/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package mc_view;
import jalview.analysis.AlignSeq;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
import jalview.gui.SequenceRenderer;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Event;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.Graphics2D;
// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
import java.awt.Image;
import java.awt.RenderingHints;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.io.PrintStream;
import java.util.List;
import java.util.Vector;
import javax.swing.JPanel;
import javax.swing.ToolTipManager;
public class PDBCanvas extends JPanel
implements MouseListener, MouseMotionListener, StructureListener
{
boolean redrawneeded = true;
int omx = 0;
int mx = 0;
int omy = 0;
int my = 0;
public StructureFile pdb;
PDBEntry pdbentry;
int bsize;
Image img;
Graphics ig;
Dimension prefsize;
float[] centre = new float[3];
float[] width = new float[3];
float maxwidth;
float scale;
String inStr;
String inType;
boolean bysequence = true;
boolean depthcue = true;
boolean wire = false;
boolean bymolecule = false;
boolean zbuffer = true;
boolean dragging;
int xstart;
int xend;
int ystart;
int yend;
int xmid;
int ymid;
Font font = new Font("Helvetica", Font.PLAIN, 10);
jalview.gui.SeqCanvas seqcanvas;
public SequenceI[] sequence;
final StringBuffer mappingDetails = new StringBuffer();
PDBChain mainchain;
Vector highlightRes;
boolean pdbAction = false;
boolean seqColoursReady = false;
jalview.renderer.seqfeatures.FeatureRenderer fr;
Color backgroundColour = Color.black;
AlignmentPanel ap;
StructureSelectionManager ssm;
String errorMessage;
void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
this.pdbentry = pdbentry;
this.sequence = seq;
ssm = ap.av.getStructureSelectionManager();
try
{
pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
ap.alignFrame);
if (protocol.equals(jalview.io.DataSourceType.PASTE))
{
pdbentry.setFile("INLINE" + pdb.getId());
}
} catch (Exception ex)
{
ex.printStackTrace();
return;
}
if (pdb == null)
{
errorMessage = "Error loading file: " + pdbentry.getId();
return;
}
pdbentry.setId(pdb.getId());
ssm.addStructureViewerListener(this);
colourBySequence();
float max = -10;
int maxchain = -1;
int pdbstart = 0;
int pdbend = 0;
int seqstart = 0;
int seqend = 0;
// JUST DEAL WITH ONE SEQUENCE FOR NOW
SequenceI sequence = seq[0];
for (int i = 0; i < pdb.getChains().size(); i++)
{
mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
+ pdb.getChains().elementAt(i).sequence
.getSequenceAsString());
mappingDetails.append("\nNo of residues = "
+ pdb.getChains().elementAt(i).residues.size() + "\n\n");
// Now lets compare the sequences to get
// the start and end points.
// Align the sequence to the pdb
AlignSeq as = new AlignSeq(sequence,
pdb.getChains().elementAt(i).sequence, "pep");
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
{
@Override
public void print(String x)
{
mappingDetails.append(x);
}
@Override
public void println()
{
mappingDetails.append("\n");
}
};
as.printAlignment(ps);
if (as.maxscore > max)
{
max = as.maxscore;
maxchain = i;
pdbstart = as.seq2start;
pdbend = as.seq2end;
seqstart = as.seq1start + sequence.getStart() - 1;
seqend = as.seq1end + sequence.getEnd() - 1;
}
mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
}
mainchain = pdb.getChains().elementAt(maxchain);
mainchain.pdbstart = pdbstart;
mainchain.pdbend = pdbend;
mainchain.seqstart = seqstart;
mainchain.seqend = seqend;
mainchain.isVisible = true;
this.pdb = pdb;
this.prefsize = new Dimension(getSize().width, getSize().height);
addMouseMotionListener(this);
addMouseListener(this);
addKeyListener(new KeyAdapter()
{
@Override
public void keyPressed(KeyEvent evt)
{
keyPressed(evt);
}
});
findCentre();
findWidth();
setupBonds();
scale = findScale();
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
}
Vector visiblebonds;
void setupBonds()
{
seqColoursReady = false;
// Sort the bonds by z coord
visiblebonds = new Vector();
for (PDBChain chain : pdb.getChains())
{
if (chain.isVisible)
{
for (Bond bond : chain.bonds)
{
visiblebonds.addElement(bond);
}
}
}
updateSeqColours();
seqColoursReady = true;
redrawneeded = true;
repaint();
}
public void findWidth()
{
float[] max = new float[3];
float[] min = new float[3];
max[0] = (float) -1e30;
