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org.biojava.nbio.structure.align.gui.DisplayAFP Maven / Gradle / Ivy
/*
* PDB web development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
*
* Created on Jun 13, 2009
* Created by Andreas Prlic
*
*/
package org.biojava.nbio.structure.align.gui;
import java.awt.Dimension;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import javax.swing.Box;
import javax.swing.JFrame;
import javax.swing.JMenuBar;
import javax.swing.JScrollPane;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.gui.aligpanel.AligPanel;
import org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay;
import org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol;
import org.biojava.nbio.structure.align.gui.jmol.JmolTools;
import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AFPAlignmentDisplay;
import org.biojava.nbio.structure.align.util.AlignmentTools;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/** A utility class for visualistion of structure alignments
*
* @author Andreas Prlic
*
*/
public class DisplayAFP {
private static final Logger logger = LoggerFactory.getLogger(DisplayAFP.class);
//TODO: same as getEqrPos??? !!!
public static final List getEQRAlignmentPos(AFPChain afpChain){
List lst = new ArrayList();
char[] s1 = afpChain.getAlnseq1();
char[] s2 = afpChain.getAlnseq2();
char[] symb = afpChain.getAlnsymb();
boolean isFatCat = afpChain.getAlgorithmName().startsWith("jFatCat");
for ( int i =0 ; i< s1.length; i++){
char c1 = s1[i];
char c2 = s2[i];
if ( isAlignedPosition(i,c1,c2,isFatCat, symb)) {
lst.add(i);
}
}
return lst;
}
private static boolean isAlignedPosition(int i, char c1, char c2, boolean isFatCat,char[]symb)
{
// if ( isFatCat){
char s = symb[i];
if ( c1 != '-' && c2 != '-' && s != ' '){
return true;
}
// } else {
//
// if ( c1 != '-' && c2 != '-')
// return true;
// }
return false;
}
/**
* Return a list of pdb Strings corresponding to the aligned positions of the molecule.
* Only supports a pairwise alignment with the AFPChain DS.
*
* @param aligPos
* @param afpChain
* @param ca
*/
public static final List getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca){
List lst = new ArrayList();
if ( aligPos > 1) {
System.err.println("multiple alignments not supported yet!");
return lst;
}
int blockNum = afpChain.getBlockNum();
int[] optLen = afpChain.getOptLen();
int[][][] optAln = afpChain.getOptAln();
if ( optLen == null)
return lst;
for(int bk = 0; bk < blockNum; bk ++) {
for ( int i=0;i< optLen[bk];i++){
int pos = optAln[bk][aligPos][i];
if ( pos < ca.length) {
String pdbInfo = JmolTools.getPdbInfo(ca[pos]);
//lst.add(ca1[pos].getParent().getPDBCode());
lst.add(pdbInfo);
}
}
}
return lst;
}
/**
* Return the atom at alignment position aligPos. at the present only works with block 0
* @param chainNr the number of the aligned pair. 0... first chain, 1... second chain.
* @param afpChain an afpChain object
* @param aligPos position on the alignment
* @param getPrevious gives the previous position if false, gives the next posible atom
* @return a CA atom that is at a particular position of the alignment
*/
public static final Atom getAtomForAligPos(AFPChain afpChain,int chainNr, int aligPos, Atom[] ca , boolean getPrevious ) throws StructureException{
int[] optLen = afpChain.getOptLen();
// int[][][] optAln = afpChain.getOptAln();
if ( optLen == null)
return null;
if (chainNr < 0 || chainNr > 1){
throw new StructureException("So far only pairwise alignments are supported, but you requested results for alinged chain nr " + chainNr);
}
//if ( afpChain.getAlgorithmName().startsWith("jFatCat")){
/// for FatCat algorithms...
