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>
<td>fileName</td>
<td>The file to open, must be on same server as the applet.</td>
</tr>
- <tr>
- <td>file2</td>
- <td>fileName</td>
- <td>A second file to open. If one file is nucleotide and the other peptide, and at least one peptide sequence
- is the translation of one of the nucleotide sequences, then alignments will be displayed linked in a split frame (<em>since 2.9</em>).</td>
+ <tr>
+ <td>file2</td>
+ <td>fileName</td>
+ <td>A second file to open and show linked in a Split Frame
+ view. If one file is nucleotide and the other peptide, and at
+ least one peptide sequence matches the translation of one of the
+ nucleotide sequences, then gaps will be inserted into the
+ sequences in this file to match the aligned columns for
+ corresponding positions in the primary alignment file. This
+ parameter is ignored if enableSplitFrame is set to false (<em>since
+ 2.9</em>).
+ </td>
+ </tr>
+ <tr>
+ <td>enableSplitFrame</td>
+ <td>true or false (default true)</td>
+ <td>Enable or disable the display of linked cDNA and Protein alignments in a split frame (<em>since 2.9</em>).</td>
</tr>
<tr>
<td>sequence1,<br>
<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>
<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>
<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>
<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><applet code="jalview.bin.JalviewLite"<em><strong>
- archive="jalviewApplet.jar, mydata.zip"</strong></em>><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 "Start Jalview"
- button by setting the embed parameter to true;<br>
- <param name="embedded"
- value="true"> </li>
- </ul>
- <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="jalviewApplet.jar,Jmol-12.2.4.jar"</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 (<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:
- "showfeaturegroups" and
- "hidefeaturegroups". Both take a list
- of feature group names (separarated by "|" 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>"debug" parameter to control verbosity of the applet's console output.</li>
- <li>"showbutton" parameter to disable launch button and open JalviewLite immediatly.</li>
- <li>"nojmol" parameter to disable check for Jmol classes.</li>
- </ul><br>
- <strong>**NEW FEATURES** in Jalview 2.3</strong></p>
- <ul>
- <li>Note that Parameter "PDBFile" 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>
- <param name="PDBFile" value="First.pdb SeqA SeqB
- SeqC"><br>
- <param name="PDBFile2" value="Second.pdb
- A=SeqA B=SeqB C=SeqC"><br>
- <param name="PDBFile3" value="Third.pdb
- D=SeqX B=SeqY C=SeqZ"><br>
- </pre>
- </li>
- <li>Note parameter "PDBSeq" 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> </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 "UserDefinedColour" - 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><param name="userDefinedColour"
- value="D,E=red; K,R,H=0022FF; C=yellow"></pre>
- </li>
- <li>Param "showFeatureSettings"
- - this will display the feature settings window when the applet starts.
- </li>
- <li>Param "Application_URL" value="http://www.jalview.org/services/launchApp"<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><param name="sequence1"
- value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI"><br>
- <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT"><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 -->
git://source.jalview.org / jalview.git / blobdiff