max[1] = (float) -1e30;
max[2] = (float) -1e30;
min[0] = (float) 1e30;
min[1] = (float) 1e30;
min[2] = (float) 1e30;
for (PDBChain chain : pdb.getChains())
{
if (chain.isVisible)
{
for (Bond tmp : chain.bonds)
{
if (tmp.start[0] >= max[0])
{
max[0] = tmp.start[0];
}
if (tmp.start[1] >= max[1])
{
max[1] = tmp.start[1];
}
if (tmp.start[2] >= max[2])
{
max[2] = tmp.start[2];
}
if (tmp.start[0] <= min[0])
{
min[0] = tmp.start[0];
}
if (tmp.start[1] <= min[1])
{
min[1] = tmp.start[1];
}
if (tmp.start[2] <= min[2])
{
min[2] = tmp.start[2];
}
if (tmp.end[0] >= max[0])
{
max[0] = tmp.end[0];
}
if (tmp.end[1] >= max[1])
{
max[1] = tmp.end[1];
}
if (tmp.end[2] >= max[2])
{
max[2] = tmp.end[2];
}
if (tmp.end[0] <= min[0])
{
min[0] = tmp.end[0];
}
if (tmp.end[1] <= min[1])
{
min[1] = tmp.end[1];
}
if (tmp.end[2] <= min[2])
{
min[2] = tmp.end[2];
}
}
}
}
/*
* System.out.println("xmax " + max[0] + " min " + min[0]);
* System.out.println("ymax " + max[1] + " min " + min[1]);
* System.out.println("zmax " + max[2] + " min " + min[2]);
*/
width[0] = Math.abs(max[0] - min[0]);
width[1] = Math.abs(max[1] - min[1]);
width[2] = Math.abs(max[2] - min[2]);
maxwidth = width[0];
if (width[1] > width[0])
{
maxwidth = width[1];
}
if (width[2] > width[1])
{
maxwidth = width[2];
}
// System.out.println("Maxwidth = " + maxwidth);
}
public float findScale()
{
int dim;
int width;
int height;
if (getWidth() != 0)
{
width = getWidth();
height = getHeight();
}
else
{
width = prefsize.width;
height = prefsize.height;
}
if (width < height)
{
dim = width;
}
else
{
dim = height;
}
return (float) (dim / (1.5d * maxwidth));
}
public void findCentre()
{
float xtot = 0;
float ytot = 0;
float ztot = 0;
int bsize = 0;
// Find centre coordinate
for (PDBChain chain : pdb.getChains())
{
if (chain.isVisible)
{
bsize += chain.bonds.size();
for (Bond bond : chain.bonds)
{
xtot = xtot + bond.start[0] + bond.end[0];
ytot = ytot + bond.start[1] + bond.end[1];
ztot = ztot + bond.start[2] + bond.end[2];
}
}
}
centre[0] = xtot / (2 * (float) bsize);
centre[1] = ytot / (2 * (float) bsize);
centre[2] = ztot / (2 * (float) bsize);
}
@Override
public void paintComponent(Graphics g)
{
super.paintComponent(g);
if (!seqColoursReady || errorMessage != null)
{
g.setColor(Color.black);
g.setFont(new Font("Verdana", Font.BOLD, 14));
g.drawString(errorMessage == null ? "Retrieving PDB data...."
: errorMessage, 20, getHeight() / 2);
return;
}
// Only create the image at the beginning -
// this saves much memory usage
if ((img == null) || (prefsize.width != getWidth())
|| (prefsize.height != getHeight()))
{
prefsize.width = getWidth();
prefsize.height = getHeight();
scale = findScale();
img = createImage(prefsize.width, prefsize.height);
ig = img.getGraphics();
Graphics2D ig2 = (Graphics2D) ig;
ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
redrawneeded = true;
}
if (redrawneeded)
{
drawAll(ig, prefsize.width, prefsize.height);
redrawneeded = false;
}
g.drawImage(img, 0, 0, this);
pdbAction = false;
}
public void drawAll(Graphics g, int width, int height)
{
g.setColor(backgroundColour);
g.fillRect(0, 0, width, height);
drawScene(g);
drawLabels(g);
}
public void updateSeqColours()
{
if (pdbAction)
{
return;
}
colourBySequence();
redrawneeded = true;
repaint();
}
// This method has been taken out of PDBChain to allow
// Applet and Application specific sequence renderers to be used
void colourBySequence()
{
SequenceRenderer sr = new SequenceRenderer(ap.av);
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
boolean showFeatures = false;
if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
{
fr = new FeatureRenderer(ap);
}
fr.transferSettings(ap.alignFrame.getFeatureRenderer());
showFeatures = true;
}
FeatureColourFinder finder = new FeatureColourFinder(fr);
PDBChain chain;
if (bysequence && pdb != null)
{
for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
chain = pdb.getChains().elementAt(ii);
for (int i = 0; i < chain.bonds.size(); i++)
{
Bond tmp = chain.bonds.elementAt(i);
tmp.startCol = Color.lightGray;
tmp.endCol = Color.lightGray;
if (chain != mainchain)
{
continue;
}
for (int s = 0; s < sequence.length; s++)
{
for (int m = 0; m < mapping.length; m++)
{
if (mapping[m].getSequence() == sequence[s])
{
int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1;
