-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathacdvalid.html
229 lines (161 loc) · 3.88 KB
/
acdvalid.html
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
<HTML>
<HEAD>
<TITLE>
EMBOSS: acdvalid
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
acdvalid
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
ACD file validation
<H2>
Description
</H2>
Acdvalid processes the ACD file for an EMBOSS program and reports any
errors or warnings caused by incorrect, deprecated or obsolete syntax.
<p>
Acdvalid does not have its own command line. Instead, it will run the
command line of any EMBOSS program by reading its ACD file and
processing the command line and user responses in exactly the same way
as the true program.
<p>
Acdvalid uses a very simple method. The first command line parameter is
the name of the EMBOSS program to be compiled. All other command line
parameters and qualifiers are processed by that program's ACD file.
<H2>
Usage
</H2>
<b>Here is a sample session with acdvalid</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>acdvalid antigenic </b>
</pre></td></tr></table><p>
<p>
<p>
<H2>
Command line arguments
</H2>
The first parameter is the name of the program to compile.
All other command line parameters and qualifiers are defined for that
program - see the documentation for the program of choice.
<P>
<H2>
Output file format
</H2>
<p>
The output file is empty, but any format available to the specified
program can be used.
<p>
<H2>
Data files
</H2>
Acdvalid will use any data files specified in the ACD file of the
specified program, but will ignore any data files that are only used
directly by the program's code.
<p>
EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by the EMBOSS environment variable EMBOSS_DATA.
<p>
To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
<pre>
% embossdata -fetch -file Exxx.dat
</pre>
<p>
Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".
<p>
The directories are searched in the following order:
<ul>
<li> . (your current directory)
<li> .embossdata (under your current directory)
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
<p>
<H2>
Notes
</H2>
<H2>
References
</H2>
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
<H2>
Exit status
</H2>
It exits with status 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="acdc.html">acdc</a></td>
<td>ACD compiler</td>
</tr>
<tr>
<td><a href="acdpretty.html">acdpretty</a></td>
<td>ACD pretty printing utility</td>
</tr>
<tr>
<td><a href="acdtable.html">acdtable</a></td>
<td>Creates an HTML table from an ACD file</td>
</tr>
<tr>
<td><a href="acdtrace.html">acdtrace</a></td>
<td>ACD compiler on-screen trace</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Peter Rice (pmr © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Written 2004
<H2>
Target users
</H2>
This program is intended to be used by developers of applications and
interfaces.
<H2>
Comments
</H2>
None
</BODY>
</HTML>