Thread: 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???

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?

Originally Posted by Haneen tar

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).