- </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</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">-tree FILE</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">-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">-dasserver nickname=URL</div>
- <td>
- <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
- nickname (alphanumeric or underscores only) for retrieval of features
- for all alignments<br>
- Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
- <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-fetchfrom nickname</div>
- <td>
- <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
- and display them</div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-groovy FILE</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">-vdoc VAMSAS DOCUMENT FILE or URL</div>
- <td>
- <div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-vsess VAMSAS SESSION URL</div>
- <td>
- <div align="left">Join the given vamsas session<br>If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).<em>New in 2.5</em></div></div>
- </td>
- </tr>
- <tr>
- <td>
- <div align="center">-groovy FILE</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">-fasta FILE</div>
- </td>
+ </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">-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">-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">-dasserver nickname=URL</div>
+ <td>
+ <div align="left">
+ Add and enable a <a href="dassettings.html">DAS server</a>
+ with given nickname (alphanumeric or underscores only) for
+ retrieval of features for all alignments<br> Sources that
+ also support the sequence command may be specified by
+ prepending the URL with 'sequence:'<br> <em>e.g.</em>
+ sequence:http://localdas.somewhere.org/das/source
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-fetchfrom nickname</div>
+ <td>
+ <div align="left">
+ Query a <a href="dassettings.html">DAS source</a> called
+ nickname for features for the alignments and display them
+ </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">-vdoc VAMSAS DOCUMENT FILE/URL</div>
+ <td>
+ <div align="left">
+ Import the given vamsas document into a new session.<br>
+ <em>New in 2.5</em>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-vsess VAMSAS SESSION URL</div>
+ <td>
+ <div align="left">
+ Join the given vamsas session<br>If a document was also
+ specified, this will be imported first and then committed as
+ new data from Jalview to the specified session (Experimental -
+ not yet enabled!).<em>New in 2.5</em>
+ </div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">-fasta FILE</div>
+ </td>