From 246d7b5d172cc9f93190c212ef13ce6dad1e696a Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Wed, 24 Nov 2010 13:04:56 +0000
Subject: [PATCH] update from JWS2

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3382 e3abac25-378b-4346-85de-24260fe3988d
---
 website/howto.html  |  251 +----------------------------------------------
 website/manual.html |  270 ++++++++++++++++++++++++++++++++++++++++++++++++---
 2 files changed, 257 insertions(+), 264 deletions(-)

diff --git a/website/howto.html b/website/howto.html
index e37cea6..4cf9f27 100644
--- a/website/howto.html
+++ b/website/howto.html
@@ -33,7 +33,7 @@ class="headeru">S</span>ervices</h2></td>
 
 
 <h2 align="center">JABAWS How To</h2>
-<h3>Table of Content </h3>
+<h3>Table of content </h3>
 <h4>About </h4>
 <ul>
   <li><a href="#wisjaba">What is JABAWS?</a></li>
@@ -72,18 +72,6 @@ class="headeru">S</span>ervices</h2></td>
   <li><a href="#toomanyreqs">What happens if the number of requests to my JABAWS installation is greater the the server can process?</a></li>
   <li><a href="#canlimit">Sometimes users sent  very large number of sequences to JABAWS server, so that it  becomes unresponsive. Can I limit the number of sequences users can submit to my server. </a></li>
 </ul>
-<h4>Using JABAWS in your program (examples in java) </h4>
-<ul>
-	<li><a href="#connectto">Connecting to JABAWS</a></li>
-	<li><a href="#validnames">Valid JABAWS service names and WSDL files</a></li>
-	<li><a href="#defalign">Aligning sequences</a></li>
-	<li><a href="#checkresults">Checking the status of the calculation </a></li>
-	<li><a href="#presetalign">Aligning with presets</a></li>
-	<li><a href="#customalign">Aligning with custom parameters</a></li>
-	<li><a href="#writingaltofile">Writing alignments to a file</a></li>
-    <li><a href="#compex">A complete client example </a></li>
-    <li><a href="#buildart">Building web services artifacts</a></li>
-</ul>
 <h4>JABAWS on Apache-Tomcat</h4>
 <ul>
   <li><a href="#tomdeploy">I dropped jaba.war file into web application directory but nothing happened. What do I do next?</a></li>
@@ -331,243 +319,6 @@ For the local execution the starting and finishing time in nano seconds can be f
 These listings are read only by default.  
 <h4><a name="canyouhelp" id="canyouhelp"></a>Sometimes something goes wrong with JABAWS, but I cannot figure out why. Can you help?</h4>
 <p>JABAWS  logs all errors to the stdout and in the file called activity.log if <a href="manual.html#logfiles">logging is enabled</a>. Stdout is usually recorded in web server log files. Have a look there and you may find the reason for the problems. If it is still unclear what went wrong try increasing the logging level. Setting the logging level to TRACE or DEBUG will give you a lot of insights in what goes on behind the scene. We would need this log if you need us to help you, or if you would like to report the bug. To change the log level, replace ERROR keyword in ACTIVITY logger to TRACE. </p>
-<h3>Using JABAWS in your program</h3>
-<h4><a name="connectto" id="connectto"></a>Connecting to JABAWS</h4>
-<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>
-<p>Download a binary JABAWS <a href="download.html">client</a>. 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>
-<p class="code">  import java.net.URL;<br />
-  import javax.xml.namespace.QName;<br />
-  import javax.xml.ws.Service;<br />
-  ...............<br />
-  1) String qualifiedName = &quot;http://msa.data.compbio/01/01/2010/&quot;;<br />
-  2) URL url = new URL(&quot;http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl&quot;);<br />
-  3) QName qname = new QName(, &quot;ClustalWS&quot;);<br />
-4) Service serv = Service.create(url, qname);<br />
-5) MsaWS msaws = serv.getPort(new QName(qualifiedName, &quot;ClustalWSPort&quot;),
-MsaWS.class);</p>
-<p>Line 1 makes a qualified name for JABA web services.<br />
-  Line 2 
-  constructs the URL to the web services WSDL. <br />
-Line 3 makes a qualified name instance for Clustal JABA web service. <br />
-Line 4 creates a service instance.<br />
-Line 5 makes a connection to the server. </p>
-<p>A more generic connection method would look like this </p>
-<p class="code"> import java.net.URL;<br />
-import javax.xml.namespace.QName;<br />
-import javax.xml.ws.Service;<br />
-import compbio.ws.client.Services<br />
-..............
