emboss-lib 6.6.0+dfsg-6 / usr / lib / emboss / include / ajacd.h

This file is indexed.

/usr/lib/emboss/include/ajacd.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. 

  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
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
/* @include ajacd *************************************************************
**
** These functions control all aspects of AJAX command definition
** syntax, command line handling and prompting of the user.
**
** The only major functions visible to callers are the initialisation
** function ajAcdInit and a series of retrieval functions ajGetAcdObject
** for each defined object type (integer, sequence, and so on).
**
** Future extensions are planned, including the ability to write out
** the ACD internal structures in a number of other interface formats.
**
** @author Copyright (C) 1998 Peter Rice
** @version $Revision: 1.17 $
** @modified Jun 25 pmr First version
** @modified May 06 2004 Jon Ison Minor mods.
** @modified $Date: 2012/09/03 14:15:18 $ 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 AJACD_H
#define AJACD_H



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

#include "ajdefine.h"

#include "ajstr.h"
#include "ajlist.h"
#include "ajarr.h"
#include "ajrange.h"

#include "ajalign.h"
#include "ajcod.h"
#include "ajgraph.h"
#include "ajpat.h"
#include "ajphylo.h"
#include "ajreg.h"
#include "ajreport.h"

#include "ajassemdata.h"
#include "ajfeatdata.h"
#include "ajobodata.h"
#include "ajrefseqdata.h"
#include "ajresourcedata.h"
#include "ajseqdata.h"
#include "ajtaxdata.h"
#include "ajtextdata.h"
#include "ajurldata.h"
#include "ajvardata.h"
#include "ajxmldata.h"

AJ_BEGIN_DECLS


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




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




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




/*
** Prototype definitions
*/

void          ajAcdExit (AjBool single);

AjPAlign      ajAcdGetAlign (const char *token);
AjPFloat      ajAcdGetArray (const char *token);
AjPAssemload  ajAcdGetAssembly (const char *token);
AjBool        ajAcdGetBoolean (const char *token);
AjPCod        ajAcdGetCodon (const char *token);
AjPFile       ajAcdGetCpdb (const char *token);
AjPFile       ajAcdGetDatafile (const char *token);
AjPDir        ajAcdGetDirectory (const char *token);
AjPStr        ajAcdGetDirectoryName (const char *token);
AjPList       ajAcdGetDirlist (const char *token);
AjPPhyloState* ajAcdGetDiscretestates (const char *token);
AjPPhyloState ajAcdGetDiscretestatesSingle (const char *token);
AjPPhyloDist* ajAcdGetDistances (const char *token);
AjPPhyloDist  ajAcdGetDistancesSingle (const char *token);
double        ajAcdGetFloatDouble (const char *token);
AjPFeattable  ajAcdGetFeatures (const char *token);
AjPFeattaball ajAcdGetFeaturesall (const char *token);
AjPFeattabOut ajAcdGetFeatout (const char *token);
AjPList       ajAcdGetFilelist (const char *token);
float         ajAcdGetFloat (const char *token);
AjPPhyloFreq  ajAcdGetFrequencies (const char *token);
AjPGraph      ajAcdGetGraph (const char *token);
AjPGraph      ajAcdGetGraphxy (const char *token);
AjPFile       ajAcdGetInfile (const char *token);
ajint         ajAcdGetInt (const char *token);
ajlong        ajAcdGetIntLong (const char *token);
AjPStr*       ajAcdGetList (const char *token);
AjPStr        ajAcdGetListSingle(const char *token);
AjPMatrix     ajAcdGetMatrix (const char *token);
AjPMatrixf    ajAcdGetMatrixf (const char *token);
AjPObo        ajAcdGetObo(const char *token);
AjPOboall     ajAcdGetOboall(const char *token);
AjPOutfile    ajAcdGetOutassembly(const char *token);
AjPOutfile    ajAcdGetOutcodon(const char *token);
AjPOutfile    ajAcdGetOutcpdb(const char *token);
AjPOutfile    ajAcdGetOutdata(const char *token);
AjPDirout     ajAcdGetOutdir (const char *token);
AjPStr        ajAcdGetOutdirName (const char *token);
AjPOutfile    ajAcdGetOutdiscrete(const char *token);
AjPOutfile    ajAcdGetOutdistance(const char *token);
AjPFile       ajAcdGetOutfile (const char *token);
AjPStr        ajAcdGetOutfileName (const char *token);
AjPOutfile    ajAcdGetOutfreq(const char *token);
AjPOutfile    ajAcdGetOutmatrix(const char *token);
AjPOutfile    ajAcdGetOutmatrixf(const char *token);
AjPOutfile    ajAcdGetOutobo(const char *token);
AjPOutfile    ajAcdGetOutproperties(const char *token);
AjPOutfile    ajAcdGetOutrefseq(const char *token);
AjPOutfile    ajAcdGetOutresource(const char *token);
AjPOutfile    ajAcdGetOutscop(const char *token);
AjPOutfile    ajAcdGetOuttaxon(const char *token);
AjPOutfile    ajAcdGetOuttext(const char *token);
AjPOutfile    ajAcdGetOuttree(const char *token);
AjPOutfile    ajAcdGetOuturl(const char *token);
AjPOutfile    ajAcdGetOutvariation(const char *token);
AjPOutfile    ajAcdGetOutxml(const char *token);
AjPPatlistSeq ajAcdGetPattern (const char *token);
AjPPhyloProp  ajAcdGetProperties (const char *token);
AjPRange      ajAcdGetRange (const char *token);
AjPRefseq     ajAcdGetRefseq (const char *token);
AjPPatlistRegex ajAcdGetRegexp (const char *token);
AjPRegexp     ajAcdGetRegexpSingle (const char *token);
AjPReport     ajAcdGetReport (const char *token);
AjPResource   ajAcdGetResource(const char *token);
AjPResourceall  ajAcdGetResourceall(const char *token);
AjPFile       ajAcdGetScop (const char *token);
AjPStr*       ajAcdGetSelect (const char *token);
AjPStr        ajAcdGetSelectSingle (const char *token);
AjPSeq        ajAcdGetSeq (const char *token);
AjPSeqall     ajAcdGetSeqall (const char *token);
AjPSeqout     ajAcdGetSeqout (const char *token);
AjPSeqout     ajAcdGetSeqoutall (const char *token);
AjPSeqout     ajAcdGetSeqoutset (const char *token);
AjPSeqset     ajAcdGetSeqset (const char *token);
AjPSeqset*    ajAcdGetSeqsetall (const char *token);
AjPSeqset     ajAcdGetSeqsetallSingle (const char *token);
AjPStr        ajAcdGetString (const char *token);
AjPTax        ajAcdGetTaxon(const char *token);
AjPTaxall     ajAcdGetTaxonall(const char *token);
AjPText       ajAcdGetText(const char *token);
AjPTextall    ajAcdGetTextall(const char *token);
AjBool        ajAcdGetToggle (const char *token);
AjPPhyloTree* ajAcdGetTree (const char *token);
AjPPhyloTree  ajAcdGetTreeSingle (const char *token);
AjPUrl        ajAcdGetUrl(const char *token);
AjPUrlall     ajAcdGetUrlall(const char *token);
AjPVarload    ajAcdGetVariation(const char *token);
AjPXml        ajAcdGetXml(const char *token);
AjPXmlall     ajAcdGetXmlall(const char *token);

