Java Code Examples for org.biojava.nbio.structure.align.model.AFPChain#getAlgorithmName()

public static void showAlignmentImage(AFPChain afpChain, String result) {

		JFrame frame = new JFrame();

		String title = afpChain.getAlgorithmName() + " V."+afpChain.getVersion() + " : " + afpChain.getName1()  + " vs. " + afpChain.getName2() ;
		frame.setTitle(title);
		frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

		AlignmentTextPanel txtPanel = new AlignmentTextPanel();
		txtPanel.setText(result);

		JMenuBar menu = MenuCreator.getAlignmentTextMenu(frame,txtPanel,afpChain,null);

		frame.setJMenuBar(menu);
		JScrollPane js = new JScrollPane();
		js.getViewport().add(txtPanel);
		js.getViewport().setBorder(null);
		//js.setViewportBorder(null);
		//js.setBorder(null);
		//js.setBackground(Color.white);

		frame.getContentPane().add(js);
		frame.pack();
		frame.setVisible(true);

	}
 

/** Takes an XML representation of the alignment and flips the positions of name1 and name2
 *
 * @param xml String representing the alignment
 * @return XML representation of the flipped alignment
 */
public static String flipAlignment(String xml) throws IOException,StructureException{
	AFPChain[] afps = parseMultiXML( xml);
	if ( afps.length < 1 )
		return null;

	if ( afps.length == 1) {
		AFPChain newChain = AFPChainFlipper.flipChain(afps[0]);
		if ( newChain.getAlgorithmName() == null) {
			newChain.setAlgorithmName(DEFAULT_ALGORITHM_NAME);
		}
		return AFPChainXMLConverter.toXML(newChain);
	}
	throw new StructureException("not Implemented yet!");
}
 

private String getAutoFileName(AFPChain afpChain){
	String fileName =afpChain.getName1()+"_" + afpChain.getName2()+"_"+afpChain.getAlgorithmName();

	if (params.isOutputPDB() )
		fileName += ".pdb";
	else
		fileName += ".xml";
	return fileName;
}
 

/**
 * Constructor using an afpChain and the atom arrays for pairwise
 * alignments. The AFPChain is converted into a MultipleAlignment.
 *
 * @param afpChain
 * @param ca1
 * @param ca2
 * @throws StructureException
 */
public MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
		AbstractAlignmentJmol jmol) throws StructureException {

	this();

	String algorithm = afpChain.getAlgorithmName();
	boolean flex = false;
	if (algorithm != null){
		if (algorithm.contains("flexible")) flex = true;
	}

	//Convert the apfChain into a MultipleAlignment object
	MultipleAlignmentEnsembleImpl ensemble =
			new MultipleAlignmentEnsembleImpl(afpChain, ca1, ca2, flex);
	this.multAln = ensemble.getMultipleAlignment(0);

	//Create the sequence alignment and the structure-sequence mapping.
	this.mapSeqToStruct = new ArrayList<Integer>();
	this.alnSeq = MultipleAlignmentTools.getSequenceAlignment(
			this.multAln, this.mapSeqToStruct);

	//Initialize other memeber variables of the panel
	this.size = multAln.size();
	this.length = alnSeq.get(0).length();

	coordManager = new MultipleAlignmentCoordManager(size, length);
	this.jmol = jmol;
}
 

/**  replace the PDB res nums with atom positions:
 *
 * @param afpChain
 * @param ca1
 * @param ca2
 */
public static void rebuildAFPChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2){

	if ( afpChain.getAlgorithmName() == null) {
		afpChain.setAlgorithmName(DEFAULT_ALGORITHM_NAME);
	}
	if ( afpChain.getVersion() == null){
		afpChain.setVersion("1.0");
	}

	int blockNum  = afpChain.getBlockNum();
	int ca1Length = afpChain.getCa1Length();
	int ca2Length = afpChain.getCa2Length();

	int minLength = Math.min(ca1Length, ca2Length);
	int[][][] optAln = new int[blockNum][2][minLength];

	int[][][] blockResList = afpChain.getBlockResList();
	if ( blockResList == null){
		blockResList = new int[blockNum][2][minLength];
	}
	int[] optLen = afpChain.getOptLen();

	String[][][] pdbAln = afpChain.getPdbAln();
	int[] verifiedOptLen = null;
	if ( optLen != null)
	  verifiedOptLen = afpChain.getOptLen().clone();
	else {
		logger.warn("did not find optimal alignment, building up empty alignment.");
		optLen = new int[1];
		optLen[0] = 0;
	}
	for (int blockNr = 0 ; blockNr < blockNum ; blockNr++){

		//System.out.println("got block " + blockNr + " size: " + optLen[blockNr]);
		int verifiedEQR = -1;
		for ( int eqrNr = 0 ; eqrNr < optLen[blockNr] ; eqrNr++ ){
			String pdbResnum1 = pdbAln[blockNr][0][eqrNr];
			String pdbResnum2 = pdbAln[blockNr][1][eqrNr];

			//System.out.println(blockNr + " " + eqrNr + " got resnum: " + pdbResnum1 + " " + pdbResnum2);
			String[] spl1 = pdbResnum1.split(":");
			String[] spl2 = pdbResnum2.split(":");

			String chain1 = spl1[0];
			String pdbres1 = spl1[1];

