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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: dbxcompress
  </TITLE>
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<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="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
dbxcompress
</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>
Compress an uncompressed dbx index
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>
    Description
</H2>

<b>dbxcompress</b> compressed EMBOSS B+tree format index files. By
default, the indexing applications in EMBOSS compress all index
files.

<p>
Indexes modified by <b>dbxuncompress</b> and indexes prior to
EMBOSS 6.4.0 are uncompressed.


<H2>
    Algorithm
</H2>

The B+tree index files contain discrete pages with a known maximum
size, filled from the first byte with a count of index terms.

<p>
<b>dbxcompress</b> reads all pages, calculating the free space at the
end of each page, and then rewrite the pages to disk removing all free space.

<p>
The final page is always written in full. This allows index reading to
assume the maximum page size in all cases without reading beyond the
end of file.

<p>
Uncompressed index files are required for updating an existing
index. Compressed index files provide more efficient storage and
retrieval.

<H2>
    Usage
</H2>

<!--  
	Example usage, as run from the command-line.
        Many examples illustrating different behaviours is good.
 -->

Here is a sample session with <b>dbxcompress</b>
<p>

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

% <b>dbxcompress embl -indexdir . -field des </b>
Compress an uncompressed dbx index
Output file [embl.dbxcompress]: <b></b>

</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>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Compress an uncompressed dbx index
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-dbname]            string     EMBOSS database name (Any string from 2 to
                                  19 characters, matching regular expression
                                  /[A-z][A-z0-9_]+/)
  [-field]             string     EMBOSS database field (Any string)
   -outfile            outfile    [*.dbxcompress] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -indexdir           directory  Index directory (optional)

   Associated qualifiers:

   "-indexdir" associated qualifiers
   -extension          string     Default file extension

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   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 bgcolor="#FFFFCC">
<td>[-dbname]<br>(Parameter 1)</td>
<td>string</td>
<td>EMBOSS database name</td>
<td>Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-field]<br>(Parameter 2)</td>
<td>string</td>
<td>EMBOSS database field</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-outfile</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.dbxcompress</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 bgcolor="#FFFFCC">
<td>-indexdir</td>
<td>directory</td>
<td>Index directory (optional)</td>
<td>Directory</td>
<td>&nbsp;</td>
</tr>

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

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-indexdir" associated directory qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -extension</td>
<td>string</td>
<td>Default file extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</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>

<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->








<H2>
    Input file format
</H2>

<!-- 
        This includes example input file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null input, etc. 
   -->

<b>dbxcompress</b> reads the index files for a database created with
an older version of one of the 'dbx' indexing programs, or
uncompressed with <b>dbxuncompress</b>.

<p>






<H2>
    Output file format
</H2>

<!-- 
        This includes example output file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null output, errors etc. 

        If you wish to include the standard description of the avalable
	report formats, use:
        #include file="inc/reportformats.ihtml"
   -->

<b>dbxcompress</b> rewrites the index files in compressed form.

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: embl.pxde</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Type         Secondary
Compress     Yes
Pages        21
Secpages     225
Order        22
Fill         21
Level        0
Pagesize     2048
Cachesize    20000
Order2       16
Fill2        24
Secpagesize  512
Seccachesize 20000
Count        223
Fullcount    445
Kwlimit      75
Idlimit      15
</pre>
</td></tr></table><p>
<p><h3>File: embl.xde</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: embl.dbxcompress</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Compressing index 'des' for database 'embl'
Index 'des' opened, compressing
Completed
</pre>
</td></tr></table><p>





<H2>
    Data files
</H2>

<!-- 
        Any data files used (e.g. translation table file)
        This includes example data file formats if they are
        not obvious.

	If you wish to include the standard description of what data
	files are and how to use embossdata to inspect and retrieve
	them, use:

        #include file="inc/localfiles.ihtml"
   -->

None.



<H2>
    Notes
</H2>

<!-- 
        Restrictions.
        Interesting behaviour.
        Useful things you can do with this program.
   -->

None.







<H2>
    References
</H2>

<!-- 
        Bibliography for methods used.
<ol>

<li>

</ol>

   -->

None.








<H2>
    Warnings
</H2>

<!-- 
        Potentially stupid things the program will let you do.
   -->

None.







<H2>
    Diagnostic Error Messages
</H2>

<!-- 
        Error messages specific to this program, eg:
        "FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
   -->

None.







<H2>
    Exit status
</H2>

<!-- 
        Description of the exit status for various error conditions
   -->

It always exits with status 0.








<H2>
    Known bugs
</H2>


<!-- 
        Bugs noted but not yet fixed.
   -->

None.








<!--
<H2>
    See also
</H2>
-->
<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="dbiblast.html">dbiblast</a></td>
<td>Index a BLAST database</td>
</tr>

<tr>
<td><a href="dbifasta.html">dbifasta</a></td>
<td>Index a fasta file database</td>
</tr>

<tr>
<td><a href="dbiflat.html">dbiflat</a></td>
<td>Index a flat file database</td>
</tr>

<tr>
<td><a href="dbigcg.html">dbigcg</a></td>
<td>Index a GCG formatted database</td>
</tr>

<tr>
<td><a href="dbxedam.html">dbxedam</a></td>
<td>Index the EDAM ontology using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxfasta.html">dbxfasta</a></td>
<td>Index a fasta file database using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxflat.html">dbxflat</a></td>
<td>Index a flat file database using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxgcg.html">dbxgcg</a></td>
<td>Index a GCG formatted database using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxobo.html">dbxobo</a></td>
<td>Index an obo ontology using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxreport.html">dbxreport</a></td>
<td>Validate index and report internals for dbx databases</td>
</tr>

<tr>
<td><a href="dbxresource.html">dbxresource</a></td>
<td>Index a data resource catalogue using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxstat.html">dbxstat</a></td>
<td>Dump statistics for dbx databases</td>
</tr>

<tr>
<td><a href="dbxtax.html">dbxtax</a></td>
<td>Index NCBI taxonomy using b+tree indices</td>
</tr>

<tr>
<td><a href="dbxuncompress.html">dbxuncompress</a></td>
<td>Uncompress a compressed dbx index</td>
</tr>

</table>
<!-- 
        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
   -->










<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>
<!--
        Date written and what changes have been made go in this file.
   -->




<H2>
    Target users
</H2>
<!--
        For general users, use this text
   -->
This program is intended to be used by administrators responsible
for software and database installation and maintenance. 

<H2>
    Comments
</H2>
<!--
        User/developer/other comments go in this file.
   -->
None


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