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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
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+<ul>
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+<li class="jvlite-nav-small"><a href="appletParameters.html">Applet Parameters</a></li>
+<li><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li><a href="formComplete.html">in-page API demo</a></li>
+<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
+<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
+</ul>
+</div>
+
+<div id="content" class="content">
<p>
<strong>Quick Links:<ul><li>Download the applet jar file from <a
href="jalviewApplet.jar">here</a>
href="jalviewLiteJs.html">here</a></li>
</ul></strong>
</p>
-
- <h3 align="left">Useful to know!!</h3>
- <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>
- <font face="Courier New, Courier, mono" align="left"><applet code="jalview.bin.JalviewLite"<em><strong>
- archive="jalviewApplet.jar, mydata.zip"</strong></em>><br>
- </font></li>
- <li> Use Jalview for input to a HTML form. For an example of how to
- code this using Javascript, click <a href="formComplete.html">here</a>.
- <br>\r
- </li>\r
- <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><font size="2">**NEW FEATURES** in Jalview 2.8</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>
-<li><font size="2">Jmol compatibility updated to Jmol 12.2.x series - <a href="JmolApplet-12.2.4.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>archive="jalviewApplet.jar,Jmol-12.2.4.jar"</pre></font>
- </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><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 (<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</font></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>
- <li><font size="2">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.</font>
- </li>
- <li><font size="2">Regular expressions can be used in URL links for sequence IDs.</font></li>
- <li><font size="2">"debug" parameter to control verbosity of the applet's console output.</font></li>
- <li><font size="2">"showbutton" parameter to disable launch button and open JalviewLite immediatly.</font></li>
- <li><font size="2">"nojmol" parameter to disable check for Jmol classes.</font></li>
- </ul><br>
- <strong><font size="2">**NEW FEATURES** in Jalview 2.3</font></strong></p>
- <ul>
- <li><font size="2">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>
- <param name="PDBFile" value="First.pdb SeqA SeqB
- SeqC"> </font><br>
- <font size="2"><param name="PDBFile2" value="Second.pdb
- A=SeqA B=SeqB C=SeqC"> </font><br>
- <font size="2"><param name="PDBFile3" value="Third.pdb
- D=SeqX B=SeqY C=SeqZ"> </font> <br>
- </li>
- <li>Note parameter "PDBSeq" is no longer required.<br>\r
- </li>
- <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="../versions.html">versions archive if you want to download the old Jmol applet</a>.</li>
- <p> </p>
- </li>
- </ul>
- <strong><font size="2">**NEW FEATURES** in Jalview 2.1</font></strong>
- <ul>
- <li>Jalview Applet can read and display JNet secondary structure annotation
- directly via the <strong>jnetfile</strong> parameter. <br>
- </li>
- <li>Param <font face="Courier New, Courier, mono">UserDefinedColour</font><em>
- </em>- 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>
- <font face="Courier New, Courier, mono"><param name="userDefinedColour"
- value="D,E=red; K,R,H=0022FF; C=yellow"></font><br>
- </li>
- <li>Param <font face="Courier New, Courier, mono">showFeatureSettings</font>
- - this will display the feature settings window when the applet starts.<br>
- </li>
- <li>Param <font face="Courier New, Courier, mono">Application_URL value="http://www.jalview.org/services/launchApp"<br>
- </font>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>
- </li>
- <li>Alignment file can be a series of parameters using eg PFAM format
- <br>
- <font face="Courier New, Courier, mono"><param name="sequence1"
- value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI"><br>
- <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT"><br>
- </font>(All the usual Jalview File formats are valid, however each
- new line in an alignment file must be entered as a parameter)<font face="Courier New, Courier, mono"><br>
- </font> </li>
- </ul>
- <a name="parameters"></a> <table width="97%" border="1" align="center" >
+ <p>Additional <a href="#appletdeploymentnotes">applet deployment notes are below</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 width="103" height="23"><strong><param name=""</strong></td>
<td width="80" ><strong>value=""></strong></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>
+ <tr><td>normaliseSequenceLogo</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 2.8</em>)</td>
</tr>
<td>Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format</td>
</tr>
</table>
- <p align="center"> </p>
- <!-- InstanceEndEditable --></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="formComplete.html">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="jalviewLiteJs.html">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="../versions.html">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>
+
</div>
+</div>
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
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