Java Code Examples for org.biojava.nbio.structure.StructureException#printStackTrace()

@Override
public void toggleSelection(AlignedPosition p) {
	if ( afpChain == null)
		return;

	char[] aligs1  = afpChain.getAlnseq1();
	char[] aligs2  = afpChain.getAlnseq2();

	char c1 = aligs1[p.getPos1()];
	char c2 = aligs2[p.getPos2()];

	try {
		Atom a1 = DisplayAFP.getAtomForAligPos(afpChain, 0, p.getPos1(), ca1,false);
		Atom a2 = DisplayAFP.getAtomForAligPos(afpChain, 1, p.getPos2(), ca2,true);

		String pdbInfo1 = JmolTools.getPdbInfo(a1);
		String pdbInfo2 = JmolTools.getPdbInfo(a2);

		String msg = "Clicked pos:" + p.getPos1()+ " " + pdbInfo1 + " ("+c1+") : " + pdbInfo2 + " ("+c2+")";

		this.setText(msg);
	} catch (StructureException e){
		e.printStackTrace();
	}

}
 

@Override
public void run() {

	MultipleStructureAligner algorithm =
			parent.getMultipleStructureAligner();
	try {

		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
		for (Structure s:structures){
			Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
			atomArrays.add(ca);
		}

		MultipleAlignment msa = algorithm.align(atomArrays);
		msa.getEnsemble().setStructureIdentifiers(names);

		MultipleAlignmentJmolDisplay.display(msa);

	} catch (StructureException e) {
		e.printStackTrace();
		logger.warn(e.getMessage());
	}

	parent.notifyCalcFinished();
}
 

@Override
protected void initCoords() {
	try {
		if (multAln == null) {
			if (structure != null)
				setStructure(structure);
			else {
				logger.error("Could not find anything to display!");
				return;
			}
		}
		Structure artificial = MultipleAlignmentTools.toMultimodelStructure(multAln, transformedAtoms);
		setStructure(artificial);
		logger.info(artificial.getPDBHeader().getTitle());
	} catch (StructureException e) {
		e.printStackTrace();
	}
}
 

/**
	 * Calculates a structural alignment and returns alignment metrics.
	 * 
	 * @param alignmentAlgorithm name of the algorithm
	 * @param key unique identifier for protein chain pair
	 * @param points1 C-alpha positions of chain 1
	 * @param points2 C-alpha positions of chain 2
	 * @return
	 */
	public static List<Row> getAlignment(String alignmentAlgorithm, String key, Point3d[] points1, Point3d[] points2) {
		// create input for BioJava alignment method
		Atom[] ca1 = getCAAtoms(points1);
		Atom[] ca2 = getCAAtoms(points2);
		
		// calculate the alignment
		AFPChain afp = null;
		try {
			StructureAlignment algorithm  = StructureAlignmentFactory.getAlgorithm(alignmentAlgorithm);
			afp = algorithm.align(ca1,ca2);
			double tmScore = AFPChainScorer.getTMScore(afp, ca1, ca2);
			afp.setTMScore(tmScore);
		} catch (StructureException e) {
			e.printStackTrace();
			return Collections.emptyList();
		} 
		
		// TODO add alignments as arrays to results
//		int[][] alignment = afp.getAfpIndex();
//		for (int i = 0; i < alignment.length; i++) {
//			System.out.println(alignment[i][0] + " - " + alignment[i][1]);
//		}

		// record the alignment metrics
		Row row = RowFactory.create(key, afp.getOptLength(), afp.getCoverage1(), 
				afp.getCoverage2(), (float) afp.getTotalRmsdOpt(), (float) afp.getTMScore());

		return Collections.singletonList(row);
	}
 

private void updateAlgorithm(String algorithmName) {

		//String algorithmName = (String)algorithmList.getSelectedItem();
		try {
			algorithm = StructureAlignmentFactory.getAlgorithm(algorithmName);
		} catch (StructureException ex){
			ex.printStackTrace();
		}

	}
 

private void updatePairwiseAlgorithm(String algorithmName) {
	try {
		pairwise = StructureAlignmentFactory.getAlgorithm(algorithmName);
		//Update also the multiple structure algorithm
		ConfigStrucAligParams params = multiple.getParameters();
		updateMultipleAlgorithm();
		multiple.setParameters(params);

	} catch (StructureException ex){
		ex.printStackTrace();
	}
}
 

@Override
public void rangeSelected(AlignedPosition start, AlignedPosition end) {
	char[] aligs1  = afpChain.getAlnseq1();
	char[] aligs2  = afpChain.getAlnseq2();

	char c1 = aligs1[start.getPos1()];
	char c3 = aligs1[end.getPos1()];

	char c2 = aligs2[start.getPos2()];
	char c4 = aligs2[end.getPos2()];

	try {
		Atom a1 = DisplayAFP.getAtomForAligPos(afpChain, 0, start.getPos1(), ca1,false);
		Atom a2 = DisplayAFP.getAtomForAligPos(afpChain, 1, start.getPos2(), ca2,true);

