<tr>
<td><code>--open <em>filename/URL ...</em></code></td>
<td>
- Opens one or more alignment files in new alignment windows.
+ Opens one or more alignment files <em>filename</em> or URLs <em>URL</em> in new alignment windows.
<a href="clarguments-ng.html#open">Examples</a>.
</td>
<td>
<tr>
<td><code>--append <em>filename/URL ...</em></code></td>
- <td>Appends one or more alignment files to an open alignment window (or opens a new alignment if none already open).</td>
+ <td>Appends one or more alignment files <em>filename</em> or URLs <em>URL</em> to the open alignment window (or opens a new alignment if none already open).</td>
<td>
<code>
- colour=<em>colourscheme</em>,
+ colour=<em>name</em>,
title=<em>title</em>,
features=<em>featurefile</em>,
annotations=<em>annotationfile</em>,
</tr>
<tr>
- <td><code>--title <em>"title"</em></code></td>
- <td>Specifies the title for the open alignment window.</td>
+ <td><code>--title <em>"string""</em></code></td>
+ <td>Specifies the title for the open alignment window as <em>string</em>.</td>
<td></td>
<td align="center">✓</td>
</tr>
<tr>
- <td><code>--colour <em>colourscheme</em></code></td>
- <td>Applies the given colour scheme to the open alignment window. Valid values are:
+ <td><code>--colour <em>name</em></code></td>
+ <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em>are:
<code>clustal</code>,
<code>blosum62</code>,
<code>pc-identity</code>,
<tr>
<td><code>--features <em>filename/URL</em></code></td>
- <td>Add a feature file to the open alignment.</td>
+ <td>Add a feature file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
<td></td>
<td align="center">✓</td>
</tr>
<tr>
<td><code>--tree <em>filename/URL</em></code></td>
- <td>Add a tree file to the open alignment.</td>
+ <td>Add a tree file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
<td></td>
<td align="center">✓</td>
</tr>
<tr>
<td><code>--annotations <em>filename/URL</em></code></td>
- <td>Add an annotations file to the open alignment.</td>
+ <td>Add an annotations file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
<td></td>
<td align="center">✓</td>
</tr>
-
+
<tr>
<td><code>--showannotations / --noshowannotations</code></td>
<td>Enforces showing (or not showing) alignment annotations.</td>
<td></td>
<td align="center">✓</td>
</tr>
-
+
+ <tr>
+ <td><code>--wrap / --nowrap</code></td>
+ <td>Enforces wrapped (or not wrapped) alignment formatting.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
<tr>
<td><code>--structure <em>filename/URL</em></code></td>
- <td>Load a structure file attached to a sequence in the open alignment.</td>
+ <td>Load a structure file <em>filename</em> or URL <em>URL</em> associated with a sequence in the open alignment. The sequence to be associated with can be specified with a following <code>--seqid</code> argument, or the subval modifier <code>seqid=<em>ID</em></code> can be used. A subval <em>INDEX</em> can also be used to specify the <em>INDEX-th</em> sequence in the open alignment.</td>
<td>
<code>
- seqid=<em>sequenceid</em></code> or <code><em>sequence index</em>,
+ seqid=<em>sequenceid</em></code> or <code><em>INDEX</em>,
paefile=<em>paefilename</em>,
tempfac=<em>temperature factor type</em>,
ssannotations,
</code></td>
<td align="center">✓</td>
</tr>
-
-
+
+
+ <tr>
+ <td><code>--seqid <em>ID</em></code></td>
+ <td>Specify the sequence name for the preceding <code>--structure</code> to be associated with.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
<tr>
<td><code>--paematrix <em>filename</em></code></td>
- <td>Add a PAE file to the preceding <code>--structure</code></td>
+ <td>Add a PAE json matrix file <em>filename</em> to the preceding <code>--structure</code>.</td>
<td></td>
<td align="center">✓</td>
</tr>
-
+
<tr>
- <td><code>--tempfac <em>temperature factor type</em></code></td>
- <td>Set the type of temperature factor. Possible values are
+ <td><code>--tempfac <em>name</em></code></td>
+ <td>Set the type of temperature factor. Possible values for <em>name</em> are
<code>default</code>,
<code>plddt</code>
</td>
<tr>
- <td><code>--structureviewer <em>structure viewer</em></code></td>
- <td>Set the structure viewer to use to open the 3d structure file specified in previous <code>--structure</code>. Possible values are:
+ <td><code>--structureviewer <em>name</em></code></td>
+ <td>Set the structure viewer to use to open the 3d structure file specified in previous <code>--structure</code> to <em>name</em>. Possible values of <em>name</em> are:
<br/>
<code>none</code>,
<br/>
-
- <p>
- Jalview processes arguments on the command line sequentially. If
- you would like to pass a <a href="jvlfiles.html">'JVL' file</a> containing
- <a href="../memory.html">memory settings</a> or any other launch
- parameters, then include it at the beginning of the command line to
- ensure they are processed before any remaining arguments.
