet(const AjPStr gvctset);
AjBool ensGvconsequenceTypesToSet(ajuint gvctbf, AjPStr *Pgvctset);
/* Ensembl Genetic Variation Transcript Variation */
EnsPGvtranscriptvariation ensGvtranscriptvariationNewCpy(
const EnsPGvtranscriptvariation gvtv);
EnsPGvtranscriptvariation ensGvtranscriptvariationNewIni(
EnsPGvtranscriptvariationadaptor gvtva,
ajuint identifier,
EnsPTranscript transcript,
EnsPGvvariationfeature gvvf,
AjPStr translationallele,
AjPStr consequencetype,
ajuint codingstart,
ajuint codingend,
ajuint transcriptstart,
ajuint transcriptend,
ajuint translationstart,
ajuint translationend);
EnsPGvtranscriptvariation ensGvtranscriptvariationNewRef(
EnsPGvtranscriptvariation gvtv);
void ensGvtranscriptvariationDel(EnsPGvtranscriptvariation *Pgvtv);
EnsPGvtranscriptvariationadaptor ensGvtranscriptvariationGetAdaptor(
const EnsPGvtranscriptvariation gvtv);
ajuint ensGvtranscriptvariationGetCodingEnd(
const EnsPGvtranscriptvariation gvtv);
ajuint ensGvtranscriptvariationGetCodingStart(
const EnsPGvtranscriptvariation gvtv);
EnsPGvvariationfeature ensGvtranscriptvariationGetGvvariationfeature(
const EnsPGvtranscriptvariation gvtv);
ajuint ensGvtranscriptvariationGetIdentifier(
const EnsPGvtranscriptvariation gvtv);
ajuint ensGvtranscriptvariationGetTranscriptEnd(
const EnsPGvtranscriptvariation gvtv);
EnsPTranscript ensGvtranscriptvariationGetTranscriptObject(
const EnsPGvtranscriptvariation gvtv);
ajuint ensGvtranscriptvariationGetTranscriptStart(
const EnsPGvtranscriptvariation gvtv);
AjPStr ensGvtranscriptvariationGetTranslationAllele(
const EnsPGvtranscriptvariation gvtv);
ajuint ensGvtranscriptvariationGetTranslationEnd(
const EnsPGvtranscriptvariation gvtv);
ajuint ensGvtranscriptvariationGetTranslationStart(
const EnsPGvtranscriptvariation gvtv);
AjBool ensGvtranscriptvariationSetAdaptor(
EnsPGvtranscriptvariation gvtv,
EnsPGvtranscriptvariationadaptor gvtva);
AjBool ensGvtranscriptvariationSetCodingEnd(
EnsPGvtranscriptvariation gvtv,
ajuint codingend);
AjBool ensGvtranscriptvariationSetCodingStart(
EnsPGvtranscriptvariation gvtv,
ajuint codingstart);
AjBool ensGvtranscriptvariationSetGvvariationfeature(
EnsPGvtranscriptvariation gvtv,
EnsPGvvariationfeature gvvf);
AjBool ensGvtranscriptvariationSetIdentifier(
EnsPGvtranscriptvariation gvtv,
ajuint identifier);
AjBool ensGvtranscriptvariationSetTranscriptEnd(
EnsPGvtranscriptvariation gvtv,
ajuint transcriptend);
AjBool ensGvtranscriptvariationSetTranscriptObject(
EnsPGvtranscriptvariation gvtv,
EnsPTranscript transcript);
AjBool ensGvtranscriptvariationSetTranscriptStart(
EnsPGvtranscriptvariation gvtv,
ajuint transcriptstart);
AjBool ensGvtranscriptvariationSetTranslationAllele(
EnsPGvtranscriptvariation gvtv,
AjPStr translationallele);
AjBool ensGvtranscriptvariationSetTranslationEnd(
EnsPGvtranscriptvariation gvtv,
ajuint translationend);
AjBool ensGvtranscriptvariationSetTranslationStart(
EnsPGvtranscriptvariation gvtv,
ajuint translationstart);
AjBool ensGvtranscriptvariationTrace(const EnsPGvtranscriptvariation gvtv,
ajuint level);
size_t ensGvtranscriptvariationCalculateMemsize(
const EnsPGvtranscriptvariation gvtv);
/* Ensembl Genetic Variation Transcript Variation Adaptor */
EnsPGvtranscriptvariationadaptor ensRegistryGetGvtranscriptvariationadaptor(
EnsPDatabaseadaptor dba);
EnsPGvtranscriptvariationadaptor ensGvtranscriptvariationadaptorNew(
EnsPDatabaseadaptor dba);
void ensGvtranscriptvariationadaptorDel(
EnsPGvtranscriptvariationadaptor *Pgvtva);
EnsPBaseadaptor ensGvtranscriptvariationadaptorGetBaseadaptor(
EnsPGvtranscriptvariationadaptor gvtva);
EnsPDatabaseadaptor ensGvtranscriptvariationadaptorGetDatabaseadaptor(
EnsPGvtranscriptvariationadaptor gvtva);
EnsPGvbaseadaptor ensGvtranscriptvariationadaptorGetGvbaseadaptor(
EnsPGvtranscriptvariationadaptor gvtva);
EnsPGvdatabaseadaptor ensGvtranscriptvariationadaptorGetGvdatabaseadaptor(
EnsPGvtranscriptvariationadaptor gvtva);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSVARIATION_H */
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