JWS-122 & JWS-116 New documentation entry with instructions on how to use the JABAWS...

[jabaws.git] / website / docs / develop.html

diff --git a/website/docs/develop.html b/website/docs/develop.html
index fb1d0f8..17bb6a5 100644 (file)
--- a/website/docs/develop.html
+++ b/website/docs/develop.html
@@ -97,6 +97,7 @@
 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Container</a></li>
 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">For Developers</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#source-code">Source Code</a></li>
@@ -177,7 +178,8 @@
       <li class="wy-breadcrumbs-aside">
         
             
-            <a href="_sources/develop.rst.txt" rel="nofollow"> View page source</a>
+            <!-- <a href="_sources/develop.rst.txt" rel="nofollow"> View page source</a> -->
+            <a href="../">Return to the JABAWS homepage</a>
           
         
       </li>
@@ -206,8 +208,8 @@
 </div>
 <div class="section" id="the-api">
 <span id="jabaws-api"></span><h2>The API<a class="headerlink" href="#the-api" title="Permalink to this headline">¶</a></h2>
-<p><a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html">Data Model JavaDoc</a> - read this if your are coding against JABA Web Services</p>
-<p><a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html">Complete JavaDoc</a> - for developers who want to use JABAWS framework and use Engines and Executables directly</p>
+<p><a class="reference external" href="dm_javadoc/index.html">Data Model JavaDoc</a> - read this if your are coding against JABA Web Services</p>
+<p><a class="reference external" href="full_javadoc/index.html">Complete JavaDoc</a> - for developers who want to use JABAWS framework and use Engines and Executables directly</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="structure-of-the-project">
@@ -337,12 +339,12 @@ JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse w
 </tbody>
 </table>
 <p>Additional utility libraries that this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.</p>
-<p>Please refer to a <a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html">Data Model JavaDoc</a> for a detailed description of each class and its methods.</p>
+<p>Please refer to a <a class="reference external" href="dm_javadoc/index.html">Data Model JavaDoc</a> for a detailed description of each class and its methods.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="connecting-to-jabaws">
 <span id="jabaws-conn-conn"></span><h3>Connecting to JABAWS<a class="headerlink" href="#connecting-to-jabaws" title="Permalink to this headline">¶</a></h3>
-<p>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 class="reference external" href="download.jsp">download page</a>. Please note that for now all the examples are in Java, other languages will follow if there is sufficient demand.</p>
+<p>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 class="reference external" href="../download.jsp">download page</a>. Please note that for now all the examples are in Java, other languages will follow if there is sufficient demand.</p>
 <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>
 <div class="highlight-java"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">java.net.URL</span><span class="o">;</span>
 <span class="kn">import</span> <span class="nn">javax.xml.namespace.QName</span><span class="o">;</span>
@@ -455,7 +457,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
 </div>
 <div class="section" id="a-complete-client-example">
 <span id="jabaws-conn-aln-example"></span><h3>A complete client example<a class="headerlink" href="#a-complete-client-example" title="Permalink to this headline">¶</a></h3>
-<p>Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service presets. All you need for this to work is a <a class="reference external" href="download.jsp#client">JABAWS CLI client</a>. Please make sure that the client is in the Java class path before running this example.</p>
+<p>Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service presets. All you need for this to work is a <a class="reference external" href="../download.jsp#client">JABAWS CLI client</a>. Please make sure that the client is in the Java class path before running this example.</p>
 <div class="highlight-java"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">java.io.ByteArrayInputStream</span><span class="o">;</span>
 <span class="kn">import</span> <span class="nn">java.io.FileNotFoundException</span><span class="o">;</span>
 <span class="kn">import</span> <span class="nn">java.io.IOException</span><span class="o">;</span>
@@ -587,7 +589,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
 <span class="o">}</span>
 </pre></div>
 </div>
-<p>For a more detailed description of all available types and their functions please refer to the <a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html">Data Model JavaDoc</a>.</p>
+<p>For a more detailed description of all available types and their functions please refer to the <a class="reference external" href="dm_javadoc/index.html">Data Model JavaDoc</a>.</p>
 <hr class="docutils" />
 </div>
 </div>
@@ -658,15 +660,8 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
 <ol class="arabic simple">
 <li>Client only (contains classes required to access JABA Web Services)</li>
 <li>Platform specific JABAWS (windows and other)</li>
-<li>JABAWS without binaries</li>
-<li>JABAWS framework</li>
-</ol>
-<p>Corresponding build task names are:</p>
-<ol class="arabic simple">
-<li>min-jaba-client</li>
-<li>jaba-windows, jaba-complete</li>
-<li>jaba-no-binaries</li>
-<li>full-jaba-client</li>
+<li>JABAWS with and without binaries</li>
+<li>JABAWS framework and complete project</li>
 </ol>
 <p>The easiest way to build all distributives is to call <code class="docutils literal"><span class="pre">build-all</span></code> ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory.</p>
 <p>If you made any changes to the data model and would like to generate a complete JABAWS distro make sure you have rebuilt jaxws artifact as described below.</p>
@@ -696,7 +691,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
 
   <div role="contentinfo">
     <p><a href="../">JABAWS 2.2</a>
-        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Alexey Drozdetskiy, Daniel Barton, Suzanne Duce, Fábio Madeira and Geoff Barton.
+        &copy; Copyright 2017, Peter Troshin, Alexander Sherstnev, Jim Procter, Daniel Barton, Fábio Madeira, Alexey Drozdetskiy, Suzanne Duce and Geoff Barton.
 
     </p>
   </div>