<td>JABAWS command line client </td>\r
</tr>\r
</table>\r
-<p>Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar. <br />\r
+<p>Additional utility libraries that 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
\r
\r
<p class="attention">\r
For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client \r
source code is available from the <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev">download page</a>. Please note that for now all \r
-the examples are in Java other languages will follow given a sufficient demand. </p>\r
+the examples are in Java, other languages will follow if there is sufficient demand. </p>\r
<p>\r
Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal \r
web service deployed in the University of Dundee. </p>\r
<p class="code">1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
2) String jobId = msaws.align(fastalist); <br />\r
3) Alignment alignment = msaws.getResult(jobId);</p>\r
-<p>Line one loads FASTA sequence from the file<br />\r
- Line two submits them to web service represented by msaws proxy <br />\r
+<p>Line one loads FASTA sequence from the file.<br />\r
+ Line two submits them to web service represented by msaws proxy. <br />\r
Line three retrieves the alignment from a web service. This line will block the execution until the result is available. \r
Use this with caution. In general, you should make sure that the calculation has been completed before attempting \r
retrieving results. This is to avoid keeping the connection to the server on hold for a prolonged periods of time. \r
5) Alignment alignment = msaws.getResult(jobId);</p>\r
<p>Line one obtains the lists of presets supported by a web service.<br />\r
Line two return a particular Preset \r
- by its name<br />\r
+ by its name.<br />\r
Lines three to five are doing the same job as in the first <a href="#defalign"> aligning sequences example</a>.</p>\r
<h3><a name="customalign" id="customalign"></a>Aligning with custom parameters</h3>\r
<p class="code"> 1) RunnerConfig options = msaws.getRunnerOptions();<br />\r
9) String jobId = msaws.customAlign(fastalist, arguments);<br />\r
10) Alignment alignment = msaws.getResult(jobId);</p>\r
<p>Line one obtains the <span class="hightlight">RunnerConfig</span> object that holds information on supported parameters and their values<br />\r
- Line two retrieve a particular parameter from the holder by its name<br />\r
+ Line two retrieve a particular parameter from the holder by its name.<br />\r
Lines three sets a value to this parameter which will be used in the calculation. <br />\r
- Line four and five do the same but for another parameter<br />\r
- Line 6 makes a List to hold the parameters <br />\r
- Line seven puts the parameters into that list<br />\r
+ Line four and five do the same but for another parameter.<br />\r
+ Line 6 makes a List to hold the parameters. <br />\r
+ Line seven puts the parameters into that list.<br />\r
Line eight \r
- and ten is the same as in previous examples<br />\r
- Line nine submit an alignment request with the sequences and the parameters <br />\r
+ and ten is the same as in previous examples.<br />\r
+ Line nine submit an alignment request with the sequences and the parameters. <br />\r
The names of all the parameters supported by a web service e.g. "PAM300" can be obtained \r
using <span class="hightlight">options.getArguments() </span>method. Further details on the methods \r
available from <span class="hightlight">RunnerConfig</span> object are available from the \r
<h3><a name="compex" id="compex"></a>A complete client example </h3>\r
<p>\r
Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using \r
-one of the Clustal web service preset. Three is also a <a href="Example_template.pdf">PDF version</a> of \r
+one of the Clustal web service presets. There is also a <a href="Example_template.pdf">PDF version</a> of \r
this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, \r
the alternatives given in the code are line commented // comment. You may want to remove line style comments to \r
test alternatives of the functions. All you need for this to work is a \r
<p>\r
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> \r
basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can \r
-generate portable artifacts to work with JABAWS from Java. However, if programming in Java we recommend using our client library as \r
+generate portable artifacts to work with JABAWS from Java. However if programming in Java, we recommend using our client library as \r
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
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git://source.jalview.org / jabaws.git / blobdiff