-<br />
-String qualifiedServiceName = &quot;http://msa.data.compbio/01/01/2010/&quot;;<br />
-String host = &quot;http://www.compbio.dundee.ac.uk/jabaws&quot;;<br />
-// In real life the service name can come from args<br />
-Services clustal = Services.ClustalWS;<br />
-URL url = new URL(host + &quot;/&quot; + clustal.toString() + &quot;?wsdl&quot;);<br />
-QName qname = new QName(qualifiedServiceName, clustal.toString());<br />
-Service serv = Service.create(url, qname);<br />
-MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, clustal<br />
-+ &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="file:///D:/workspace/JWS2/website/dm_javadoc/compbio/data/msa/MsaWS.html">javadoc</a>. </p>
-<h4><a name="validnames" id="validnames"></a>Valid JABAWS service names and WSDL files </h4>
-<ul>
-  <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>
-<h4><a name="defalign" id="defalign"></a>Aligning sequences  </h4>
-<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 />
-  2) String jobId = msaws.align(fastalist);
-  <br />
-  3) Alignment alignment = msaws.getResult(jobId);</p>
-<p>Line  one loads FASTA sequence from the file<br />
-  Line two submits them to web service represented by msaws proxy <br />
-  Line three retrieves the alignment from a web service. This line will block the execution until the result is available. Use this with caution. In general, you should make sure that the calculation has been completed before attempting retrieving results. This is to avoid keeping the connection to the server on hold for a prolonged periods of time. While this may be ok with your local server, our public server (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) will not let you hold the connection for longer than 10 minutes. This is done to prevent excessive load on the server. The next section describes how to check the status of the calculation.<br />
-Methods and classes mentioned in the excerpt are available from the JABAWS client library.  </p>
-<h4><a name="checkresults" id="checkresults"></a>Checking the status of the calculation </h4>
-<p> You may have noticed that there was no pause between submitting the job and retrieving of the results. This is because <span class="hightlight">getResult(jobId)</span> method block the processing until the calculation is completed. However, taking into account that the connection holds server resources, our public server (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) is configured to reset the connection after 10 minutes of waiting. To work around the connection reset you are encouraged to check whether the calculation has been completed before accessing the results.	You can do it like this: </p>
-<p> <span class="code">while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {<br />
-   &nbsp;&nbsp;&nbsp;&nbsp;Thread.sleep(2000); // wait two  seconds, then recheck the status
-   <br />
-  }</span></p>
-<h4><a name="presetalign" id="presetalign"></a>Aligning with presets</h4>
-<p class="code">1) PresetManager presetman = msaws.getPresets();<br />
-  2) Preset preset = presetman.getPresetByName(presetName);<br />
-  3) List&lt;FastaSequence&gt; fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />
-  4) String jobId = msaws.presetAlign(fastalist, preset);<br />
-  5) Alignment alignment = msaws.getResult(jobId);</p>
-<p>Line one obtains the lists of presets supported by a web service.<br />
-  Line two return a particular Preset 
-  by its name<br />
-  Lines three to five  are doing the same job as in the first <a href="#defalign"> aligning sequences example</a>.</p>
-<h4><a name="customalign" id="customalign"></a>Aligning with  custom parameters</h4>
-<p class="code">  1) RunnerConfig options = msaws.getRunnerOptions();<br />
-  2) Argument matrix = options.getArgument(&quot;MATRIX&quot;);<br />
-  3) matrix.setValue(&quot;PAM300&quot;);<br />
-  4) Argument gapopenpenalty = options.getArgument(&quot;GAPOPEN&quot;);<br />
-  5) gapopenpenalty.setValue(&quot;20&quot;);<br />
-  6) List&lt;Argument&gt; arguments = new ArrayList&lt;Argument&gt;();
-  <br />
-  7) arguments.add(matrix);
-  arguments.add(gapopenpenalty);<br />
-  8) List&lt;FastaSequence&gt; fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />
-  9) String jobId = msaws.customAlign(fastalist, arguments);<br />
-  10) Alignment alignment = msaws.getResult(jobId);</p>
-<p>Line one obtains the RunnerConfig object that holds information on supported parameters and their values<br />
