button by setting the embed parameter to true;<br>
<param name="embedded"
value="true"> </li>
- </ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>
\r <ul>
\r <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>
\r<li>To use Jmol as the structure viewer for Jalview, you must include
\r the jar file in the applet archive argument thus:<br>
\r <pre><font size="2">archive="jalviewApplet.jar,Jmol-12.1.13.jar"</font></pre>
\r </li>
\r <li>Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have
\r Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the
\r original Jalview structure viewer will still be available. <br>
\r </li>
\r <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
\r the Jmol binary distribution available at the Jmol Sourceforge site,
\r or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
\r <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>
\r </ul>
+ </ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>
\r <ul>
\r <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>
\r <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 (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul></font>
\r </li>
\r <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.
\r </font></li></ul>
\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>
\r <ul>
\r <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>
\r<li>To use Jmol as the structure viewer for Jalview, you must include
\r the jar file in the applet archive argument thus:<br>
\r <pre><font size="2">archive="jalviewApplet.jar,Jmol-12.1.13.jar"</font></pre>
\r </li>
\r <li>Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have
\r Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the
\r original Jalview structure viewer will still be available. <br>
\r </li>
\r <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
\r the Jmol binary distribution available at the Jmol Sourceforge site,
\r or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>
\r <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>
\r </ul>
<br><strong><font size="2">**NEW FEATURES** in Jalview 2.5</font></strong></p>
\r <ul>
\r <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>
\r </ul>
\r <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>
<td>true</td>
<td>Show the jalview button on the page. When false, JalviewLite will open immediately.</td>
</tr>\r </tr>\r <tr><td>sortByTree</td>\r <td>true or false (default is false)</td>\r <td>automatically sort the associated alignment view by the tree when a new tree is opened.</td>\r </tr>\r <tr>\r <td>showTreeBootstraps</td><td>true or false (default is true)</td><td>show or hide branch bootstraps</td>\r </tr>\r <tr><td>showTreeDistances</td><td>true or false (default is true)</td><td>show or hide branch lengths</td></tr>\r <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>\r </tr>\r <tr><td>heightScale</td>\r <td>1.0 or greater</td>\r <td>Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font.</td>\r </tr>
- <tr><td>widthScale</td>\r <td>1.0 or greater</td>\r <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font.</td>\r </tr>\r </table>
+ <tr><td>widthScale</td>\r <td>1.0 or greater</td>\r <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font.</td>\r </tr>\r <tr><td>centrecolumnlabels</td>\r <td>true of false (default is false)</td>\r <td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column.</td>\r <tr><td>showUnconserved</td>\r <td>true of false (default is false)</td>\r <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>\r </tr>\r <tr><td>upperCase</td>\r <td><em>bold</em> or other value</td>\r <td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>\r </tr>\r <tr><td>showUnconserved</td>\r <td>true of false (default is false)</td>\r <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>\r </tr>\r \r <tr><td>automaticScrolling</td>\r <td>true of false (default is false)</td>\r <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>\r </tr>\r \r <tr><td>showGroupConsensus</td>\r <td>true of false (default is false)</td>\r <td>When true, shows consensus annotation row for any groups on the alignment.</td>\r </tr>\r \r <tr><td>showGroupConservation</td>\r <td>true of false (default is false)</td>\r <td>When true, shows amino-acid property conservation annotation row for any groups on the alignment.</td>\r </tr>\r <tr><td>showConsensusHistogram</td>\r <td>true of false (default is true)</td>\r <td>When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row.</td>\r </tr>\r <tr><td>showSequenceLogo</td>\r <td>true of false (default is false)</td>\r <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>\r </tr>\r <tr><td>oninit</td>\r <td><em>after_init()</em></td>\r <td>name of javascript function that will be called after the jalviewLite instance has completed its initialisation.</em></td>\r </tr>\r <tr><td>relaxedidmatch</td>\r <td><em>true or false (default is false)</em></td>\r <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>\r </tr>\r <tr><td>alignpdbfiles</td>\r <td><em>true or false (default is false)</em></td>\r <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>\r </tr>\r <tr><td>externalstructureviewer</td>\r <td><em>true or false (default is false)</em></td>\r <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental]</td>\r </tr>\r <tr><td>externalstructureviewer</td>\r <td><em>true or false (default is false)</em></td>\r <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental]</td>\r </tr>\r \r </table>
<p align="center"> </p>
<!-- InstanceEndEditable --></td>\r </tr>\r </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r
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git://source.jalview.org / jalview.git / commitdiff