		Atom a3 = DisplayAFP.getAtomForAligPos(afpChain, 0, end.getPos1(), ca1,false);
		Atom a4 = DisplayAFP.getAtomForAligPos(afpChain, 1, end.getPos2(), ca2,true);

		String pdbInfo1 = JmolTools.getPdbInfo(a1);
		String pdbInfo2 = JmolTools.getPdbInfo(a2);

		String pdbInfo3 = JmolTools.getPdbInfo(a3);
		String pdbInfo4 = JmolTools.getPdbInfo(a4);

		String msg =  "Selected range1: " + pdbInfo1 + " ("+c1+") - " + pdbInfo3 + " ("+c3+")";
		msg       +=  " range2: "         + pdbInfo2 + " ("+c2+") - " + pdbInfo4 + " ("+c4+")";


		this.setText(msg);
	} catch (StructureException e){
		e.printStackTrace();
	}


}
 

private void updateJmolDisplay() {

		if ( jmol == null)
			return;

		int size = afpChain.getAlnLength();

		StringBuffer cmd = new StringBuffer("select ");

		int nrSelected = 0;
		try {

			for (int i = 0 ; i< size ; i++){
				if ( selection.get(i)){

					Atom a1 = DisplayAFP.getAtomForAligPos(afpChain, 0,i, ca1, false);
					Atom a2 = DisplayAFP.getAtomForAligPos(afpChain, 1,i, ca2, false);

					String select1 = "";

					if ( a1 != null )
						select1 = JmolTools.getPdbInfo(a1);
					String select2 = "" ;
					if ( a2 != null)
						select2 = JmolTools.getPdbInfo(a2);

					// nothing to display
					if ( select1.equals("") && select2.equals(""))
						continue;

					if ( nrSelected > 0)
						cmd.append(", ");

					cmd.append(select1);
					cmd.append("/1, ");
					cmd.append(select2);
					cmd.append("/2");
					nrSelected++;
				}
			}


		} catch (StructureException e){
			e.printStackTrace();
		}
		if ( nrSelected == 0)
			cmd.append(" none;");
		else
			cmd.append("; set display selected;");

		jmol.evalString(cmd.toString());


	}
 

@Override
public void mouseOverPosition(AlignedPosition p) {

	if ( afpChain == null)
		return;

	char[] aligs1  = afpChain.getAlnseq1();
	char[] aligs2  = afpChain.getAlnseq2();

	char c1 = aligs1[p.getPos1()];
	char c2 = aligs2[p.getPos2()];

	try {
		Atom a1 = DisplayAFP.getAtomForAligPos(afpChain, 0, p.getPos1(), ca1,false);
		Atom a2 = DisplayAFP.getAtomForAligPos(afpChain, 1, p.getPos2(), ca2,true);

		String pdbInfo1 = JmolTools.getPdbInfo(a1);
		String pdbInfo2 = JmolTools.getPdbInfo(a2);

		String msg = "alig pos:" + p.getPos1()+ " " +  pdbInfo1 + " ("+c1+") : " + pdbInfo2 + " ("+c2+")";

		this.setText(msg);



	} catch (StructureException e){
		e.printStackTrace();
	}

	this.repaint();

}
 

@Override
public void run() {

	// both structure have been downloaded, now calculate the alignment ...

	StructureAlignment algorithm = parent.getStructureAlignment();
	//StructurePairAligner aligner = new StructurePairAligner();
	//aligner.setDebug(true);
	try {

		Atom[] ca1 = StructureTools.getRepresentativeAtomArray(structure1);
		Atom[] ca2 = StructureTools.getRepresentativeAtomArray(structure2);

		//System.out.println("ca1 size:" + ca1.length + " ca2 size: " + ca2.length);
		AFPChain afpChain = algorithm.align(ca1, ca2);

		afpChain.setName1(name1);
		afpChain.setName2(name2);

		StructureAlignmentJmol jmol =   StructureAlignmentDisplay.display(afpChain, ca1, ca2);

		String title = jmol.getTitle();
		ConfigStrucAligParams params = algorithm.getParameters();
		if ( params != null)
			title += " " + algorithm.getParameters().toString();
		jmol.setTitle(title);

		DisplayAFP.showAlignmentPanel(afpChain,ca1,ca2,jmol);

		System.out.println(afpChain.toCE(ca1,ca2));

	} catch (StructureException e){
		e.printStackTrace();
		logger.warn(e.getMessage());
	}



	//logger.info("done!");

	parent.notifyCalcFinished();

}