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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: acdpretty
  </TITLE>
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<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="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
acdpretty
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Correctly reformat an application ACD file
<H2>
    Description
</H2>
<p><b>acdpretty</b> will generate a correctly, fully formatted ACD file from one which is parsable but which is partly or incorrectly formatted.</p>

<p><b>acdpretty</b> reads the ACD file and rewrites it with clean formatting to the file (<tt>ApplicationName</tt>).<b>acdpretty</b> which can be used to overwrite the original ACD file.  The new file might contain many differences.  For example, abbreviations will be expanded, all sections and attributes will be indented, all values will be quoted and lines will be wrapped at a reasonable width.  



<H2>
    Usage
</H2>
Here is a sample session with <b>acdpretty</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>acdpretty qatest </b>

Created qatest.acdpretty

</pre></td></tr></table><p>
<p>
<a href="#output.1">Go to the output files for this example</a><p><p>

<H2>
    Command line arguments
</H2>


The first parameter is the name of the program to pretty print.

<p>
All other command line parameters and qualifiers are essentially
ignored as processing stops once the ACD file is printed. A few of the
general qualifiers have the potential to conflict with the function of
acdpretty.

<P>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Correctly reformat an application ACD file
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>



<H2>
    Input file format
</H2>


The input file is the ACD file for the specified program

<p>


<H2>
    Output file format
</H2>

<p>

The output file is a pretty printed copy of the original ACD file.

<p>
All sections and attributed will be indented. All values will be
quoted. Lines will be wrapped at a reasonable width.

<p>
The output file is intended as a standard format for parsers used by
GUI and other interface wrappers, rather than using the original ACD
file directly.



<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: qatest.acdpretty</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Example ACD file for QA testing
#

application: qatest [
  groups: "test"
  documentation: "ACD file for QA testing"
]

sequence: asequence [
  parameter: "Y"
  features: "Y"
]

sequence: bsequence [
  parameter: "Y"
]

outfile: outfile [
  parameter: "Y"
]

integer: aint [
  prompt: "first integer"
]

integer: bint [
  prompt: "second integer, first was $(aint)"
  default: "57"
]

string: testalen [
  standard: "Y"
  information: "asequence length $(asequence.length)"
]

string: testblen [
  standard: "Y"
  information: "bsequence length $(bsequence.length)"
]

string: outdir [
  information: "output directory"
]

boolean: logic [
  information: "boolean value"
]

outfile: outtest [
  parameter: "Y"
  odirectory: "$(outdir)"
]

seqout: outseq [
  parameter: "Y"
  features: "Y"
  osdirectory: "$(outdir)"
  ofdirectory: "$(outdir)"
]
</pre>
</td></tr></table><p>

<H2>
    Data files
</H2>


None

<H2>
    Notes
</H2>
<p><b>acdpretty</b> does not have its own options, but takes a single parameter which is the name of the ACD file that is being processed.  It is invoked by specifying the name of the ACD file after the name of the utility application itself:</p>

<p><tt><b>acdpretty</b> ApplicationName</tt></p>

<p>Any command line parameters that would normally be specified for the application are essentially ignored as processing stops once the reformatted ACD file is printed.</p> 

<p>The format generated by <b>acdpretty</b> is intended as a standard for parsers used by GUI and other interface developers. It is far easier writing a parser to cope with <b>acdpretty</b> output than one which can cope with the ACD sytax in general.</p>


<H2>
    References
</H2>


<H2>
    Warnings
</H2>

<p>A few of the global qualifiers have the potential to conflict with the function of <b>acdpretty</b>.</p>


<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>Test an application ACD file</td>
</tr>

<tr>
<td><a href="acdtable.html">acdtable</a></td>
<td>Generate an HTML table of parameters from an application ACD file</td>
</tr>

<tr>
<td><a href="acdtrace.html">acdtrace</a></td>
<td>Trace processing of an application ACD file (for testing)</td>
</tr>

<tr>
<td><a href="acdvalid.html">acdvalid</a></td>
<td>Validate an application ACD file</td>
</tr>

</table>

<H2>
    Author(s)
</H2>
Peter Rice
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.
<H2>
    History
</H2>
Completed 9th March 1999


<H2>
    Target users
</H2>

This program is intended to be used by developers of applications and
interfaces. 

<H2>
    Comments
</H2>
None



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