			String chain2 = spl2[0];
			String pdbres2 = spl2[1];

			int pos1 = getPositionForPDBresunm(pdbres1,chain1,ca1);
			int pos2 = getPositionForPDBresunm(pdbres2,chain2,ca2);

			if ( pos1 == -1 || pos2 == -1 ){
				// this can happen when parsing old files that contained Calcium atoms...
				logger.warn("pos1: {} (residue {}), pos2: {} (residue {}), should never be -1. Probably parsing an old file.",
						pos1, pdbResnum1, pos2, pdbResnum2);
				verifiedOptLen[blockNr]-- ;
				continue;
			}

			verifiedEQR++;
			//System.out.println(blockNr + " " + eqrNr + " " + pos1 + " " + pos2);
			optAln[blockNr][0][verifiedEQR] = pos1;
			optAln[blockNr][1][verifiedEQR] = pos2;
			blockResList[blockNr][0][verifiedEQR] = pos1;
			blockResList[blockNr][1][verifiedEQR] = pos2;
		}
	}

	afpChain.setOptLen(verifiedOptLen);
	afpChain.setOptAln(optAln);
	afpChain.setBlockResList(blockResList);
	// build up alignment image:
	AFPAlignmentDisplay.getAlign(afpChain, ca1, ca2);


}
 

/** check if the result should be written to the local file system
 *
 * @param params2
 * @param afpChain
 * @param ca1
 * @param ca2
 * @throws IOException If an error occurs when writing the afpChain to XML
 * @throws ClassNotFoundException If an error occurs when invoking jmol
 * @throws NoSuchMethodException If an error occurs when invoking jmol
 * @throws InvocationTargetException If an error occurs when invoking jmol
 * @throws IllegalAccessException If an error occurs when invoking jmol
 * @throws StructureException
 */
private void checkWriteFile( AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean dbsearch) throws IOException, ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException, StructureException
		{
	String output = null;
	if ( params.isOutputPDB()){
		if (! GuiWrapper.isGuiModuleInstalled()) {
			System.err.println("The biojava-structure-gui module is not installed. Please install!");
			output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
		} else {

			Structure tmp = AFPAlignmentDisplay.createArtificalStructure(afpChain, ca1, ca2);
			output = "TITLE  " + afpChain.getAlgorithmName() + " " + afpChain.getVersion()  + " ";
			output += afpChain.getName1() + " vs. " + afpChain.getName2();
			output += newline;
			output += tmp.toPDB();
		}
	} else  if ( params.getOutFile() != null) {
		// output by default is XML
		// write the XML to a file...
		output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);

	} else if ( params.getSaveOutputDir() != null){
		output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
	}

	// no output requested.
	if ( output == null)
		return;

	String fileName = null;

	if ( dbsearch ){
		if ( params.getSaveOutputDir() != null) {

			// we currently don't have a naming convention for how to store results for custom files
			// they will be re-created on the fly
			if ( afpChain.getName1().startsWith("file:") || afpChain.getName2().startsWith("file:"))
				return;
			fileName = params.getSaveOutputDir();
			fileName += getAutoFileName(afpChain);

		} else {
			return;
		}

		//
		//else {
		//	fileName = getAutoFileName(afpChain);
		//}
	} else

		if ( params.getOutFile() != null) {
			fileName = params.getOutFile();
		}

	if (fileName == null) {
		System.err.println("Can't write outputfile. Either provide a filename using -outFile or set -autoOutputFile to true .");
		System.exit(1); return;
	}
	//System.out.println("writing results to " + fileName + " " + params.getSaveOutputDir());

	FileOutputStream out; // declare a file output object
	PrintStream p; // declare a print stream object

		// Create a new file output stream
		out = new FileOutputStream(fileName);

		// Connect print stream to the output stream
		p = new PrintStream( out );

		p.println (output);

		p.close();



}
 

/** Note: ca2, hetatoms2 and nucleotides2 should not be rotated. This will be done here...
 * */

public static final StructureAlignmentJmol display(AFPChain afpChain,Group[] twistedGroups, Atom[] ca1, Atom[] ca2,List<Group> hetatms1, List<Group> hetatms2 ) throws StructureException {

	List<Atom> twistedAs = new ArrayList<Atom>();

	for ( Group g: twistedGroups){
		if ( g == null )
			continue;
		if ( g.size() < 1)
			continue;
		Atom a = g.getAtom(0);
		twistedAs.add(a);
	}
	Atom[] twistedAtoms = twistedAs.toArray(new Atom[twistedAs.size()]);
	twistedAtoms = StructureTools.cloneAtomArray(twistedAtoms);

	Atom[] arr1 = getAtomArray(ca1, hetatms1);
	Atom[] arr2 = getAtomArray(twistedAtoms, hetatms2);

	//

	//if ( hetatms2.size() > 0)
		//	System.out.println("atom after:" + hetatms2.get(0).getAtom(0));

	//if ( hetatms2.size() > 0)
	//	System.out.println("atom after:" + hetatms2.get(0).getAtom(0));

	String title =  afpChain.getAlgorithmName() + " V." +afpChain.getVersion() + " : " + afpChain.getName1() + " vs. " + afpChain.getName2();

	//System.out.println(artificial.toPDB());



	StructureAlignmentJmol jmol = new StructureAlignmentJmol(afpChain,arr1,arr2);
	//jmol.setStructure(artificial);

	System.out.format("CA2[0]=(%.2f,%.2f,%.2f)%n", arr2[0].getX(), arr2[0].getY(), arr2[0].getZ());

	//jmol.setTitle("Structure Alignment: " + afpChain.getName1() + " vs. " + afpChain.getName2());
	jmol.setTitle(title);
	return jmol;
}