-  Line two retrieve a particular parameter from the holder by its name<br />
-  Lines three sets a value to this parameter which will be used in the calculation. <br />
-  Line four and five do the same but for another parameter<br />
-  Line 6 makes a List to hold the parameters <br />
-  Line seven puts the parameters into that list<br />
-  Line eight 
-  and ten is the same as in previous examples<br />
-  Line nine submit an alignment request with the sequences and the parameters <br /> 
-  The names of all the parameters supported by a web service e.g. &quot;PAM300&quot; can be obtained using options.getArguments() method. Further details on the methods available from RunnerConfig object are available from the <a href="dm_javadoc/index.html">javadoc</a>. </p>
-<h4><a name="writingaltofile" id="writingaltofile"></a>Writing alignments to a file</h4>
-<p>There is a utility method in the client library that does exactly that. </p>
-<p> <span class="code">Alignment alignment = align(...) <br />
-  FileOutputStream outStream = new FileOutputStream(file);<br />
-  ClustalAlignmentUtil.writeClustalAlignment(outStream, align);</span></p>
-<h4><a name="compex" id="compex"></a>A complete client example </h4>
-<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 nicely colorized <a href="Example_template.pdf">PDF version</a> of this example. 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>
-<pre class="code" style="line-height:1em;">
-import java.io.ByteArrayInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.net.URL;
-import java.util.List;
-
-import javax.xml.namespace.QName;
-import javax.xml.ws.Service;
-
-import compbio.data.msa.MsaWS;
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.SequenceUtil;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.LimitExceededException;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.UnsupportedRuntimeException;
-import compbio.metadata.WrongParameterException;
-
-public class Example {
-
-	/*
-	 * Input sequences for alignment
-	 */
-	static final String input = &quot;&gt;Foo\r\n&quot;
-			+ &quot;MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGR&quot;
-			+ &quot;VRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQ&quot;
-			+ &quot;LLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPL&quot;
-			+ &quot;APTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQA&quot;
-			+ &quot;STLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMD&quot;
-			+ &quot;YVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLN&quot;
-			+ &quot;PQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHAD&quot;
-			+ &quot;LFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALAS&quot;
-			+ &quot;DPAALTALHARVDVLRRESGVFEMDGFADDFGALLQALARRHGWLGI\r\n&quot;
-			+ &quot;\r\n&quot;
-			+ &quot;&gt;Bar\r\n&quot;
-			+ &quot;MGDTTAGEMAVQRGLALHQQRHAEAAVLLQQASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAH&quot;
-			+ &quot;QLLPEEPYITAQLLNAVAQGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGA&quot;
-			+ &quot;HPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHG&quot;
-			+ &quot;IDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVL&quot;
-			+ &quot;RLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLL&quot;
-			+ &quot;SGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGC&quot;
-			+ &quot;PVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESGV&quot;
-			+ &quot;FEMDGFADDFGALLQALARRHGWLGI\r\n&quot;
-			+ &quot;\r\n&quot;
-			+ &quot;&gt;Friends\r\n&quot;
-			+ &quot;MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRV&quot;
-			+ &quot;RWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDHQLLPEEPYITAQLDVLSAQVRAAVAQG&quot;
-			+ &quot;VGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLL&quot;
-			+ &quot;TVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFD&quot;
-			+ &quot;LRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAF&quot;
-			+ &quot;QPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEA&quot;
-			+ &quot;DARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTP&quot;
-			+ &quot;GETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESI&quot;;
-
-	public static void main(String[] args) throws UnsupportedRuntimeException,
-			LimitExceededException, JobSubmissionException,
-			WrongParameterException, FileNotFoundException, IOException,
-			ResultNotAvailableException, InterruptedException {
-
