Java Code Examples for org.biojava.nbio.structure.align.model.AFPChain#getName1()

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);

	}
 

/** new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
*
* @param xml
* @param name1
* @param name1
* @param ca1
* @param ca2
* @return
*/
public static AFPChain fromXML(String xml, String name1, String name2, Atom[] ca1, Atom[] ca2) throws IOException, StructureException{
	AFPChain[] afps = parseMultiXML( xml);
	if ( afps.length > 0 ) {

		AFPChain afpChain = afps[0];

		String n1 = afpChain.getName1();
		String n2 = afpChain.getName2();

		if ( n1 == null )
			n1 = "";
		if ( n2 == null)
			n2 = "";

		//System.out.println("from AFPCHAIN: " + n1 + " " + n2);
		if ( n1.equals(name2) && n2.equals(name1)){
			// flipped order
			//System.out.println("AfpChain in wrong order, flipping...");
			afpChain  = AFPChainFlipper.flipChain(afpChain);
		}
		rebuildAFPChain(afpChain, ca1, ca2);

		return afpChain;
	}
	return null;

}
 

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

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

/**
 * Swaps the order of structures in an AFPChain
 * @param a
 * @return
 */
public AFPChain invertAlignment(AFPChain a) {
	String name1 = a.getName1();
	String name2 = a.getName2();
	a.setName1(name2);
	a.setName2(name1);

	int len1 = a.getCa1Length();
	a.setCa1Length( a.getCa2Length() );
	a.setCa2Length( len1 );

	int beg1 = a.getAlnbeg1();
	a.setAlnbeg1(a.getAlnbeg2());
	a.setAlnbeg2(beg1);

	char[] alnseq1 = a.getAlnseq1();
	a.setAlnseq1(a.getAlnseq2());
	a.setAlnseq2(alnseq1);

	Matrix distab1 = a.getDisTable1();
	a.setDisTable1(a.getDisTable2());
	a.setDisTable2(distab1);

	int[] focusRes1 = a.getFocusRes1();
	a.setFocusRes1(a.getFocusRes2());
	a.setFocusRes2(focusRes1);

	//What are aftIndex and befIndex used for? How are they indexed?
	//a.getAfpAftIndex()


	String[][][] pdbAln = a.getPdbAln();
	if( pdbAln != null) {
		for(int block = 0; block < a.getBlockNum(); block++) {
			String[] paln1 = pdbAln[block][0];
			pdbAln[block][0] = pdbAln[block][1];
			pdbAln[block][1] = paln1;
		}
	}

	int[][][] optAln = a.getOptAln();
	if( optAln != null ) {
		for(int block = 0; block < a.getBlockNum(); block++) {
			int[] aln1 = optAln[block][0];
			optAln[block][0] = optAln[block][1];
			optAln[block][1] = aln1;
		}
	}
	a.setOptAln(optAln); // triggers invalidate()

	Matrix distmat = a.getDistanceMatrix();
	if(distmat != null)
		a.setDistanceMatrix(distmat.transpose());


	// invert the rotation matrices
	Matrix[] blockRotMat = a.getBlockRotationMatrix();
	Atom[] shiftVec = a.getBlockShiftVector();
	if( blockRotMat != null) {
		for(int block = 0; block < a.getBlockNum(); block++) {
			if(blockRotMat[block] != null) {
				// if y=x*A+b, then x=y*inv(A)-b*inv(A)
				blockRotMat[block] = blockRotMat[block].inverse();

				Calc.rotate(shiftVec[block],blockRotMat[block]);
				shiftVec[block] = Calc.invert(shiftVec[block]);
			}
		}
	}

	return a;
}
 

/** 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;
}