X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=04cc235164ee30368f32b1253282173f3a7016d5;hb=282350839f47b2a7b05994638d4202511a41bc8f;hp=ed822d3d4a443b8372dcae6c8d81435382e5231b;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index ed822d3..04cc235 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -1,6 +1,6 @@
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -28,7 +28,7 @@ which are described <a href="#parameters"> below</a>. Once initialised,
 the applet can be interacted with <em>via</em> its 
 <a href="javascript:doSubmit('jalviewLiteJs')">Javascript API</a>. 
 </p><p><strong>Issues arising from tightening of Java Security default settings</strong><br/>JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java may not be compatible with these settings. </p>
-    <p>For additional deployment notes, <a href="#appletdeploymentnotes">see below</a>.</p>
+    <p>For additional deployment notes, <a href="javascript:doSubmit('appletDeployment')">see Applet Deployment</a>.</p>
 	    <p><h2>Applet Parameters</h2><br/>The applet takes the following initialisation parameters.</p>
         <a name="parameters"></a>        <table width="97%" class="borderTable" align="center" >
           <tr> 
@@ -91,8 +91,9 @@ the applet can be interacted with <em>via</em> its
             <td>jnetfile</td>
             <td>fileName</td>
             <td>Secondary structure predictions from a <a
-            href="http://www.compbio.dundee.ac.uk/~www-jpred/">Jnet</a> Concise 
-              file will be added to the first sequence in the alignment.</td>
+            href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred</a> Concise 
+              file will be added to the first sequence in the alignment.<br/>
+              <em>jpredfile</em> can be used interchangeably with this parameter.</td>
           </tr>
           <tr> 
             <td>PDBfile(x)</td>
@@ -114,10 +115,18 @@ the applet can be interacted with <em>via</em> its
             <td>defaultColour</td>
             <td> <em>One of: </em><br>
               Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix 
-              Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices</td>
+              Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, T-Coffee Scores, RNA Helices</td>
             <td>Default is no colour.</td>
           </tr>
           <tr> 
+            <td>defaultColourNuc</td>
+            <td>A colour scheme (from the list above) to apply to Nucleotide alignments</td><td>This overrides defaultColour if it is specified.</td>
+          </tr>
+          <tr> 
+            <td>defaultColourProt</td>
+            <td>A colour scheme (from the list above) to apply to Peptide alignments</td><td>This overrides defaultColour if it is specified.</td>
+          </tr>
+          <tr> 
             <td>userDefinedColour</td>
             <td><p><em>Example:</em><br>
                 D,E=red; K,R,H=0022FF; c=yellow</p></td>
@@ -150,6 +159,11 @@ the applet can be interacted with <em>via</em> its
             <td>Default is true.</td>
           </tr>
           <tr> 
+            <td>showOccupancy</td>
+            <td>true <em>or</em> false</td>
+            <td>Default is true.</td>
+          </tr>
+          <tr> 
             <td>sortBy</td>
             <td> Id <em>, </em> Pairwise Identity<em>, or</em> Length</td>
             <td> Sorts the alignment on startup</td>
@@ -349,133 +363,4 @@ the applet can be interacted with <em>via</em> its
           <td>Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format</td>
           </tr>
                   </table>
-                  <p><h2><a name="appletdeploymentnotes"/>Notes on applet deployment</h2><br/>
-        <ul>
-          <li>Package all your data files into a single (or multiple) zip / jar 
-            files. This is very useful to reduce download time of large data files. 
-            The applet archive tag can take multiple entries separated by commas, 
-            eg<br>
-            <pre>&lt;applet code=&quot;jalview.bin.JalviewLite&quot;<em><strong> 
-            archive=&quot;jalviewApplet.jar, mydata.zip&quot;</strong></em>&gt;<br>
-            </pre></li>
-          <li> Use Jalview for input to a HTML form. For an example of how to 
-            code this using Javascript, click <a href="javascript:doSubmit('formComplete')">here</a>. 