-		String qualifiedServiceName = &quot;http://msa.data.compbio/01/01/2010/&quot;;
-
-		/* Make a URL pointing to web service WSDL */
-		URL url = new URL(
-				&quot;http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl&quot;);
-
-		/*
-		 * If you are making a client that connects to different web services
-		 * you can use something like this:
-		 */
-		// URL url = new URL(host + &quot;/&quot; + Services.ClustalWS.toString() +
-		// &quot;?wsdl&quot;);
-
-		QName qname = new QName(qualifiedServiceName, &quot;ClustalWS&quot;);
-		Service serv = Service.create(url, qname);
-		/*
-		 * Multiple sequence alignment interface for Clustal web service
-		 * instance
-		 */
-		MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, &quot;ClustalWS&quot;
-				+ &quot;Port&quot;), MsaWS.class);
-
-		/* Get the list of available presets */
-		PresetManager presetman = msaws.getPresets();
-
-		/* Get the Preset object by preset name */
-		Preset preset = presetman
-				.getPresetByName(&quot;Disable gap weighting (Speed-oriented)&quot;);
-
-		/*
-		 * Load sequences in FASTA format from the file You can use something
-		 * like new FileInputStream(<filename>) to load sequence from the file
-		 */
-		List<FastaSequence> fastalist = SequenceUtil
-				.readFasta(new ByteArrayInputStream(input.getBytes()));
-
-		/*
-		 * Submit loaded sequences for an alignment using preset. The job
-		 * identifier is returned by this method, you can retrieve the results
-		 * with it sometime later.
-		 */
-		String jobId = msaws.presetAlign(fastalist, preset);
-
-		/* This method will block for the duration of the calculation */
-		Alignment alignment = msaws.getResult(jobId);
-
-		/*
-		 * This is a better way of obtaining results, it does not involve
-		 * holding the connection open for the duration of the calculation,
-		 * Besides, as the University of Dundee public server will reset the
-		 * connection after 10 minutes of idling, this is the only way to obtain
-		 * the results of long running task from our public server.
-		 */
-		// while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {
-		// Thread.sleep(1000); // wait a second, then recheck the status
-		// }
-
-		/* Output the alignment to standard out */
-		System.out.println(alignment);
-
-		// Alternatively, you can record retrieved alignment into the file in
-		// ClustalW format
-
-		// ClustalAlignmentUtil.writeClustalAlignment(new FileOutputStream(
-		// &quot;output.al&quot;), alignment);
-
-	}
-}
-</pre>
-For a more detailed description of all available types and their functions please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>. 
-<h4><a name="buildart" id="buildart"></a>Building web services artifacts</h4>
-<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 <a href="#connectto"> client library</a> as it provides a handful of useful methods in addition to plain data types. </p>
-<p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl</p>
 <h3>JABAWS on Apache-Tomcat</h3>
 <h4><a name="tomdeploy" id="tomdeploy"></a>I dropped jaba.war file into web application directory but nothing happened. What do I do next?</h4>
 <ul>
diff --git a/website/manual.html b/website/manual.html
index 5941807..95f1d27 100644
--- a/website/manual.html
+++ b/website/manual.html
@@ -40,8 +40,8 @@ href="manual.html">Manual</a> <a href="howto.html">How To</a>
 <h2 align="center">JABAWS Manual</h2>
 
 <h3>Table of content</h3>
-<p>
-<h4>JABAWS Virtual Appliance </h4>
+<h4>JABAWS Virtual Appliance 
+</h4>
 <ul>
     <li><a href="#whenvm">When to use virtual appliance</a> </li>
 	<li><a href="#virtualbox">VirtualBox appliance configuration</a></li>
@@ -71,10 +71,19 @@ href="manual.html">Manual</a> <a href="howto.html">How To</a>
   <li><a href="#setexecenv">Defining Environment Variables for
     Executables</a></li>
 </ul>
-<h4>For Developers  </h4>
+<h4>Using JABAWS in your program </h4>
 <ul>
-  <li><a href="#wsfunctions">Web service functions </a></li>
+  <li><a href="#wsfunctions">Web services functions overview </a></li>
   <li><a href="#templatestr">The template client structure</a></li>
+  <li><a href="#connectto">Connecting to JABAWS</a></li>
+  <li><a href="#validnames">Valid JABAWS service names and WSDL files</a></li>
+  <li><a href="#defalign">Aligning sequences</a></li>
+  <li><a href="#checkresults">Checking the status of the calculation </a></li>
+  <li><a href="#presetalign">Aligning with presets</a></li>
+  <li><a href="#customalign">Aligning with custom parameters</a></li>
