[Biojava-l] An exception is being thrown while using the code related to phylogeny from BioJava cookbook

[Muhammad Tariq Pervez]

Dear concerns,
I want to develop an application for phylogenetic 
analysis. To get started, I took some lines of code from BioJava cookbook, modified them
 as per my requirement and have been trying to get the results for a few
 days but in vain. The code is as follows. 


package biojavademo;


import java.io.File;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map.Entry;

import org.biojava3.alignment.template.Profile;
import org.biojava3.alignment.Alignments;
import org.biojava3.alignment.template.AlignedSequence;
import org.biojava3.core.sequence.MultipleSequenceAlignment;
import org.biojava3.core.sequence.ProteinSequence;
import org.biojava3.core.sequence.compound.AminoAcidCompound;
import org.biojava3.core.sequence.io.FastaReaderHelper;
import org.biojava3.core.sequence.template.Compound;
import org.biojava3.core.sequence.template.Sequence;
import org.biojava3.core.util.ConcurrencyTools;
import org.biojava3.phylo.ProgessListenerStub;
import org.biojava3.phylo.TreeConstructionAlgorithm;
import org.biojava3.phylo.TreeConstructor;
import org.biojava3.phylo.TreeType;

public class MSA {

  
    MSA(){
              multipleSequenceAlignment = new MultipleSequenceAlignment <ProteinSequence, AminoAcidCompound>();
}
    public void multipleSequenceAlignment(List<String> ids) throws Exception {
        List<ProteinSequence> lst = new ArrayList<ProteinSequence>();
       
        for (String id : ids) {
            lst.add(getSequenceForId(id));
           
        }
     
        profile = Alignments.getMultipleSequenceAlignment(lst);
        System.out.println("Compound == "+ profile.getCompoundSet());
        seq=new  ProteinSequence(profile.toString(),profile.getCompoundSet());
        multipleSequenceAlignment.addAlignedSequence(seq);
       
 TreeConstructor<ProteinSequence, AminoAcidCompound> 
treeConstructor = new TreeConstructor<ProteinSequence, 
AminoAcidCompound>(multipleSequenceAlignment,  TreeType.NJ, 
TreeConstructionAlgorithm.PID, new ProgessListenerStub());
           treeConstructor.process();
           String newick = treeConstructor.getNewickString(true, true);
        System.out.println("Clustalw:\n Multisequence Alignment\n"+ profile.toString(Profile.StringFormat.CLUSTALW));
       System.out.println("Tree === "+ newick);
              ConcurrencyTools.shutdown();
    }

      private static ProteinSequence getSequenceForId(String fileName) throws Exception {
        
        LinkedHashMap<String, ProteinSequence> a = FastaReaderHelper.readFastaProteinSequence(new File(fileName));
     
                String seqStr;
                ProteinSequence seq=null;
        for (  Entry<String, ProteinSequence> entry : a.entrySet() ) {
                        seqStr=entry.getValue().getSequenceAsString();
                        seq=new ProteinSequence(seqStr);//entry.getValue();
                        
        }
        return seq;
    }
    public Profile<ProteinSequence, AminoAcidCompound> getMSAProfile(){
        return profile;
    }

Profile<ProteinSequence, AminoAcidCompound> profile;
MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> multipleSequenceAlignment;
 ProteinSequence seq=null;
}

When I run this code the following exception is thrown

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.ArrayListSequenceReader.setContents(ArrayListSequenceReader.java:196)
        at org.biojava3.core.sequence.template.AbstractSequence.<init>(AbstractSequence.java:88)
        at org.biojava3.core.sequence.ProteinSequence.<init>(ProteinSequence.java:52)
        at biojavademo.MSA.multipleSequenceAlignment(MSA.java:41)
        at biojavademo.MSAJFrame.jButton2ActionPerformed(MSAJFrame.java:160)
        at biojavademo.MSAJFrame.access$100(MSAJFrame.java:27)
        at biojavademo.MSAJFrame$2.actionPerformed(MSAJFrame.java:72)
        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
        at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
        at java.awt.Component.processMouseEvent(Component.java:6038)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3265)
        at java.awt.Component.processEvent(Component.java:5803)
        at java.awt.Container.processEvent(Container.java:2058)
        at java.awt.Component.dispatchEventImpl(Component.java:4410)
        at java.awt.Container.dispatchEventImpl(Container.java:2116)
        at java.awt.Component.dispatchEvent(Component.java:4240)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4322)
        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3986)
        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3916)
        at java.awt.Container.dispatchEventImpl(Container.java:2102)
        at java.awt.Window.dispatchEventImpl(Window.java:2429)
        at java.awt.Component.dispatchEvent(Component.java:4240)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)

Actually I don't know how to construct the multiple sequence alignment object which is given as a parameter while constructing the  'TreeConstructor' object.

Kindly guide/help me to resolve this issue.


Muhammad Tariq Pervez

Ph.D (Scholar) - Bioinformatics,
University of Veterinary and Animal Science, Lahore, Pakistan