From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 4 Jul 2011 13:47:43 +0000 (+0100)
Subject: jmb isn't created yet, so use another SSM provider
X-Git-Tag: Release_2_7~158
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=98b0965366ac8705c7592844b5403fbebd888cd9;p=jalview.git

jmb isn't created yet, so use another SSM provider
---

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 5078c69..9a26f15 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -22,7 +22,7 @@
             button by setting the embed parameter to true;<br>
             &lt;param name=&quot;embedded&quot;
           value=&quot;true&quot;&gt; </li>
-        </ul>
        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>
        <ul>
        <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series - <a href="JmolApplet-12.1.13.jar">download the JmolApplet here</a></font></li>
<li>To use Jmol as the structure viewer for Jalview, you must include 
            the jar file in the applet archive argument thus:<br>
            <pre><font size="2">archive=&quot;jalviewApplet.jar,Jmol-12.1.13.jar&quot;</font></pre>
          </li>
          <li>Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have 
            Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the 
            original Jalview structure viewer will still be available. <br>
          </li>
          <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from 
          the Jmol binary distribution available at the Jmol Sourceforge site, 
          or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
          <li><font size="2">Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</font></li>
		</ul>
+        </ul>
        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>
        <ul>
        <li><font size="2">Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>
        <li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (&lt;param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul></font>
        </li>
        <li><font size="2">New <a href="jalviewLiteJsApi.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
        </font></li></ul>
        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>
        <ul>
        <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series - <a href="JmolApplet-12.1.13.jar">download the JmolApplet here</a></font></li>
<li>To use Jmol as the structure viewer for Jalview, you must include 
            the jar file in the applet archive argument thus:<br>
            <pre><font size="2">archive=&quot;jalviewApplet.jar,Jmol-12.1.13.jar&quot;</font></pre>
          </li>
          <li>Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have 
            Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the 
            original Jalview structure viewer will still be available. <br>
          </li>
          <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from 
          the Jmol binary distribution available at the Jmol Sourceforge site, 
          or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
          <li><font size="2">Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</font></li>
		</ul>
         <br><strong><font size="2">**NEW FEATURES** in Jalview 2.5</font></strong></p>
        <ul>
        <li><font size="2">New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</font></li>
		</ul>        
        <br><strong><font size="2">**NEW FEATURES** in Jalview 2.4</font></strong></p>
         <ul>
         <li><font size="2">New applet API methods for feature display control, views, and obtaining current selection via javascript.</font></li>
@@ -289,6 +289,6 @@
           <td>true</td>
           <td>Show the jalview button on the page. When false, JalviewLite will open immediately.</td>
           </tr>
          </tr>
		  <tr><td>sortByTree</td>
		  <td>true or false (default is false)</td>
		  <td>automatically sort the associated alignment view by the tree when a new tree is opened.</td>
		  </tr>
		  <tr>
		   <td>showTreeBootstraps</td><td>true or false (default is true)</td><td>show or hide branch bootstraps</td>
			</tr>
	<tr><td>showTreeDistances</td><td>true or false (default is true)</td><td>show or hide branch lengths</td></tr>
	<tr><td>showUnlinkedTreeNodes</td><td>true or false (default is false)</td><td>indicate if unassociated nodes should be highlighted in the tree view</td>
	</tr>
          <tr><td>heightScale</td>
          <td>1.0 or greater</td>
          <td>Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font.</td>
          </tr>
-          <tr><td>widthScale</td>
          <td>1.0 or greater</td>
          <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font.</td>
          </tr>
        </table>
+          <tr><td>widthScale</td>
          <td>1.0 or greater</td>
          <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font.</td>
          </tr>
          <tr><td>centrecolumnlabels</td>
          <td>true of false (default is false)</td>
          <td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column.</td>
          <tr><td>showUnconserved</td>
          <td>true of false (default is false)</td>
          <td>When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations.</td>
          </tr>
          <tr><td>upperCase</td>
          <td><em>bold</em> or other value</td>
          <td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>
          </tr>
          <tr><td>showUnconserved</td>
          <td>true of false (default is false)</td>
          <td>When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations.</td>
          </tr>
          
          <tr><td>automaticScrolling</td>
          <td>true of false (default is false)</td>
          <td>When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure.</td>
          </tr>
          
          <tr><td>showGroupConsensus</td>
          <td>true of false (default is false)</td>
          <td>When true, shows consensus annotation row for any groups on the alignment.</td>
          </tr>
          
          <tr><td>showGroupConservation</td>
          <td>true of false (default is false)</td>
          <td>When true, shows amino-acid property conservation annotation row for any groups on the alignment.</td>
          </tr>
          <tr><td>showConsensusHistogram</td>
          <td>true of false (default is true)</td>
          <td>When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row.</td>
          </tr>
          <tr><td>showSequenceLogo</td>
          <td>true of false (default is false)</td>
          <td>When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme).</td>
          </tr>
          <tr><td>oninit</td>
          <td><em>after_init()</em></td>
          <td>name of javascript function that will be called after the jalviewLite instance has completed its initialisation.</em></td>
          </tr>
          <tr><td>relaxedidmatch</td>
          <td><em>true or false (default is false)</em></td>
          <td>When true, use stem based matching to identify sequences that match features imported from a GFF or Jalview sequence features file, and for associating PDB data (passed on PDBfile parguments) with sequences (based on a given destination sequence ID).</td>
          </tr>
          <tr><td>alignpdbfiles</td>
          <td><em>true or false (default is false)</em></td>
          <td>When true, and jalviewLite is able to use jmol as a structure viewer, attempt to show a superposition of all structures loaded onto the alignment, superimposed using the aligned regions of corresponding sequences. [experimental]</td>
          </tr>
          <tr><td>externalstructureviewer</td>
          <td><em>true or false (default is false)</em></td>
          <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental]</td>
          </tr>
          <tr><td>externalstructureviewer</td>
          <td><em>true or false (default is false)</em></td>
          <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental]</td>
          </tr>
          
                  </table>
         <p align="center">&nbsp;</p>
         <!-- InstanceEndEditable --></td>
    </tr>
  </table>
</div>
</body>
<!-- InstanceEnd --></html>
\ No newline at end of file
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index e598e00..c292af3 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -246,7 +246,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
       if (option == JOptionPane.YES_OPTION)
       {
-        jmb.ssm.setMapping(seq, chains, alreadyMapped,
+        ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped,
                         AppletFormatAdapter.FILE);
         if (ap.seqPanel.seqCanvas.fr != null)
         {