int capos = getUngappedFatCatPos(afpChain, chainNr, aligPos);
if ( capos < 0) {
capos = getNextFatCatPos(afpChain, chainNr, aligPos,getPrevious);
//System.out.println(" got next" + capos + " for " + chainNr + " alignedPos: " + aligPos);
} else {
//System.out.println("got aligned fatcat position: " + capos + " " + chainNr + " for alig pos: " + aligPos);
}
if ( capos < 0) {
System.err.println("could not match position " + aligPos + " in chain " + chainNr +". Returing null...");
return null;
}
if ( capos > ca.length){
System.err.println("Atom array "+ chainNr + " does not have " + capos +" atoms. Returning null.");
return null;
}
return ca[capos];
//}
//
//
// int ungappedPos = getUngappedPos(afpChain, aligPos);
// System.out.println("getAtomForAligPOs " + aligPos + " " + ungappedPos );
// return ca[ungappedPos];
//
// if ( ungappedPos >= optAln[bk][chainNr].length)
// return null;
// int pos = optAln[bk][chainNr][ungappedPos];
// if ( pos > ca.length)
// return null;
// return ca[pos];
}
private static int getNextFatCatPos(AFPChain afpChain, int chainNr,
int aligPos, boolean getPrevious) {
char[] aseq;
if ( chainNr == 0 )
aseq = afpChain.getAlnseq1();
else
aseq = afpChain.getAlnseq2();
if ( aligPos > aseq.length)
return -1;
if ( aligPos < 0)
return -1;
int blockNum = afpChain.getBlockNum();
int[] optLen = afpChain.getOptLen();
int[][][] optAln = afpChain.getOptAln();
int p1, p2;
int p1b = 0;
int p2b = 0;
int len = 0;
boolean terminateNextMatch = false;
for(int i = 0; i < blockNum; i ++) {
for(int j = 0; j < optLen[i]; j ++) {
p1 = optAln[i][0][j];
p2 = optAln[i][1][j];
if(len > 0) {
int lmax = (p1 - p1b - 1)>(p2 - p2b - 1)?(p1 - p1b - 1):(p2 - p2b - 1);
// lmax gives the length of an alignment gap
//System.out.println(" pos "+ len+" p1-p2: " + p1 + " - " + p2 + " lmax: " + lmax + " p1b-p2b:"+p1b + " " + p2b + " terminate? "+ terminateNextMatch);
for(int k = 0; k < lmax; k ++) {
if(k >= (p1 - p1b - 1)) {
// a gap position in chain 0
if ( aligPos == len && chainNr == 0 ){
if ( getPrevious)
return p1b;
else
terminateNextMatch = true;
}
}
else {
if ( aligPos == len && chainNr == 0)
return p1b+1+k;
}
if(k >= (p2 - p2b - 1)) {
// a gap position in chain 1
if ( aligPos == len && chainNr == 1){
if ( getPrevious)
return p2b;
else
terminateNextMatch = true;
}
}
else {
if ( aligPos == len && chainNr == 1) {
return p2b+1+k;
}
}
len++;
}
}
if ( aligPos == len && chainNr == 0)
return p1;
if ( aligPos == len && chainNr == 1)
return p2;
if ( terminateNextMatch)
if ( chainNr == 0)
return p1;
else
return p2;
if ( len > aligPos) {
if ( getPrevious) {
if ( chainNr == 0)
return p1b;
else
return p2b;
} else {
terminateNextMatch = true;
}
}
len++;
p1b = p1;
p2b = p2;
}
}
// we did not find an aligned position
return -1;
}
private static final int getUngappedFatCatPos(AFPChain afpChain, int chainNr, int aligPos){
char[] aseq;
if ( chainNr == 0 )
aseq = afpChain.getAlnseq1();
else
aseq = afpChain.getAlnseq2();
if ( aligPos > aseq.length)
return -1;
if ( aligPos < 0)
return -1;
int blockNum = afpChain.getBlockNum();
int[] optLen = afpChain.getOptLen();
int[][][] optAln = afpChain.getOptAln();
int p1, p2;
int p1b = 0;
int p2b = 0;
int len = 0;
for(int i = 0; i < blockNum; i ++) {
for(int j = 0; j < optLen[i]; j ++) {
p1 = optAln[i][0][j];
p2 = optAln[i][1][j];
if(len > 0) {
int lmax = (p1 - p1b - 1)>(p2 - p2b - 1)?(p1 - p1b - 1):(p2 - p2b - 1);
// lmax gives the length of an alignment gap
//System.out.println(" p1-p2: " + p1 + " - " + p2 + " lmax: " + lmax + " p1b-p2b:"+p1b + " " + p2b);
for(int k = 0; k < lmax; k ++) {
