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documented the -colour command line argument.
authorjprocter <Jim Procter>
Sat, 12 Jun 2010 12:45:49 +0000 (12:45 +0000)
committerjprocter <Jim Procter>
Sat, 12 Jun 2010 12:45:49 +0000 (12:45 +0000)
help/html/features/clarguments.html patch | blob | history
src/jalview/bin/Jalview.java patch | blob | history

diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 9bca344..9b527d6 100644 (file)
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -16,33 +16,55 @@
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 -->
-<title>Jalview Command Line Arguments
-</title>
+<title>Jalview Command Line Arguments</title>
 <body>
- <p><strong>The Jalview Executable's Command Line
- Arguments</strong></p>
- See <a href="commandline.html">running Jalview from the command
- line</a> for more information.<br>
- <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>
+<p><strong>The Jalview Executable's Command Line Arguments</strong></p>
+See
+<a href="commandline.html">running Jalview from the command line</a>
+for more information.
+<br>
+<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">-props FILE</div></td>
- <td><div align="left">Use the given Jalview properties file instead 
- of users default.</div></td>
- </tr>
- <tr> 
- <td><div align="center">-features FILE</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>
+       <tr>
+               <td>
+               <div align="center">-props FILE</div>
+               </td>
+               <td>
+               <div align="left">Use the given Jalview properties file instead
+               of users default.</div>
+               </td>
+       </tr>
+       <tr>
+               <td>
+               <div align="center">-features FILE</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>
+               </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>
@@ -74,26 +96,30 @@
                <div align="left">Turn off questionnaire check</div>
                </td>
        </tr>
-       <tr><td>
+       <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>
+       <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>
+               <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>
+               <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>
@@ -101,38 +127,47 @@
                <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>
+               <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>
+               <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>
+               <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>
+               <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>
+               <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>
+               <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>
@@ -144,51 +179,91 @@
                <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>
+       <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 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">-jalview 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">-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 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>
- </table>
+               <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>
+</table>
 </body>
 </html>
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 04f68f3..b62c83f 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -94,6 +94,7 @@ public class Jalview
               .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
                       + "-nodisplay\tRun Jalview without User Interface.\n"
                       + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+                      + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
                       + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
                       + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
                       + "-features FILE\tUse the given file to mark features on the alignment.\n"