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/*
* BioJava 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.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.align.gui.jmol;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;
import javax.swing.Box;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JMenuBar;
import javax.swing.JPanel;
import javax.swing.JTextField;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.gui.MenuCreator;
import org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI;
import org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay;
import org.biojava.nbio.structure.align.multiple.Block;
import org.biojava.nbio.structure.align.multiple.BlockSet;
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
import org.biojava.nbio.structure.align.webstart.AligUIManager;
import org.biojava.nbio.structure.gui.WrapLayout;
import org.biojava.nbio.structure.jama.Matrix;
import org.forester.archaeopteryx.Archaeopteryx;
import org.forester.phylogeny.Phylogeny;
import org.jcolorbrewer.ColorBrewer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* A class that provides a 3D visualization Frame in Jmol for
* {@link MultipleAlignment}s.
*
* @author Aleix Lafita
* @since 4.1.0
*
*/
public class MultipleAlignmentJmol extends AbstractAlignmentJmol {
private MultipleAlignment multAln;
private List<Atom[]> transformedAtoms;
private JCheckBox colorByBlocks;
private List<JCheckBox> selectedStructures;
private static final String LIGAND_DISPLAY_SCRIPT = "select ligand; wireframe 40; spacefill 120; color CPK;";
private static final Logger logger = LoggerFactory
.getLogger(MultipleAlignmentJmol.class);
/**
* Default constructor creates an empty JmolPanel window, from where
* alignments can be made through the align menu.
*/
public MultipleAlignmentJmol() {
this(null, null);
}
/**
* The constructor displays the Mutltiple Alignment in a new JmolPanel
* Frame.
*
* @param msa
* : contains the aligned residues.
* @param rotatedAtoms
* : contains the transformed Atom coordinates.
*/
public MultipleAlignmentJmol(MultipleAlignment msa,
List<Atom[]> rotatedAtoms) {
AligUIManager.setLookAndFeel();
nrOpenWindows++;
jmolPanel = new JmolPanel();
frame = new JFrame();
JMenuBar menu = MenuCreator.initJmolMenu(frame, this, null, msa);
frame.setJMenuBar(menu);
this.multAln = msa;
this.transformedAtoms = rotatedAtoms;
this.selectedStructures = new ArrayList<>();
frame.addWindowListener(new WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
nrOpenWindows--;
destroy();
if (nrOpenWindows > 0)
frame.dispose();
else {
MultipleAlignmentGUI gui = MultipleAlignmentGUI
.getInstanceNoVisibilityChange();
if (gui.isVisible()) {
frame.dispose();
gui.requestFocus();
} else
System.exit(0);
}
}
});
Container contentPane = frame.getContentPane();
jmolPanel.addMouseMotionListener(this);
jmolPanel.addMouseListener(this);
jmolPanel.setPreferredSize(new Dimension(DEFAULT_WIDTH, DEFAULT_HEIGHT));
contentPane.add(jmolPanel,BorderLayout.CENTER);
Box vBox = Box.createVerticalBox();
// / USER SCRIPTING COMMAND
JTextField field = new JTextField();
field.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
field.setText(COMMAND_LINE_HELP);
RasmolCommandListener listener = new RasmolCommandListener(jmolPanel,
field);
field.addActionListener(listener);
field.addMouseListener(listener);
field.addKeyListener(listener);
vBox.add(field);
// / STRUCTURE SELECTION
if (multAln != null) {
JPanel modelSelection = new JPanel();
modelSelection.setLayout(new WrapLayout(WrapLayout.LEFT));
modelSelection.setSize(new Dimension(DEFAULT_WIDTH,30));
vBox.add(modelSelection);
JButton show = new JButton("Show Only: ");
show.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
jmolPanel.evalString("save selection;");
String cmd = getJmolString(multAln,
transformedAtoms, colorPalette,
colorByBlocks.isSelected());
cmd += "; restrict ";
for (int st = 0; st < multAln.size(); st++) {
if (selectedStructures.get(st).isSelected()) {
cmd += "*/" + (st + 1) + ", ";
}
}
cmd += "none;";
jmolPanel.executeCmd(cmd + " restore selection;");
}
});
modelSelection.add(show);
// Check boxes for all models
for(int str = 0; str < multAln.size();str++) {
JCheckBox structureSelection = new JCheckBox(multAln
.getEnsemble().getStructureIdentifiers().get(str)
.getIdentifier());
modelSelection.add(structureSelection);
structureSelection.setSelected(true);
selectedStructures.add(structureSelection);
}
}
// / COMBO BOXES
Box hBox1 = Box.createHorizontalBox();
hBox1.add(Box.createGlue());
String[] styles = new String[] { "Cartoon", "Backbone", "CPK",
"Ball and Stick", "Ligands", "Ligands and Pocket" };
JComboBox<String> style = new JComboBox<>(styles);
hBox1.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
hBox1.add(new JLabel("Style"));
hBox1.add(style);
vBox.add(hBox1);
style.addActionListener(jmolPanel);