+  <li><a href="#writingaltofile">Writing alignments to a file</a></li>
+  <li><a href="#compex">A complete client example </a></li>
+  <li><a href="#buildart">Building web services artifacts</a></li>
 </ul>
 <h4>JABA Web Services Internals </h4>
 <ul>
@@ -199,8 +208,8 @@ libraries or other problems, then you probably need to <a href=
 <li>Restart the Tomcat.</li>
 </ol>
 
-That's it! JABAWS should work at this point. Try it out using the<a
-href="howto.html#usingWsTester">JABAWS test client</a>. If not,
+That's it! JABAWS should work at this point. Try it out using the JABAWS<a
+href="howto.html#usingWsTester"> test client</a>. If not,
 read on... or have a look at <a href=
 "howto.html#usingtomcat">deploying on Tomcat</a> tips.<br />
  <em>Note: You may want to enable logging, <a href="#logfiles">see
@@ -236,7 +245,7 @@ the <a href="howto.html#usingWsTester">JABAWS test client</a> to
 check that JABAWS can use the new binaries.</li>
 </ol>
 
-<p>If you couldn't compile everthing, then it may be that your system does
+<p>If you couldn't compile everything, then it may be that your system does
 not have all the tools required for compiling the programs. At the very
 least check that you have gcc, g++ and make installed in your
 system. If not install these packages and repeat the compilation
@@ -284,7 +293,7 @@ look at the <a href="#warfile">war file content table</a>).</p>
 enabled, with job output written to directory called "jobsout"
 within the web application itself. This means that JABAWS will work
 out of the box, but may not be suitable for serving a whole lab or
-instute.</p>
+a university.</p>
 
 <h4><a name="locEngConf" id="locEngConf"></a>Local Engine Configuration</h4>
 
@@ -376,9 +385,9 @@ optional&gt;</span></p>
 
 <p>Default JABAWS configuration includes path to local executables
 to be run by the local engine only, all cluster related settings
-are commened out, but they are there for you as example. Cluster
+are commented out, but they are there for you as example. Cluster
 engine is disabled by default. To configure executable for cluster
-execution uncomment the X.cluster settings and change them
+execution un comment the X.cluster settings and change them
 appropriately. </p>
 <p>By default limits are set well in excess of what you may want to offer to the users outside your lab, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services.  You can adjust the limits according to your needs by editing <span class="hightlight">conf/settings/&lt;X&gt;Limit.xml</span> files.<br />
   After you have completed the editing your configuration may look like
@@ -464,8 +473,8 @@ by providing an absolute path to them. All these settings are
 defined in <span class=
 "hightlight">conf/Executable.properties</span> file.</p>
 
-<h3>For Developers</h3>
-<h4><a name="wsfunctions" id="wsfunctions"></a>Web service functions description </h4>
+<h3>Using JABAWS in your program </h3>
+<h4><a name="wsfunctions" id="wsfunctions"></a>Web services functions overview </h4>
 <p>All JABA multiple sequence alignment web services comply to the same interface, thus the function described below are available from all the services. </p>
 <p><strong>Functions for initiating the alignment </strong><span class="code">  String id = align(List&lt;FastaSequence&gt; list)<br />
   String id = customAlign(List&lt;FastaSequence&gt; sequenceList, List&lt;Option&gt; optionList)<br />
@@ -506,6 +515,239 @@ defined in <span class=
 </table>
 <p>Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar. <br />
   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>
+<h4><a name="connectto" id="connectto"></a>Connecting to JABAWS</h4>
+<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>
+<p>Download a binary JABAWS <a href="download.html">client</a>. 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>
+<p class="code"> import java.net.URL;<br />
+  import javax.xml.namespace.QName;<br />
+  import javax.xml.ws.Service;<br />
+  ...............<br />
+  1) String qualifiedName = &quot;http://msa.data.compbio/01/01/2010/&quot;;<br />
+  2) URL url = new URL(&quot;http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl&quot;);<br />
+  3) QName qname = new QName(, &quot;ClustalWS&quot;);<br />
+  4) Service serv = Service.create(url, qname);<br />
+  5) MsaWS msaws = serv.getPort(new QName(qualifiedName, &quot;ClustalWSPort&quot;),
+  MsaWS.class);</p>