- <br>
- Typical command line execution follows the following pattern:
- <pre>
- jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
- </pre>
-
- <table width="100%" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td width="27%"><div align="center">-nodisplay</div></td>
- <td width="73%"><div align="left">Run Jalview without
- User Interface. (automatically disables questionnaire, version
- and usage stats checks)</div></td>
- </tr>
- <tr>
- <td><div align="center">-nowebservicediscovery</div></td>
- <td><div align="left">Do not query configured servers to
- discover web services (<em>Since 2.11.2.0</em>)</div></td>
- </tr>
- <tr>
- <td><div align="center">-open FILE/URL</div></td>
- <td><div align="left">Specify the alignment file to
- open or process by providing additional arguments.</div></td>
- </tr>
- <tr>
- <td><div align="center">-props FILE/URL</div></td>
- <td><div align="left">Use the given Jalview properties
- file instead of users default.</div></td>
- </tr>
- <tr>
- <td><div align="center">-setprop PROPERTY=value</div></td>
- <td><div align="left">(JalviewJS ONLY) sets the given
- property to the given value</div></td>
- </tr>
- <tr>
- <td><div align="center">-features FILE/URL</div></td>
- <td><div align="left">
- <p>
- Use the given file to add sequence features to an alignment.
- See <a href="featuresFormat.html" target="NEW">Features
- File</a> (Known as Groups file prior to 2.08) description.
- </p>
-
- </div></td>
- </tr>
- <tr>
- <td>
- <div align="center">-colour COLOURSCHEME</div>
- </td>
- <td>Set the colourscheme for the alignment. This can be any
- of the built-in colourschemes, a name of a predefined
- colourscheme (defined in the Jalview properties file), or an
- 'inline' colourscheme (see the applet's colour parameter for
- more information).</td>
- </tr>
- <tr>
- <td>
- <div align="center">-annotations FILE/URL</div>
- </td>
- <td>Add precalculated annotations to the alignment. See <a
- href="annotationsFormat.html" target="NEW">Annotation
- File</a> description.
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-no-annotation</div>
- </td>
- <td>Do not display annotation below the alignment.
