X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fman_dev.html;h=f5c087cd4bd84020823c554f72a12d477706740f;hb=0d3b931076cf21ff2800c2de77d72f81efa5a7e5;hp=73dee0840af9132e07d293c121f98929ef687cd5;hpb=b0423691d9a44eae86799ad242c4fea58f9acd8d;p=jabaws.git

diff --git a/website/man_dev.html b/website/man_dev.html
index 73dee08..f5c087c 100644
--- a/website/man_dev.html
+++ b/website/man_dev.html
@@ -15,11 +15,12 @@
 <div id="page">
 <div id="banner">
 <table> 
-<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>
-<td class="bg"><img src="images/jabaws.png" title="JABAWS:MSA" alt="JABAWS:MSA"/></td>
-<td class="bg"><img src="images/align.png"/></td>
+<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>
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
 </tr>
-</table></div><!-- banner end-->
+</table>
+</div><!-- banner end-->
 
 <div id="wrapper">
 <div id="panel"><a href="index.html">Home</a> 
@@ -28,16 +29,21 @@
 	<div id="submenu">
 		<a href="man_about.html">About</a>
 		<a href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>
+		<a href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>
 		<a href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>
 		<a href="man_configuration.html" >Server<br/>
 		Configuration</a>
 		<a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>
+		<a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>
 		<a class="selected" href="man_dev.html" title="Accessing JABAWS from your program">Accessing<br/>
 		JABAWS</a>	
+		<a href="man_server_dev.html" >JABAWS Development</a>
 	</div>
 <a href="download.html">Download</a> 
 <a href="contacts.html">Contact Us</a>
-<a href="http://www.compbio.dundee.ac.uk">Barton Group</a> 
+<a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>
+<a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>
+
 </div>
 
 <!-- panel end-->
@@ -135,13 +141,26 @@
   + &quot;Port&quot;), MsaWS.class);</p>
 <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>
 <h3><a name="validnames" id="validnames"></a>Valid JABAWS service names and WSDL files </h3>
-<ul>
+<p>Multiple sequence alignment services </p>
+<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>
   <li><a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl">ClustalWS</a> (http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl) </li>
   <li><a href="http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl">MuscleWS</a> (http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl) </li>
   <li><a href="http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl">MafftWS</a> (http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl) </li>
   <li><a href="http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl">TcoffeeWS</a> (http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl) </li>
   <li><a href="http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl">ProbconsWS</a> (http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl) </li>
-</ul>
+  </ul>
+<p>Protein disorder prediction services </p>
+<ul>
+  <li><a href="http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl">IUPredWS</a> (http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl) </li>
+  <li><a href="http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl">GlobPlotWS</a> (http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl) </li>
+  <li><a href="http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl">DisemblWS</a> (http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl) </li>
+  <li><a href="http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl">JronnWS</a> (http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl) </li>
+  </ul>
+<p>Amino acid conservation service</p>
+<ul>
+  <li><a href="http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl">AAConWS</a> (http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl) </li>
+  </ul>
+<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>
 <h3><a name="defalign" id="defalign"></a>Aligning sequences </h3>
 <p>Given that <span class="hightlight">msaws</span> is web service proxy, created as described in &quot;Connecting to JABAWS&quot; section, the actual alignment can be obtained as follows: </p>
 <p class="code">1) List&lt;FastaSequence&gt; fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />
@@ -334,7 +353,7 @@ For a more detailed description of all available types and their functions pleas
 </div>
 
 <!-- content end-->
-<div id="copyright">Last update: 1 April 2011<br />
+<div id="copyright">Last update: 10 August 2011<br />
  Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of
 Dundee, UK</div>
 </div>