String[] colorModes = new String[] { "Secondary Structure", "By Chain",
"Rainbow", "By Element", "By Amino Acid", "Hydrophobicity",
"Suggest Domains", "Show SCOP Domains" };
JComboBox<String> jcolors = new JComboBox<>(colorModes);
jcolors.addActionListener(jmolPanel);
hBox1.add(Box.createGlue());
hBox1.add(new JLabel("Color"));
hBox1.add(jcolors);
String[] cPalette = { "Spectral", "Set1", "Set2", "Pastel" };
JComboBox<String> palette = new JComboBox<>(cPalette);
palette.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
@SuppressWarnings("unchecked")
JComboBox<String> source = (JComboBox<String>) e.getSource();
String value = source.getSelectedItem().toString();
evalString("save selection; select *; color grey; "
+ "select ligand; color CPK;");
if (value == "Set1") {
colorPalette = ColorBrewer.Set1;
} else if (value == "Set2") {
colorPalette = ColorBrewer.Set2;
} else if (value == "Spectral") {
colorPalette = ColorBrewer.Spectral;
} else if (value == "Pastel") {
colorPalette = ColorBrewer.Pastel1;
}
String script = getJmolString(multAln, transformedAtoms,
colorPalette, colorByBlocks.isSelected());
evalString(script + "; restore selection; ");
}
});
hBox1.add(Box.createGlue());
hBox1.add(new JLabel("Palette"));
hBox1.add(palette);
// / CHECK BOXES
Box hBox2 = Box.createHorizontalBox();
hBox2.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
JButton resetDisplay = new JButton("Reset Display");
resetDisplay.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
logger.info("reset!!");
jmolPanel.executeCmd("restore STATE state_1");
}
});
hBox2.add(resetDisplay);
hBox2.add(Box.createGlue());
JCheckBox toggleSelection = new JCheckBox("Show Selection");
toggleSelection.addItemListener(new ItemListener() {
@Override
public void itemStateChanged(ItemEvent e) {
boolean showSelection = (e.getStateChange() == ItemEvent.SELECTED);
if (showSelection) {
jmolPanel.executeCmd("set display selected");
} else
jmolPanel.executeCmd("set display off");
}
});
hBox2.add(toggleSelection);
hBox2.add(Box.createGlue());
colorByBlocks = new JCheckBox("Color By Block");
colorByBlocks.addItemListener(new ItemListener() {
@Override
public void itemStateChanged(ItemEvent e) {
evalString("save selection; "
+ getJmolString(multAln, transformedAtoms,
colorPalette, colorByBlocks.isSelected())
+ "; restore selection;");
}
});
hBox2.add(colorByBlocks);
hBox2.add(Box.createGlue());
vBox.add(hBox2);
// STATUS DISPLAY
Box hBox = Box.createHorizontalBox();
status = new JTextField();
status.setBackground(Color.white);
status.setEditable(false);
status.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
status.setPreferredSize(new Dimension(DEFAULT_WIDTH / 2, 30));
status.setMinimumSize(new Dimension(DEFAULT_WIDTH / 2, 30));
hBox.add(status);
text = new JTextField();
text.setBackground(Color.white);
text.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
text.setPreferredSize(new Dimension(DEFAULT_WIDTH / 2, 30));
text.setMinimumSize(new Dimension(DEFAULT_WIDTH / 2, 30));
text.setText("Display of Atom info");
text.setEditable(false);
hBox.add(text);
vBox.add(hBox);
contentPane.add(vBox,BorderLayout.SOUTH);
MyJmolStatusListener li = (MyJmolStatusListener) jmolPanel
.getStatusListener();
li.setTextField(status);
frame.pack();
frame.setVisible(true);
initCoords();
resetDisplay();
}
@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();
}
}
@Override
public void destroy() {
super.destroy();
multAln = null;
transformedAtoms = null;
}
@Override
public void actionPerformed(ActionEvent ae) {
String cmd = ae.getActionCommand();
if (multAln == null) {
logger.error("Currently not viewing an alignment!");
return;
}
try {
if (cmd.equals(MenuCreator.TEXT_ONLY)) {
logger.warn("Option not available for MultipleAlignments");
} else if (cmd.equals(MenuCreator.PAIRS_ONLY)) {
String result = MultipleAlignmentWriter
.toAlignedResidues(multAln);
MultipleAlignmentJmolDisplay
.showAlignmentImage(multAln, result);
} else if (cmd.equals(MenuCreator.ALIGNMENT_PANEL)) {
MultipleAlignmentJmolDisplay.showMultipleAlignmentPanel(multAln,
this);
} else if (cmd.equals(MenuCreator.FATCAT_TEXT)) {
String result = MultipleAlignmentWriter.toFatCat(multAln)
+ "\n";
result += MultipleAlignmentWriter.toTransformMatrices(multAln);
MultipleAlignmentJmolDisplay
.showAlignmentImage(multAln, result);
} else if (cmd.equals(MenuCreator.PHYLOGENETIC_TREE)) {
// Kimura, Structural and Fractional Dissimilarity Score
Phylogeny kimura = MultipleAlignmentTools
.getKimuraTree(multAln);
Phylogeny sdm = MultipleAlignmentTools.getHSDMTree(multAln);
// Phylogeny structural = MultipleAlignmentTools
// .getStructuralTree(multAln);
Archaeopteryx
.createApplication(new Phylogeny[] { kimura, sdm });
}
} catch (Exception e) {
logger.error("Could not complete display option.", e);
}
}
/**
* Generate a Jmol command String that colors the aligned residues of every
* structure.
