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Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.
Please refer to a data model javadoc for a detailed description of each class and its methods.
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 download page. Please note that for now all the examples are in Java other languages will follow given a sufficient demand.
+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 download page. Please note that for now all the examples are in Java other languages will follow given a sufficient demand.
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.
import java.net.URL;
import javax.xml.namespace.QName;
@@ -135,13 +142,26 @@
+ "Port"), MsaWS.class);
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 javadoc.
Multiple sequence alignment services
+Protein disorder prediction services
+Amino acid conservation service
+Please replace http://www.compbio.dundee.ac.uk/ with your JABAWS instance host name, and jabaws with your JABAWS context name to access your local version of JABAWS web services. For example http://localhost:8080/jabaws would be a valid URL for the default Apache-Tomcat installation and jabaws.war file deployment.
Given that msaws is web service proxy, created as described in "Connecting to JABAWS" section, the actual alignment can be obtained as follows:
1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));
@@ -194,7 +214,7 @@
FileOutputStream outStream = new FileOutputStream(file);
ClustalAlignmentUtil.writeClustalAlignment(outStream, align);
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 PDF version 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 JABAWS binary client. Please make sure that the client is in the Java class path before running this example.
+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 PDF version 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 JABAWS binary client. Please make sure that the client is in the Java class path before running this example.
import java.io.ByteArrayInputStream; import java.io.FileNotFoundException; @@ -334,7 +354,7 @@ For a more detailed description of all available types and their functions pleas