From 1ce0262fabd88d6bf4ac6e2ef3d6253561baf18c Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 14 Oct 2011 12:41:06 +0100
Subject: [PATCH] (JAL-958) documented normalised sequence logo parameter
 (JAL-826) documented introduction of WUSS annotation vis'n

---
 FEATURETODO                    |    3 +--
 examples/appletParameters.html |    4 ++--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/FEATURETODO b/FEATURETODO
index 5a5c5c1..636cb53 100644
--- a/FEATURETODO
+++ b/FEATURETODO
@@ -1,8 +1,7 @@
 Normalised logo feature todo
 
-* transfer and update calcs in applet
+* add gui switches in applet for normalised logo display
 * add flags for normalised logo display to AnnotationFile and Jalview Project
-* add parameter for applet
 * add preference for application
 * consider rationalising flag model for N types of consensus/logo calculation methods
 
diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 24452b6..5b0af6c 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -19,7 +19,7 @@
             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 2.7</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="jalviewLiteJs.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>
+        </ul>
        <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7.1</font></strong></p>
        <ul>
        <li><font size="2">Normalised sequence logo display
        </font></li>
        <li><font size="2">RNA secondary structure annotation row
        </font></li>
        </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.</font></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="jalviewLiteJs.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>
@@ -286,6 +286,6 @@
           <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. (<em>since 2.5.1</em>)</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. (<em>since 2.5.1</em>)</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. (<em>since 2.4</em>)</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. (<em>since 2.5</em>)</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>automaticScrolling</td>
          <td>true of false (default is true)</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. (<em>since 2.6</em>)</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. (<em>since 2.7</em>)</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. (<em>since 2.7</em>)</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. (<em>since 2.7</em>)</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). (<em>since 2.7</em>)</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>since 2.7</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). (<em>since 2.7</em>)</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] (<em>since 2.7</em>)</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] (<em>since 2.7</em>)</td>
          
          </tr>
          <tr><td>annotationcolour_max</td>
          <td>colour name or RGB hex triplet (default is red)</td>
          <td>Default colour used for maximum value when shading by annotation. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>annotationcolour_min</td>
          <td>colour name or RGB hex triplet (default is orange)</td>
          <td>Default colour used for minimum value when shading by annotation. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>jalviewhelpurl</td>
          <td>absolute or relative url or javascript function prefixed by <em>javascript:</em> (default is http://www.jalview.org/help.html)</td>
          <td>Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>resolvetocodebase</td>
          <td>True or False (False)</td>
          <td>Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (<em>since 2.7</em>)</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. (<em>since 2.5.1</em>)</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. (<em>since 2.4</em>)</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. (<em>since 2.5</em>)</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>automaticScrolling</td>
          <td>true of false (default is true)</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. (<em>since 2.6</em>)</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. (<em>since 2.7</em>)</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. (<em>since 2.7</em>)</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. (<em>since 2.7</em>)</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). (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>normaliseLogo</td>
          <td>true of false (default is false)</td>
          <td>When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (<em>since 2.7.1</em>)</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>since 2.7</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). (<em>since 2.7</em>)</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] (<em>since 2.7</em>)</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] (<em>since 2.7</em>)</td>
          
          </tr>
          <tr><td>annotationcolour_max</td>
          <td>colour name or RGB hex triplet (default is red)</td>
          <td>Default colour used for maximum value when shading by annotation. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>annotationcolour_min</td>
          <td>colour name or RGB hex triplet (default is orange)</td>
          <td>Default colour used for minimum value when shading by annotation. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>jalviewhelpurl</td>
          <td>absolute or relative url or javascript function prefixed by <em>javascript:</em> (default is http://www.jalview.org/help.html)</td>
          <td>Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>resolvetocodebase</td>
          <td>True or False (False)</td>
          <td>Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (<em>since 2.7</em>)</td>
          </tr>
          
                  </table>
         <p align="center">&nbsp;</p>
         <!-- InstanceEndEditable --></td>
    </tr>
  </table>
</div>
</body>
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