*/
public static String getJmolString(MultipleAlignment multAln,
List<Atom[]> transformedAtoms, ColorBrewer colorPalette,
boolean colorByBlocks) {
// Color by blocks if specified
if (colorByBlocks)
return getMultiBlockJmolString(multAln, transformedAtoms,
colorPalette, colorByBlocks);
Color[] colors = colorPalette.getColorPalette(multAln.size());
StringBuffer j = new StringBuffer();
j.append(DEFAULT_SCRIPT);
// Color the equivalent residues of every structure
StringBuffer sel = new StringBuffer();
sel.append("select *; color lightgrey; backbone 0.1; ");
List<List<String>> allPDB = new ArrayList<>();
// Get the aligned residues of every structure
for (int i = 0; i < multAln.size(); i++) {
List<String> pdb = MultipleAlignmentJmolDisplay.getPDBresnum(i,
multAln, transformedAtoms.get(i));
allPDB.add(pdb);
sel.append("select ");
int pos = 0;
for (String res : pdb) {
if (pos > 0)
sel.append(",");
pos++;
sel.append(res);
sel.append("/" + (i + 1));
}
if (pos == 0)
sel.append("none");
sel.append("; backbone 0.3 ; color [" + colors[i].getRed() + ","
+ colors[i].getGreen() + "," + colors[i].getBlue() + "]; ");
}
j.append(sel);
j.append("model 0; ");
j.append(LIGAND_DISPLAY_SCRIPT);
return j.toString();
}
/**
* Colors every Block of the structures with a different color, following
* the palette. It colors each Block differently, no matter if it is from
* the same or different BlockSet.
*/
public static String getMultiBlockJmolString(MultipleAlignment multAln,
List<Atom[]> transformedAtoms, ColorBrewer colorPalette,
boolean colorByBlocks) {
StringWriter jmol = new StringWriter();
jmol.append(DEFAULT_SCRIPT);
jmol.append("select *; color lightgrey; backbone 0.1; ");
int blockNum = multAln.getBlocks().size();
Color[] colors = colorPalette.getColorPalette(blockNum);
// For every structure color all the blocks with the printBlock method
for (int str = 0; str < transformedAtoms.size(); str++) {
jmol.append("select */" + (str + 1) + "; color lightgrey; model "
+ (str + 1) + "; ");
int index = 0;
for (BlockSet bs : multAln.getBlockSets()) {
for (Block b : bs.getBlocks()) {
List<List<Integer>> alignRes = b.getAlignRes();
printJmolScript4Block(transformedAtoms.get(str), alignRes,
colors[index], jmol, str, index, blockNum);
index++;
}
}
}
jmol.append("model 0; ");
jmol.append(LIGAND_DISPLAY_SCRIPT);
return jmol.toString();
}
private static void printJmolScript4Block(Atom[] atoms,
List<List<Integer>> alignRes, Color blockColor, StringWriter jmol,
int str, int colorPos, int blockNum) {
// Obtain the residues aligned in this block of the structure
List<String> pdb = new ArrayList<>();
for (int i = 0; i < alignRes.get(str).size(); i++) {
// Handle gaps - only color if it is not null
if (alignRes.get(str).get(i) != null) {
int pos = alignRes.get(str).get(i);
pdb.add(JmolTools.getPdbInfo(atoms[pos]));
}
}
// Select the aligned residues
StringBuffer buf = new StringBuffer("select ");
int count = 0;
for (String res : pdb) {
if (count > 0)
buf.append(",");
buf.append(res);
buf.append("/" + (str + 1));
count++;
}
buf.append("; backbone 0.3 ; color [" + blockColor.getRed() + ","
+ blockColor.getGreen() + "," + blockColor.getBlue() + "]; ");
jmol.append(buf);
}
@Override
public void resetDisplay() {
if (multAln != null && transformedAtoms != null) {
String script = getJmolString(multAln, transformedAtoms,
colorPalette, colorByBlocks.isSelected());
logger.debug(script);
evalString(script);
jmolPanel.evalString("save STATE state_1");
}
}
@Override
public List<Matrix> getDistanceMatrices() {
if (multAln == null)
return null;
else
return multAln.getEnsemble().getDistanceMatrix();
}
public void setColorByBlocks(boolean colorByBlocks) {
this.colorByBlocks.setSelected(colorByBlocks);
resetDisplay();
}
public JFrame getFrame() {
return frame;
}
public MultipleAlignment getMultipleAlignment() {
return multAln;
}
}