-            <br>
-          </li>
-          <li>Embed Jalview into the web page, without the &quot;Start Jalview&quot; 
-            button by setting the embed parameter to true;<br>
-            &lt;param name=&quot;embedded&quot;
-          value=&quot;true&quot;&gt; </li>
-        </ul>
-        
-        <p><strong>**NEW FEATURES** in Jalview 2.9</strong></p> 
-        <ul>
-        <li>Split Views for cDNA and Protein alignments<br/>Specify second alignment with 'file2' parameter, and set cDNA/Protein column scaling with scaleProteinAsCdna
-        </li>
-        </ul>
-        </p>
-        <p><strong>**NEW FEATURES** in Jalview 2.8</strong></p> 
-        <ul>
-        <li>Normalised sequence logo display
-        </li>
-        <li>RNA secondary structure annotation row
-        </li>
-<li>Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.jar">download the JmolApplet here</a></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>archive=&quot;jalviewApplet.jar,Jmol-12.2.4.jar&quot;</pre>
-          </li>
-          <li>Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have 
-            Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the 
-            original Jalview structure viewer will still be available. <br>
-          </li>
-          
-        </ul>
-        <p><strong>**NEW FEATURES** in Jalview 2.7</strong></p>
-        <ul>
-        <li>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>
-        </li>
-        <li>New <a href="javascript:doSubmit('jalviewLiteJs')">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
-        </li></ul>
-        <p><strong>**NEW FEATURES** in Jalview 2.6</strong></p>
-        <ul>
-        <li>Jmol compatibility updated to Jmol 12.1.x series</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>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).</li>
-  </ul>
-        <br><strong>**NEW FEATURES** in Jalview 2.5</strong></p>
-        <ul>
-        <li>New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</li>
-  </ul>        
-        <br><strong>**NEW FEATURES** in Jalview 2.4</strong></p>
-        <ul>
-        <li>New applet API methods for feature display control, views, and obtaining current selection via javascript.</li>
-          <li>Group show and hide parameters:
-        &quot;showfeaturegroups&quot; and
-        &quot;hidefeaturegroups&quot;. Both take a list
-        of feature group names (separarated by &quot;|&quot; by default) to hide or show on the displayed
-        alignment.
-        </li>
-        <li>Regular expressions can be used in URL links for sequence IDs.</li>
-        <li>&quot;debug&quot; parameter to control verbosity of the applet's console output.</li>
-        <li>&quot;showbutton&quot; parameter to disable launch button and open JalviewLite immediatly.</li>
-        <li>&quot;nojmol&quot; parameter to disable check for Jmol classes.</li>
-        </ul><br>
-        <strong>**NEW FEATURES** in Jalview 2.3</strong></p>
-        <ul>
-          <li>Note that Parameter &quot;PDBFile&quot; now takes 
-            the PDB file followed by a space separated list of alignment sequence 
-            ids to associate the structure to. It is also possible to associate 
-            multiple PDB files by adding an incremental value to PDBFile (up to 
-            10). It is also possible to map specific sequences to specific chains 
-            by using the following notation:<br>
-            <br>
-            <pre>
-            &lt;param name=&quot;PDBFile&quot; value=&quot;First.pdb SeqA SeqB 
-            SeqC&quot;&gt;<br>
-            &lt;param name=&quot;PDBFile2&quot; value=&quot;Second.pdb 
-            A=SeqA B=SeqB C=SeqC&quot;&gt;<br>
-            &lt;param name=&quot;PDBFile3&quot; value=&quot;Third.pdb 
-            D=SeqX B=SeqY C=SeqZ&quot;&gt;<br>
-            </pre>
-          </li>
-          <li>Note parameter &quot;PDBSeq&quot; is no longer required.<br>
-          </li>
-          <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="/development">versions archive if you want to download the old Jmol applet</a>.</li> 
-            <p>&nbsp;</p>
-          </li>
-        </ul>
-        <strong>**NEW FEATURES** in Jalview 2.1</strong> 
-        <ul>
-          <li>Jalview Applet can read and display JNet secondary structure annotation 
-            directly via the <strong>jnetfile</strong> parameter. <br>
-          </li>
-          <li>Param &quot;UserDefinedColour&quot; - specify your own colours for each residue using a semi colon 
-            separated list. Multiple residues can be assigned the same colour 
-            using commas. eg:<br>
-            <pre>&lt;param name=&quot;userDefinedColour&quot; 
-            value=&quot;D,E=red; K,R,H=0022FF; C=yellow&quot;&gt;</pre>
-          </li>
-          <li>Param &quot;showFeatureSettings&quot;
-            - this will display the feature settings window when the applet starts.
-          </li>
-          <li>Param &quot;Application_URL&quot; value=&quot;http://www.jalview.org/services/launchApp&quot;<br/>
-            This calls a servlet which creates a JNLP file with the alignment 
-            file, annotations file and features file of the applet as arguments. 
-            If the user has Java installed, the returned JNLP file should start 
-            up the full Jalview Application. BUT this does not currently work 
-            for alignment files added to the applet in a zip file.
-            <br/>Look at the XML comments in the file downloaded from <a href="http://www.jalview.org/services/launchApp">The LaunchApp page</a> for full documentation.
-          </li>
-          <li>Alignment file can be a series of parameters using eg PFAM format 
-            <br>
-            <pre>&lt;param name=&quot;sequence1&quot; 
-            value=&quot;Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI&quot;&gt;<br>
-            &lt;param name=&quot;sequence2&quot; value=&quot;FER1_PEA/14-29 TSFLRTQPMPMSVTTT&quot;&gt;<br>
-            </pre>(All the usual Jalview File formats are valid, however each 
-            new line in an alignment file must be entered as a parameter)</li>
-        </ul>
-<!-- content end -->
+                  <!-- content end -->