const AjPStr  ajAcdGetValue (const char* token);
const AjPStr  ajAcdGetValueDefault (const char* token);

void          ajAcdInit(const char *pgm, ajint argc, char * const argv[]);
void          ajAcdInitPV(const char *pgm, ajint argc, char * const argv[],
			  const char *package, const char *packversion);
AjBool        ajAcdIsUserdefinedC(const char* token);
AjBool        ajAcdIsUserdefinedS(const AjPStr);
const AjPStr  ajAcdGetpathC(const char *token);
const AjPStr  ajAcdGetpathS(const AjPStr);
void          ajAcdPrintAppl(AjPFile outf, AjBool full);
void          ajAcdPrintQual(AjPFile outf, AjBool full);
void          ajAcdPrintType (AjPFile outf, AjBool full);
AjBool        ajAcdSetControl (const char* optionName);
void          ajAcdUnused(void);
AjBool        ajAcdedamParse(const AjPStr relation, AjPStr* id,
                             AjPStr* namespace,  AjPStr* name);
const char*   ajAcdtypeGetGroup(const AjPStr type);

/*
** End of prototype definitions
*/

#ifdef AJ_COMPILE_DEPRECATED_BOOK
#endif
#ifdef AJ_COMPILE_DEPRECATED

__deprecated AjBool         ajAcdIsUserdefined(const char* token);
__deprecated AjBool         ajAcdDebug (void);
__deprecated AjBool         ajAcdDebugIsSet (void);
__deprecated AjBool         ajAcdFilter (void);
__deprecated AjPPhyloState  ajAcdGetDiscretestatesI (const char *token,
						    ajint num);
__deprecated AjPStr         ajAcdGetListI (const char *token, ajint num);
__deprecated AjPStr         ajAcdGetSelectI (const char *token, ajint num);
__deprecated AjPSeqset      ajAcdGetSeqsetallI (const char *token, ajint num);
__deprecated AjPPhyloTree   ajAcdGetTreeI (const char *token, ajint num);
__deprecated const AjPStr   ajAcdValue (const char* token);
__deprecated AjBool         ajAcdStdout (void);

__deprecated AjBool        ajAcdGetBool (const char *token);
__deprecated AjPFeattable  ajAcdGetFeat (const char *token);

__deprecated void          ajAcdGraphicsInit(const char *pgm,
                                             ajint argc, char * const argv[]);
__deprecated void          ajAcdGraphicsInitPV(const char *pgm,
                                               ajint argc,char * const argv[],
                                               const char *package,
                                               const char *packversion);

__deprecated void          ajGraphicsInit(const char *pgm,
					  ajint argc, char * const argv[]);
__deprecated void          ajGraphicsInitPV(const char *pgm,
					    ajint argc,char * const argv[],
					    const char *package,
					    const char *packversion);

#endif

AJ_END_DECLS

#endif  /* !AJACD_H */

APT Browse - Built by Thomas Orozco.