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-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt.gif" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws.png" title="JABAWS:MSA" alt="JABAWS:MSA"/></td>\r
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+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0" title="Java Bioinformatics Analysis Web Services version 2.0"/></td>\r
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+ <a href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
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Configuration</a>\r
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+ <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
<a class="selected" href="man_dev.html" title="Accessing JABAWS from your program">Accessing<br/>\r
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+<a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
+<a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
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-<a href="http://www.compbio.dundee.ac.uk">Barton Group</a> \r
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<p>Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar. <br />\r
Please refer to a <a href="dm_javadoc/index.html">data model javadoc</a> for a detailed description of each class and its methods. </p>\r
<h3><a name="connectto" id="connectto"></a>Connecting to JABAWS</h3>\r
-<p class="attention">For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client source code is available from the <a href="download.html">download page</a>. Please note that for now all the examples are in Java other languages will follow given a sufficient demand. </p>\r
+<p class="attention">For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client source code is available from the <a href="http://www.compbio.dundee.ac.uk/download">download page</a>. Please note that for now all the examples are in Java other languages will follow given a sufficient demand. </p>\r
<p>Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee. </p>\r
<p class="code"> import java.net.URL;<br />\r
import javax.xml.namespace.QName;<br />\r
+ "Port"), MsaWS.class);</p>\r
<p>Where Services is enumeration of JABAWS web services. All JABAWS multiple sequence alignment methods confirm to MsaWS specification, thus from the caller point of view all JABAWS web services can be represented by MsaWS interface. The full documentation of MsaWS functions is available from the <a href="dm_javadoc/compbio/data/msa/MsaWS.html">javadoc</a>. </p>\r
<h3><a name="validnames" id="validnames"></a>Valid JABAWS service names and WSDL files </h3>\r
-<ul>\r
+<p>Multiple sequence alignment services </p>\r
+<ul><li><a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalOWS?wsdl">ClustalOWS</a> (http://www.compbio.dundee.ac.uk/jabaws/ClustalOWS?wsdl) </li>\r
<li><a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl">ClustalWS</a> (http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl) </li>\r
<li><a href="http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl">MuscleWS</a> (http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl) </li>\r
<li><a href="http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl">MafftWS</a> (http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl) </li>\r
<li><a href="http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl">TcoffeeWS</a> (http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl) </li>\r
<li><a href="http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl">ProbconsWS</a> (http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl) </li>\r
-</ul>\r
+ </ul>\r
+<p>Protein disorder prediction services </p>\r
+<ul>\r
+ <li><a href="http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl">IUPredWS</a> (http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl) </li>\r
+ <li><a href="http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl">GlobPlotWS</a> (http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl) </li>\r
+ <li><a href="http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl">DisemblWS</a> (http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl) </li>\r
+ <li><a href="http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl">JronnWS</a> (http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl) </li>\r
+ </ul>\r
+<p>Amino acid conservation service</p>\r
+<ul>\r
+ <li><a href="http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl">AAConWS</a> (http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl) </li>\r
+ </ul>\r
+<p>Please replace <span class="hightlight">http://www.compbio.dundee.ac.uk/</span> with your JABAWS instance host name, and <span class="hightlight">jabaws</span> with your JABAWS context name to access your local version of JABAWS web services. For example <span class="hightlight">http://localhost:8080/jabaws</span> would be a valid URL for the default Apache-Tomcat installation and jabaws.war file deployment. </p>\r
<h3><a name="defalign" id="defalign"></a>Aligning sequences </h3>\r
<p>Given that <span class="hightlight">msaws</span> is web service proxy, created as described in "Connecting to JABAWS" section, the actual alignment can be obtained as follows: </p>\r
<p class="code">1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
FileOutputStream outStream = new FileOutputStream(file);<br />\r
ClustalAlignmentUtil.writeClustalAlignment(outStream, align);</span></p>\r
<h3><a name="compex" id="compex"></a>A complete client example </h3>\r
-<p>Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service preset. Three is also a <a href="Example_template.pdf">PDF version</a> of this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, the alternatives given in the code are line commented // comment. You may want to remove line style comments to test alternatives of the functions. All you need for this to work is a <a href="download.html">JABAWS binary client</a>. Please make sure that the client is in the Java class path before running this example.</p>\r
+<p>Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service preset. Three is also a <a href="Example_template.pdf">PDF version</a> of this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, the alternatives given in the code are line commented // comment. You may want to remove line style comments to test alternatives of the functions. All you need for this to work is a <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">JABAWS binary client</a>. Please make sure that the client is in the Java class path before running this example.</p>\r
<pre class="code" style="line-height:1em;">\r
import java.io.ByteArrayInputStream;\r
import java.io.FileNotFoundException;\r
</div>\r
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<!-- content end-->\r
-<div id="copyright">Last update: 1 April 2011<br />\r
+<div id="copyright">Last update: 16 September 2011<br />\r
Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
</div>\r
git://source.jalview.org / jabaws.git / blobdiff