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    <p>This is pretty broad question. So I will keep my answer at a high level and we can dig deeper as you have more questions.</p> <p>Initially this is how I would structure the application.</p> <ol> <li>Pick a MVC framework. I would pick <a href="http://www.oracle.com/technetwork/java/javaee/javaserverfaces-139869.html" rel="nofollow">JSF2</a> but anything else is fine too. Your view and controller layer will be defined here.</li> <li>Create 3 DAO classes at bare minimum - one for reading data from XML, one for reading data from mySql, and one for reading text files. To parse XML files you can use <a href="http://www.w3.org/TR/xpath/" rel="nofollow">XPath</a> and ofcourse SQLs to get data from the database.</li> <li>Create a <a href="http://java.sun.com/j2ee/tutorial/1_3-fcs/doc/EJBConcepts5.html" rel="nofollow">MDB</a> to asynchronously kick off the EXE process via <a href="http://download.oracle.com/javaee/1.3/jms/tutorial/" rel="nofollow">JMS</a>. </li> <li>Package the application as an EAR file.</li> </ol> <p><strong>Tools you can use:</strong></p> <ol> <li>Eclipse for IDE</li> <li>JBoss-AS (or any other container that you have access to)</li> <li>Some sort of build/packaging tool (ANT, Maven, etc) </li> </ol> <p>I am not familiar with image manipulation so I can't comment on that part. However, I think you need to break down your design into various components first. That's why I started listing the ones that I could think of without enough details. So image query will be one of the components. Try to create a black box diagram of the system with each major component in &amp; out. After that start developing each of them and then I bet a lot more folks here can help you with more specific questions. Does this make sense?</p>
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    1. POArchitecture Java EE ? many ressources : database, xml
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    1. COCan you see again my question please, I added some details !!
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    2. COThis is the problem, image manipulation is different than other things ,so do you have any other comment? because there are a lot of I/O of txt and XML files and calling matlab ...
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    3. COYes for text files you will need to create file parsers (read lines from a file, parse them using some token) and for XML files as I mentioned above you can use XPath.
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