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Thread: Biojava and netbean

  1. #1
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    Question Biojava and netbean

    welcome
    When I using the Jcreator with biojava to create a protein sequenc and multiple sequence alignment it work well
    but when I copy this code to netbean it not work and it gave me this exception:

    Exception in thread "AWT-EventQueue-0" org.biojava3.core.exceptions.CompoundNotFoundError : Compound not found for: Cannot find compound for:

    at org.biojava3.core.sequence.storage.ArrayListSequen ceReader.setContents(ArrayListSequenceReader.java: 201)
    at org.biojava3.core.sequence.template.AbstractSequen ce.<init>(AbstractSequence.java:88)
    at org.biojava3.core.sequence.ProteinSequence.<init>( ProteinSequence.java:52)
    at main.jButton1ActionPerformed(main.java:191)
    at main.access$000(main.java:29)
    at main$1.actionPerformed(main.java:68)
    at javax.swing.AbstractButton.fireActionPerformed(Abs tractButton.java:2018)
    at javax.swing.AbstractButton$Handler.actionPerformed (AbstractButton.java:2341)
    at javax.swing.DefaultButtonModel.fireActionPerformed (DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultB uttonModel.java:259)
    at javax.swing.plaf.basic.BasicButtonListener.mouseRe leased(BasicButtonListener.java:252)
    at java.awt.Component.processMouseEvent(Component.jav a:6505)
    at javax.swing.JComponent.processMouseEvent(JComponen t.java:3321)
    at java.awt.Component.processEvent(Component.java:627 0)
    at java.awt.Container.processEvent(Container.java:222 9)
    at java.awt.Component.dispatchEventImpl(Component.jav a:4861)
    at java.awt.Container.dispatchEventImpl(Container.jav a:2287)
    at java.awt.Component.dispatchEvent(Component.java:46 87)
    at java.awt.LightweightDispatcher.retargetMouseEvent( Container.java:4832)
    at java.awt.LightweightDispatcher.processMouseEvent(C ontainer.java:4492)
    at java.awt.LightweightDispatcher.dispatchEvent(Conta iner.java:4422)
    at java.awt.Container.dispatchEventImpl(Container.jav a:2273)
    at java.awt.Window.dispatchEventImpl(Window.java:2719 )
    at java.awt.Component.dispatchEvent(Component.java:46 87)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.j ava:703)
    at java.awt.EventQueue.access$000(EventQueue.java:102 )
    at java.awt.EventQueue$3.run(EventQueue.java:662)
    at java.awt.EventQueue$3.run(EventQueue.java:660)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPri vilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$1.doIntersectionPri vilege(ProtectionDomain.java:87)
    at java.awt.EventQueue$4.run(EventQueue.java:676)
    at java.awt.EventQueue$4.run(EventQueue.java:674)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPri vilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java: 673)
    at java.awt.EventDispatchThread.pumpOneEventForFilter s(EventDispatchThread.java:244)
    at java.awt.EventDispatchThread.pumpEventsForFilter(E ventDispatchThread.java:163)
    at java.awt.EventDispatchThread.pumpEventsForHierarch y(EventDispatchThread.java:151)
    at java.awt.EventDispatchThread.pumpEvents(EventDispa tchThread.java:147)
    at java.awt.EventDispatchThread.pumpEvents(EventDispa tchThread.java:139)
    at java.awt.EventDispatchThread.run(EventDispatchThre ad.java:97)



    this is my code ProteinSequence [] seqs= new ProteinSequence[length];
    for (int i=0;i<length;i++)
    {seqs[i]= new ProteinSequence (ar2[i]);
    System.out.println(seqs[i]);}

    where the ar2 is array of strings


    can any one help me , please???
    Last edited by Haneen tar; June 16th, 2012 at 01:07 PM.


  2. #2
    Administrator copeg's Avatar
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    Default Re: Biojava and netbean

    Make sure the String's you pass contain valid AminoAcid characters. The Exception should show the invalid character...are there spaces in the Sequence? What is the contents of ar2?

  3. The Following User Says Thank You to copeg For This Useful Post:

    Haneen tar (June 16th, 2012)

  4. #3
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    Default Re: Biojava and netbean

    Thank you for reply i return to my code my there is a space in the ar2 I will rewrite the code and I will see what happened
    I have a question for you
    you have an experience in the biojava?
    I am a informatics student and I will work to develop an bioinformatic tool, so I hope I can ask you problems if it appear for me if there isn't any problem for you
    Thank you again

  5. #4
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    Default Re: Biojava and netbean

    Quote Originally Posted by Haneen tar View Post
    you have an experience in the biojava?
    I am a informatics student and I will work to develop an bioinformatic tool, so I hope I can ask you problems if it appear for me if there isn't any problem for you
    Thank you again
    You are welcome, and yes I do have experience. I am glad to help, and if you have further questions please pose your question to the forums (there also might be biojava specific forums that might be more geared for questions regarding its API).

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