+<p>Line 1 makes a qualified name for JABA web services.<br />
+  Line 2 
+  constructs the URL to the web services WSDL. <br />
+  Line 3 makes a qualified name instance for Clustal JABA web service. <br />
+  Line 4 creates a service instance.<br />
+  Line 5 makes a connection to the server. </p>
+<p>A more generic connection method would look like this </p>
+<p class="code"> import java.net.URL;<br />
+  import javax.xml.namespace.QName;<br />
+  import javax.xml.ws.Service;<br />
+  import compbio.ws.client.Services<br />
+  .............. <br />
+  String qualifiedServiceName = &quot;http://msa.data.compbio/01/01/2010/&quot;;<br />
+  String host = &quot;http://www.compbio.dundee.ac.uk/jabaws&quot;;<br />
+  // In real life the service name can come from args<br />
+  Services clustal = Services.ClustalWS;<br />
+  URL url = new URL(host + &quot;/&quot; + clustal.toString() + &quot;?wsdl&quot;);<br />
+  QName qname = new QName(qualifiedServiceName, clustal.toString());<br />
+  Service serv = Service.create(url, qname);<br />
+  MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, clustal<br />
+  + &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="file:///D:/workspace/JWS2/website/dm_javadoc/compbio/data/msa/MsaWS.html">javadoc</a>. </p>
+<h4><a name="validnames" id="validnames"></a>Valid JABAWS service names and WSDL files </h4>
+<ul>
+  <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>
+<h4><a name="defalign" id="defalign"></a>Aligning sequences </h4>
+<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 />
+  2) String jobId = msaws.align(fastalist); <br />
+  3) Alignment alignment = msaws.getResult(jobId);</p>
+<p>Line  one loads FASTA sequence from the file<br />
+  Line two submits them to web service represented by msaws proxy <br />
+  Line three retrieves the alignment from a web service. This line will block the execution until the result is available. Use this with caution. In general, you should make sure that the calculation has been completed before attempting retrieving results. This is to avoid keeping the connection to the server on hold for a prolonged periods of time. While this may be ok with your local server, our public server (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) will not let you hold the connection for longer than 10 minutes. This is done to prevent excessive load on the server. The next section describes how to check the status of the calculation.<br />
+  Methods and classes mentioned in the excerpt are available from the JABAWS client library. </p>
+<h4><a name="checkresults" id="checkresults"></a>Checking the status of the calculation </h4>
+<p> You may have noticed that there was no pause between submitting the job and retrieving of the results. This is because <span class="hightlight">getResult(jobId)</span> method block the processing until the calculation is completed. However, taking into account that the connection holds server resources, our public server (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) is configured to reset the connection after 10 minutes of waiting. To work around the connection reset you are encouraged to check whether the calculation has been completed before accessing the results.	You can do it like this: </p>
+<p> <span class="code">while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {<br />
+  &nbsp;&nbsp;&nbsp;&nbsp;Thread.sleep(2000); // wait two  seconds, then recheck the status <br />
+  }</span></p>
+<h4><a name="presetalign" id="presetalign"></a>Aligning with presets</h4>
+<p class="code">1) PresetManager presetman = msaws.getPresets();<br />
+  2) Preset preset = presetman.getPresetByName(presetName);<br />
+  3) List&lt;FastaSequence&gt; fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />
+  4) String jobId = msaws.presetAlign(fastalist, preset);<br />
+  5) Alignment alignment = msaws.getResult(jobId);</p>
+<p>Line one obtains the lists of presets supported by a web service.<br />
+  Line two return a particular Preset 
+  by its name<br />
+  Lines three to five  are doing the same job as in the first <a href="#defalign"> aligning sequences example</a>.</p>
+<h4><a name="customalign" id="customalign"></a>Aligning with  custom parameters</h4>
+<p class="code"> 1) RunnerConfig options = msaws.getRunnerOptions();<br />
+  2) Argument matrix = options.getArgument(&quot;MATRIX&quot;);<br />
+  3) matrix.setValue(&quot;PAM300&quot;);<br />