- </td>
- </tr>
-
- <tr>
- <td>
- <div align="center">-tree FILE/URL</div>
- <td>
- <div align="left">Load the given newick format tree file
- onto the alignment</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-questionnaire URL</div>
- <td>
- <div align="left">Queries the given URL for information
- about any Jalview user questionnaires</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-noquestionnaire</div>
- <td>
- <div align="left">Turn off questionnaire check</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-nonews</div>
- <td>
- <div align="left">
- Disable check for <a href="../webServices/newsreader.html">Jalview
- news</a> on startup (not recommended other than for classroom /
- demo usage)
- </div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-nousagestats</div>
- <td>
- <div align="left">Turn off google analytics usage tracking</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-[no]sortbytree</div>
- <td>
- <div align="left">Enable or disable automatic sorting of
- associated view when a new tree is displayed</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-groovy FILE/URL</div>
- <td>
- <div align="left">Execute groovy script in FILE (where
- FILE may be 'STDIN' to read from the standard input) after all
- other arguments have been processed</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-jabaws URL</div>
- <td>
- <div align="left">Specify the URL of the preferred JABAWS
- server</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-fasta FILE</div>
- </td>
-
- <td>
- <div align="left">Create alignment file FILE in Fasta
- format.</div>
- </td>
- </tr>
- <tr>
- <td><div align="center">-clustal FILE</div></td>
- <td><div align="left">Create alignment file FILE in
- Clustal format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-msf FILE</div></td>
-
- <td><div align="left">Create alignment file FILE in MSF
- format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pileup FILE</div></td>
- <td><div align="left">Create alignment file FILE in
- Pileup format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pir FILE</div></td>
-
- <td><div align="left">Create alignment file FILE in PIR
- format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-pfam FILE</div></td>
- <td><div align="left">Create alignment file FILE in
- PFAM format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-blc FILE</div></td>
- <td><div align="left">Create alignment file FILE in BLC
- format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-json FILE</div></td>
- <td><div align="left">Create alignment file FILE in
- JSON format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-jalview FILE</div></td>
-
- <td><div align="left">Create alignment file FILE in
- Jalview format.</div></td>
- </tr>
- <tr>
- <td><div align="center">-png FILE</div></td>
- <td><div align="left">Create PNG image FILE from
- alignment.</div></td>
- </tr>
- <tr>
- <td><div align="center">-imgMap FILE</div></td>
-
- <td><div align="left">Create HTML file FILE with image
- map of PNG image.</div></td>
- </tr>
- <tr>
- <td><div align="center">-eps FILE</div></td>
- <td><div align="left">Create EPS file FILE from
- alignment.</div></td>
- </tr>
- <tr>
- <td><div align="center">-svg FILE</div></td>
- <td><div align="left">Create Scalable Vector Graphics
- file FILE from alignment.</div></td>
- </tr>
- <tr>
- <td><div align="center">-biojsMSA FILE</div></td>
- <td><div align="left">Write an HTML page to display
- the alignment with the <a href="biojsmsa.html">
- BioJS MSAviewer MSA</a>
- </div>
- </td>
- </tr>
- <tr>
- <td><div align="center">-jvmmempc=PERCENT</div></td>
- <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
- Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
- This defaults to 90 if total physical memory can be detected.
- See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
- </div>
- </td>
- </tr>
- <tr>
- <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
- <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
- Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
- gigabytes(g) or if you're lucky enough, terabytes(t).
- This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
- See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
- </div>
- </td>
- </tr>
- </table>
</body>
</html>
{
String val = av.getValue();
SubVals subVals = av.getSubVals();
- SequenceI seq = getSpecifiedSequence(af, subVals);
+ SequenceI seq = getSpecifiedSequence(af, avm, av);
if (seq == null)
{
// Could not find sequence from subId, let's assume the first
return true;
}
- private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
+ private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
+ ArgValue av)
{
- if (subId == null)
+ SubVals subVals = av.getSubVals();
+ ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID);
+ SequenceI seq = null;
+ if (subVals == null && idAv == null)
return null;
AlignmentI al = af.getCurrentView().getAlignment();
- if (subId.has("seqid"))
+ if (al == null)
+ return null;
+ if (subVals != null)
{
- return al.findName(subId.get("seqid"));
+ if (subVals.has("seqid"))
+ {
+ seq = al.findName(subVals.get("seqid"));
+ }
+ else if (-1 < subVals.getIndex()
+ && subVals.getIndex() < al.getSequences().size())
+ {
+ seq = al.getSequenceAt(subVals.getIndex());
+ }
}
- else if (-1 < subId.getIndex()
- && subId.getIndex() < al.getSequences().size())
+ else if (idAv != null)
{
- return al.getSequenceAt(subId.getIndex());
+ seq = al.findName(idAv.getValue());
}
- return null;
+ return seq;
}
// returns the first Arg value intended for the structure structFilename
git://source.jalview.org / jalview.git / commitdiff