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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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- <tr>
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-
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- <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
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- </tr>
- <tr>
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- Version</a></td>
- </tr>
- <tr>
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- </tr>
- <tr>
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- Code</a></td>
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- Mailing List</a></td>
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- href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
- class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
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+<body>
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- <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
- </div>
- </td>
- <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p>
- <strong>Quick Links:<ul><li>Download the applet jar file from <a
- href="jalviewApplet.jar">here</a>
- </li>
- <li>Parameters are described <a href="#parameters">below</a></li>
- <li>The javascript API is described <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>
- </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><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>
- </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" >
+
+ <div id="header">
+ <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+ <ul id="buttons">
+ <li id="applet"><a href="applets.html" title="applet"></a></li>
+ <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+ </ul>
+ </div>
+
+
+ <div id ="nav">
+ <div id="navInner">
+
+ <ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+ </ul>
+ <div style="clear:both"></div>
+ </div>
+
+ </div>
+<div id="pageWrap">
+
+<div id="sideNav">
+ <ul>
+ <li ><a href="applets.html">JalviewLite Examples</a></li>
+ <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li class="jvlite-nav-small"><a href="appletParameters.html">Applet Parameters</a></li>
+ <li ><a href="embedded.html">Embedded Alignment</a></li>
+ <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="formComplete.html">Access from Javascript</a></li>
+ <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
+</div>
+
+<div id="content" class="content">
+
+
+<!-- content start -->
+<p>
+<ul>
+<li>Parameters are described <a href="#parameters">below</a></li>
+<li>The javascript API is described <a
+href="jalviewLiteJs.html">here</a></li>
+</ul></strong>
+</p>
+ <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 width="100%"><strong>Description</strong></td>
</tr>
+ <tr>
+ <td>permissions</td>
+ <td>sandbox</td>
+ <td><strong>This parameter is necessary, and must have the value <em>sandbox</em> to allow the JalviewLite applet to run.</strong></td>
+ </tr>
<tr>
<td>file</td>
<td>fileName</td>
</tr>
<tr>
<td>linkLabel_1</td>
- <td>Uniprot</td>
+ <td>EMBL-EBI Search</td>
<td rowspan="2"><p>Right click on sequence id to see list of available
links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n
value. For multiple links, increment the label and url name by
<br>Regex URL links are also applied to the description line (since Jalview 2.4.+).</em></p></td>
</tr>
<tr>
- <td> <p><br>
+ <td> <p>
+ <br>
linkUrl_1<br>
</p></td>
<td><p><br>
- http://us.expasy.org/cgi-bin/<br>
- niceprot.pl?$SEQUENCE_ID$</p>
+ http://www.ebi.ac.uk/ebisearch/<br/>search.ebi?db=allebi&query=$SEQUENCE_ID$</p>
</td>
</tr>
<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="/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 -->
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
+<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>
</div>
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