if(k >= (p1 - p1b - 1)) {
// a gap position in chain 0
if ( aligPos == len && chainNr == 0){
return -1;
}
}
else {
if ( aligPos == len && chainNr == 0)
return p1b+1+k;
}
if(k >= (p2 - p2b - 1)) {
// a gap position in chain 1
if ( aligPos == len && chainNr == 1){
return -1;
}
}
else {
if ( aligPos == len && chainNr == 1) {
return p2b+1+k;
}
}
len++;
}
}
if ( aligPos == len && chainNr == 0)
return p1;
if ( aligPos == len && chainNr == 1)
return p2;
len++;
p1b = p1;
p2b = p2;
}
}
// we did not find an aligned position
return -1;
}
/**
* Returns the first atom for each group
* @param ca
* @param hetatms
* @return
* @throws StructureException
*/
public static final Atom[] getAtomArray(Atom[] ca,List hetatms ) throws StructureException{
List atoms = new ArrayList();
Collections.addAll(atoms, ca);
logger.debug("got {} hetatoms", hetatms.size());
// we only add atom nr 1, since the getAlignedStructure method actually adds the parent group, and not the atoms...
for (Group g : hetatms){
if (g.size() < 1)
continue;
//if (debug)
// System.out.println("adding group " + g);
Atom a = g.getAtom(0);
//if (debug)
// System.out.println(a);
a.setGroup(g);
atoms.add(a);
}
Atom[] arr = atoms.toArray(new Atom[atoms.size()]);
return arr;
}
/** 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 hetatms1, List hetatms2 ) throws StructureException {
List twistedAs = new ArrayList();
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;
}
public static void showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol) throws StructureException {
AligPanel me = new AligPanel();
me.setAlignmentJmol(jmol);
me.setAFPChain(afpChain);
me.setCa1(ca1);
me.setCa2(ca2);
JFrame frame = new JFrame();
frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
frame.setTitle(afpChain.getName1() + " vs. " + afpChain.getName2() + " | " + afpChain.getAlgorithmName() + " V. " + afpChain.getVersion());
me.setPreferredSize(new Dimension(me.getCoordManager().getPreferredWidth() , me.getCoordManager().getPreferredHeight()));
JMenuBar menu = MenuCreator.getAlignmentPanelMenu(frame,me,afpChain,null);
frame.setJMenuBar(menu);
JScrollPane scroll = new JScrollPane(me);
scroll.setAutoscrolls(true);
StatusDisplay status = new StatusDisplay();
status.setAfpChain(afpChain);
status.setCa1(ca1);
status.setCa2(ca2);
me.addAlignmentPositionListener(status);
Box vBox = Box.createVerticalBox();
vBox.add(scroll);
vBox.add(status);
frame.getContentPane().add(vBox);
frame.pack();
frame.setVisible(true);
// make sure they get cleaned up correctly:
frame.addWindowListener(me);
frame.addWindowListener(status);
}
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);
}
/** Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
*
* @param afpChain the container of the alignment
* @param ca1 atoms for protein 1
* @param ca2 atoms for protein 2
* @return a protein structure with 2 models.
* @throws StructureException
*/
public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
Atom[] ca2) throws StructureException{
if ( afpChain.getNrEQR() < 1){
return AlignmentTools.getAlignedStructure(ca1, ca2);
}
Group[] twistedGroups = AlignmentTools.prepareGroupsForDisplay(afpChain,ca1, ca2);
List twistedAs = new ArrayList();
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()]);
List hetatms = StructureTools.getUnalignedGroups(ca1);
List hetatms2 = StructureTools.getUnalignedGroups(ca2);
Atom[] arr1 = DisplayAFP.getAtomArray(ca1, hetatms);
Atom[] arr2 = DisplayAFP.getAtomArray(twistedAtoms, hetatms2);
Structure artificial = AlignmentTools.getAlignedStructure(arr1,arr2);
return artificial;
}
}