+  4) Argument gapopenpenalty = options.getArgument(&quot;GAPOPEN&quot;);<br />
+  5) gapopenpenalty.setValue(&quot;20&quot;);<br />
+  6) List&lt;Argument&gt; arguments = new ArrayList&lt;Argument&gt;(); <br />
+  7) arguments.add(matrix);
+  arguments.add(gapopenpenalty);<br />
+  8) List&lt;FastaSequence&gt; fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />
+  9) String jobId = msaws.customAlign(fastalist, arguments);<br />
+  10) Alignment alignment = msaws.getResult(jobId);</p>
+<p>Line one obtains the RunnerConfig object that holds information on supported parameters and their values<br />
+  Line two retrieve a particular parameter from the holder by its name<br />
+  Lines three sets a value to this parameter which will be used in the calculation. <br />
+  Line four and five do the same but for another parameter<br />
+  Line 6 makes a List to hold the parameters <br />
+  Line seven puts the parameters into that list<br />
+  Line eight 
+  and ten is the same as in previous examples<br />
+  Line nine submit an alignment request with the sequences and the parameters <br />
+  The names of all the parameters supported by a web service e.g. &quot;PAM300&quot; can be obtained using options.getArguments() method. Further details on the methods available from RunnerConfig object are available from the <a href="dm_javadoc/index.html">javadoc</a>. </p>
+<h4><a name="writingaltofile" id="writingaltofile"></a>Writing alignments to a file</h4>
+<p>There is a utility method in the client library that does exactly that. </p>
+<p> <span class="code">Alignment alignment = align(...) <br />
+  FileOutputStream outStream = new FileOutputStream(file);<br />
+  ClustalAlignmentUtil.writeClustalAlignment(outStream, align);</span></p>
+<h4><a name="compex" id="compex"></a>A complete client example </h4>
+<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>
+<pre class="code" style="line-height:1em;">
+import java.io.ByteArrayInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.URL;
+import java.util.List;
+
+import javax.xml.namespace.QName;
+import javax.xml.ws.Service;
+
+import compbio.data.msa.MsaWS;
+import compbio.data.sequence.Alignment;
+import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.SequenceUtil;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.LimitExceededException;
+import compbio.metadata.Preset;
+import compbio.metadata.PresetManager;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.metadata.UnsupportedRuntimeException;
+import compbio.metadata.WrongParameterException;
+
+public class Example {
+
+	/*
+	 * Input sequences for alignment
+	 */
+	static final String input = &quot;&gt;Foo\r\n&quot;
+			+ &quot;MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGR&quot;
+			+ &quot;VRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQ&quot;
+			+ &quot;LLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPL&quot;
+			+ &quot;APTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQA&quot;
+			+ &quot;STLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMD&quot;
+			+ &quot;YVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLN&quot;
+			+ &quot;PQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHAD&quot;
+			+ &quot;LFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALAS&quot;
+			+ &quot;DPAALTALHARVDVLRRESGVFEMDGFADDFGALLQALARRHGWLGI\r\n&quot;
+			+ &quot;\r\n&quot;
+			+ &quot;&gt;Bar\r\n&quot;
+			+ &quot;MGDTTAGEMAVQRGLALHQQRHAEAAVLLQQASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAH&quot;
+			+ &quot;QLLPEEPYITAQLLNAVAQGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGA&quot;
+			+ &quot;HPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHG&quot;
+			+ &quot;IDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVL&quot;
+			+ &quot;RLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLL&quot;
+			+ &quot;SGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGC&quot;
+			+ &quot;PVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESGV&quot;
+			+ &quot;FEMDGFADDFGALLQALARRHGWLGI\r\n&quot;
+			+ &quot;\r\n&quot;
+			+ &quot;&gt;Friends\r\n&quot;
+			+ &quot;MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRV&quot;
+			+ &quot;RWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDHQLLPEEPYITAQLDVLSAQVRAAVAQG&quot;
+			+ &quot;VGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLL&quot;
+			+ &quot;TVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFD&quot;
+			+ &quot;LRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAF&quot;
