"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
<head>\r
-<meta name="Last-modified" content="Mon, 4 Apr 2011 12:00:00 GMT"/>\r
+<meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
<title>Java Bioinformatics Analyses Web Services (JABAWS) client developers manual</title>\r
-<link href="ws.css" rel="stylesheet" type="text/css" media=\r
-"screen, projection, handheld, tv" />\r
-<link rel="stylesheet" type="text/css" media="print" href=\r
-"print.css" />\r
+<link href="ws.css" rel="stylesheet" type="text/css" media="screen, projection, handheld, tv" />\r
+<link rel="stylesheet" type="text/css" media="print" href="print.css" />\r
<script type="text/javascript" src="prototype-1.6.0.3.js"></script>\r
</head>\r
+\r
<body>\r
<div id="page">\r
<div id="banner">\r
-<table> \r
-<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:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
-<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
-</tr>\r
+<table>\r
+ <tr>\r
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" 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/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
+ <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
+ </tr>\r
</table>\r
-</div><!-- banner end-->\r
+</div>\r
+<!-- banner end-->\r
+\r
\r
<div id="wrapper">\r
<div id="panel"><a href="index.html">Home</a> \r
- <a href="quick_start.html">Getting Started</a> \r
- <a class="selected" href="man_about.html">Manual</a> \r
- <div id="submenu">\r
- <a href="man_about.html">About</a>\r
- <a href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
- <a href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
- <a href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
- <a href="man_configuration.html" >Server<br/>\r
- Configuration</a>\r
- <a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
- <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
- JABAWS</a> \r
- <a href="man_server_dev.html" >JABAWS Development</a>\r
- </div>\r
-<a href="download.html">Download</a> \r
-<a href="contacts.html">Contact Us</a>\r
-<a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
-<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
-\r
+ <a href="quick_start.html">Getting Started</a> \r
+ <a class="selected" href="man_about.html">Manual</a> \r
+ <div id="submenu">\r
+ <a href="man_about.html">About</a>\r
+ <a href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>\r
+ <a href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
+ <a href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
+ <a href="man_configuration.html" >Server Configuration</a>\r
+ <a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
+ <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 JABAWS</a>\r
+ <a href="man_server_dev.html" >JABAWS Development</a>\r
+ </div>\r
+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
+ <a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
+ <a href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
+ <a href="contacts.html">Contact Us</a>\r
+ <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
+ <a href="jabaws_funding.html">Funding</a>\r
</div>\r
-\r
<!-- panel end-->\r
+\r
+\r
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<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
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
<h3><a name="buildart" id="buildart"></a>Building web services artifacts</h3>\r
<p>JABAWS are the standard <a href="http://jax-ws.java.net/">JAX-WS</a> SOAP web services, which are <a href="http://www.ws-i.org/">WS-I</a> basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can generate portable artifacts to work with JABAWS from Java. However, if programming in Java we recommend using our client library as it provides a handful of useful methods in addition to plain data types. </p>\r
<p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl</p>\r
-</div>\r
+</div><!-- content end-->\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+</div><!-- wrapper end-->\r
+</div><!-- page end-->\r
\r
-<!-- content end-->\r
-<div id="copyright">Last update: 10 August 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
-</div>\r
-\r
-<!-- wrapper end-->\r
-</div>\r
-<!-- page end-->\r
\r
<!-- Google analitics -->\r
<script type="text/javascript">\r
</script>\r
</body>\r
</html>\r
-\r
git://source.jalview.org / jabaws.git / blobdiff