/usr/lib/emboss/include/enssimple.h is in emboss-lib 6.6.0-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 | /* @include enssimple *********************************************************
**
** Ensembl Simple Feature functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.8 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2012/08/05 11:31:15 $ 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 ENSSIMPLE_H
#define ENSSIMPLE_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ensfeature.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* @const EnsPSimplefeatureadaptor ********************************************
**
** Ensembl Simple Feature Adaptor.
** Defined as an alias in EnsPFeatureadaptor.
**
**
** #cc Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor
** ##
******************************************************************************/
#define EnsPSimplefeatureadaptor EnsPFeatureadaptor
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* @data EnsPSimplefeature ****************************************************
**
** Ensembl Simple Feature.
**
** @alias EnsSSimplefeature
** @alias EnsOSimplefeature
**
** @attr Use [ajuint] Use counter
** @cc Bio::EnsEMBL::Storable
** @attr Identifier [ajuint] SQL database-internal identifier
** @attr Adaptor [EnsPSimplefeatureadaptor] Ensembl Simple Feature Adaptor
** @cc Bio::EnsEMBL::Feature
** @attr Feature [EnsPFeature] Ensembl Feature
** @cc Bio::EnsEMBL::Simplefeature
** @attr Displaylabel [AjPStr] Display label
** @attr Score [double] Score
** @@
******************************************************************************/
typedef struct EnsSSimplefeature
{
ajuint Use;
ajuint Identifier;
EnsPSimplefeatureadaptor Adaptor;
EnsPFeature Feature;
AjPStr Displaylabel;
double Score;
} EnsOSimplefeature;
#define EnsPSimplefeature EnsOSimplefeature*
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
/* Ensembl Simple Feature */
EnsPSimplefeature ensSimplefeatureNewCpy(const EnsPSimplefeature object);
EnsPSimplefeature ensSimplefeatureNewIni(EnsPSimplefeatureadaptor pfa,
ajuint identifier,
EnsPFeature feature,
AjPStr label,
double score);
EnsPSimplefeature ensSimplefeatureNewRef(EnsPSimplefeature sf);
void ensSimplefeatureDel(EnsPSimplefeature *Psf);
EnsPSimplefeatureadaptor ensSimplefeatureGetAdaptor(
const EnsPSimplefeature sf);
AjPStr ensSimplefeatureGetDisplaylabel(
const EnsPSimplefeature sf);
EnsPFeature ensSimplefeatureGetFeature(
const EnsPSimplefeature sf);
ajuint ensSimplefeatureGetIdentifier(
const EnsPSimplefeature sf);
double ensSimplefeatureGetScore(
const EnsPSimplefeature sf);
AjBool ensSimplefeatureSetAdaptor(EnsPSimplefeature sf,
EnsPSimplefeatureadaptor sfa);
AjBool ensSimplefeatureSetDisplaylabel(EnsPSimplefeature sf, AjPStr label);
AjBool ensSimplefeatureSetFeature(EnsPSimplefeature sf, EnsPFeature feature);
AjBool ensSimplefeatureSetIdentifier(EnsPSimplefeature sf, ajuint identifier);
AjBool ensSimplefeatureSetScore(EnsPSimplefeature sf, double score);
AjBool ensSimplefeatureTrace(const EnsPSimplefeature sf, ajuint level);
size_t ensSimplefeatureCalculateMemsize(const EnsPSimplefeature sf);
/* AJAX List of Ensembl Simple Feature objects */
AjBool ensListSimplefeatureSortEndAscending(AjPList sfs);
AjBool ensListSimplefeatureSortEndDescending(AjPList sfs);
AjBool ensListSimplefeatureSortIdentifierAscending(AjPList sfs);
AjBool ensListSimplefeatureSortStartAscending(AjPList sfs);
AjBool ensListSimplefeatureSortStartDescending(AjPList sfs);
/* Ensembl Simple Feature Adaptor */
EnsPSimplefeatureadaptor ensRegistryGetSimplefeatureadaptor(
EnsPDatabaseadaptor dba);
EnsPSimplefeatureadaptor ensSimplefeatureadaptorNew(
EnsPDatabaseadaptor dba);
void ensSimplefeatureadaptorDel(EnsPSimplefeatureadaptor *Psfa);
EnsPBaseadaptor ensSimplefeatureadaptorGetBaseadaptor(
EnsPSimplefeatureadaptor sfa);
EnsPDatabaseadaptor ensSimplefeatureadaptorGetDatabaseadaptor(
EnsPSimplefeatureadaptor sfa);
EnsPFeatureadaptor ensSimplefeatureadaptorGetFeatureadaptor(
EnsPSimplefeatureadaptor sfa);
AjBool ensSimplefeatureadaptorFetchAllbyAnalysisname(
EnsPSimplefeatureadaptor sfa,
const AjPStr anname,
AjPList sfs);
AjBool ensSimplefeatureadaptorFetchAllbySlice(EnsPSimplefeatureadaptor sfa,
EnsPSlice slice,
const AjPStr anname,
AjPList sfs);
AjBool ensSimplefeatureadaptorFetchAllbySlicescore(
EnsPSimplefeatureadaptor sfa,
EnsPSlice slice,
double score,
const AjPStr anname,
AjPList sfs);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !ENSSIMPLE_H */
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