+			+ &quot;QPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEA&quot;
+			+ &quot;DARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTP&quot;
+			+ &quot;GETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESI&quot;;
+
+	public static void main(String[] args) throws UnsupportedRuntimeException,
+			LimitExceededException, JobSubmissionException,
+			WrongParameterException, FileNotFoundException, IOException,
+			ResultNotAvailableException, InterruptedException {
+
+		String qualifiedServiceName = &quot;http://msa.data.compbio/01/01/2010/&quot;;
+
+		/* Make a URL pointing to web service WSDL */
+		URL url = new URL(
+				&quot;http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl&quot;);
+
+		/*
+		 * If you are making a client that connects to different web services
+		 * you can use something like this:
+		 */
+		// URL url = new URL(host + &quot;/&quot; + Services.ClustalWS.toString() +
+		// &quot;?wsdl&quot;);
+
+		QName qname = new QName(qualifiedServiceName, &quot;ClustalWS&quot;);
+		Service serv = Service.create(url, qname);
+		/*
+		 * Multiple sequence alignment interface for Clustal web service
+		 * instance
+		 */
+		MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, &quot;ClustalWS&quot;
+				+ &quot;Port&quot;), MsaWS.class);
+
+		/* Get the list of available presets */
+		PresetManager presetman = msaws.getPresets();
+
+		/* Get the Preset object by preset name */
+		Preset preset = presetman
+				.getPresetByName(&quot;Disable gap weighting (Speed-oriented)&quot;);
+
+		/*
+		 * Load sequences in FASTA format from the file You can use something
+		 * like new FileInputStream(<filename>) to load sequence from the file
+		 */
+		List<FastaSequence> fastalist = SequenceUtil
+				.readFasta(new ByteArrayInputStream(input.getBytes()));
+
+		/*
+		 * Submit loaded sequences for an alignment using preset. The job
+		 * identifier is returned by this method, you can retrieve the results
+		 * with it sometime later.
+		 */
+		String jobId = msaws.presetAlign(fastalist, preset);
+
+		/* This method will block for the duration of the calculation */
+		Alignment alignment = msaws.getResult(jobId);
+
+		/*
+		 * This is a better way of obtaining results, it does not involve
+		 * holding the connection open for the duration of the calculation,
+		 * Besides, as the University of Dundee public server will reset the
+		 * connection after 10 minutes of idling, this is the only way to obtain
+		 * the results of long running task from our public server.
+		 */
+		// while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {
+		// Thread.sleep(1000); // wait a second, then recheck the status
+		// }
+
+		/* Output the alignment to standard out */
+		System.out.println(alignment);
+
+		// Alternatively, you can record retrieved alignment into the file in
+		// ClustalW format
+
+		// ClustalAlignmentUtil.writeClustalAlignment(new FileOutputStream(
+		// &quot;output.al&quot;), alignment);
+
+	}
+}
+</pre>
+For a more detailed description of all available types and their functions please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.
+<h4><a name="buildart" id="buildart"></a>Building web services artifacts</h4>
+<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 <a href="#connectto"> client library</a> as it provides a handful of useful methods in addition to plain data types. </p>
+<p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl</p>
+<p>&nbsp;</p>
 <h3>JABA Web Services Internals </h3>
 <h4><a name="testingJaba" id="testingJaba"></a>Testing JABA Web Services</h4>
 <p>You can use a command line client (part of the client only
@@ -531,7 +773,7 @@ lines in this file are commented out. The reason why the logging is
 disabled by default it simple, log4j have to know the exact
 location where the log files should be stored. This is not known up
 until the deployment time. To enable the logging you need to
-define<span class="hightlight">logDir</span> property in the <span
+define<span class="hightlight"> logDir</span> property in the <span
 class="hightlight">log4j.properties</span> and uncomment section of
 the file which corresponds to your need. More information is given
 in the <span class="hightlight">log4j.properties</span> file
@@ -625,7 +867,7 @@ pages)</td>
 
 <tr>
 <td>prog_docs</td>
-<td>documentation for programmes that JABAWS uses</td>
+<td>documentation for programs that JABAWS uses</td>
 </tr>
 
 <tr>
-- 
1.7.10.2