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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
<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/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
+ </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
\r
<!-- 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