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
tmp.startCol = sr.getResidueColour(sequence[s], pos,
finder);
}
pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
tmp.endCol = sr.getResidueColour(sequence[s], pos,
finder);
}
}
}
}
}
}
}
}
Zsort zsort;
public void drawScene(Graphics g)
{
if (zbuffer)
{
if (zsort == null)
{
zsort = new Zsort();
}
zsort.sort(visiblebonds);
}
Bond tmpBond = null;
for (int i = 0; i < visiblebonds.size(); i++)
{
tmpBond = visiblebonds.elementAt(i);
xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
+ (getWidth() / 2));
ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
+ (getHeight() / 2));
xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
+ (getWidth() / 2));
yend = (int) (((centre[1] - tmpBond.end[1]) * scale)
+ (getHeight() / 2));
xmid = (xend + xstart) / 2;
ymid = (yend + ystart) / 2;
if (depthcue && !bymolecule)
{
if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
{
g.setColor(tmpBond.startCol.darker().darker());
drawLine(g, xstart, ystart, xmid, ymid);
g.setColor(tmpBond.endCol.darker().darker());
drawLine(g, xmid, ymid, xend, yend);
}
else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
{
g.setColor(tmpBond.startCol.darker());
drawLine(g, xstart, ystart, xmid, ymid);
g.setColor(tmpBond.endCol.darker());
drawLine(g, xmid, ymid, xend, yend);
}
else
{
g.setColor(tmpBond.startCol);
drawLine(g, xstart, ystart, xmid, ymid);
g.setColor(tmpBond.endCol);
drawLine(g, xmid, ymid, xend, yend);
}
}
else if (depthcue && bymolecule)
{
if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
{
g.setColor(Color.green.darker().darker());
drawLine(g, xstart, ystart, xend, yend);
}
else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
{
g.setColor(Color.green.darker());
drawLine(g, xstart, ystart, xend, yend);
}
else
{
g.setColor(Color.green);
drawLine(g, xstart, ystart, xend, yend);
}
}
else if (!depthcue && !bymolecule)
{
g.setColor(tmpBond.startCol);
drawLine(g, xstart, ystart, xmid, ymid);
g.setColor(tmpBond.endCol);
drawLine(g, xmid, ymid, xend, yend);
}
else
{
drawLine(g, xstart, ystart, xend, yend);
}
if (highlightBond1 != null && highlightBond1 == tmpBond)
{
g.setColor(
tmpBond.endCol.brighter().brighter().brighter().brighter());
drawLine(g, xmid, ymid, xend, yend);
}
if (highlightBond2 != null && highlightBond2 == tmpBond)
{
g.setColor(tmpBond.startCol.brighter().brighter().brighter()
.brighter());
drawLine(g, xstart, ystart, xmid, ymid);
}
}
}
public void drawLine(Graphics g, int x1, int y1, int x2, int y2)
{
if (!wire)
{
if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
{
g.drawLine(x1, y1, x2, y2);
g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
g.drawLine(x1, y1 - 1, x2, y2 - 1);
}
else
{
g.setColor(g.getColor().brighter());
g.drawLine(x1, y1, x2, y2);
g.drawLine(x1 + 1, y1, x2 + 1, y2);
g.drawLine(x1 - 1, y1, x2 - 1, y2);
}
}
else
{
g.drawLine(x1, y1, x2, y2);
}
}
public Dimension minimumsize()
{
return prefsize;
}
public Dimension preferredsize()
{
return prefsize;
}
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_UP)
{
scale = (float) (scale * 1.1);
redrawneeded = true;
repaint();
}
else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
{
scale = (float) (scale * 0.9);
redrawneeded = true;
repaint();
}
}
@Override
public void mousePressed(MouseEvent e)
{
pdbAction = true;
Atom fatom = findAtom(e.getX(), e.getY());
if (fatom != null)
{
fatom.isSelected = !fatom.isSelected;
redrawneeded = true;
repaint();
if (foundchain != -1)
{
PDBChain chain = pdb.getChains().elementAt(foundchain);
if (chain == mainchain)
{
if (fatom.alignmentMapping != -1)
{
if (highlightRes == null)
{
highlightRes = new Vector();
}
final String atomString = Integer
.toString(fatom.alignmentMapping);
if (highlightRes.contains(atomString))
{
highlightRes.remove(atomString);
}
else
{
highlightRes.add(atomString);
}
}
}
}
}
mx = e.getX();
my = e.getY();
omx = mx;
omy = my;
dragging = false;
}
@Override
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
if (highlightBond1 != null)
{
highlightBond1.at2.isSelected = false;
highlightBond2.at1.isSelected = false;
highlightBond1 = null;
highlightBond2 = null;
}
Atom fatom = findAtom(e.getX(), e.getY());
PDBChain chain = null;
if (foundchain != -1)
{
chain = pdb.getChains().elementAt(foundchain);
if (chain == mainchain)
{
mouseOverStructure(fatom.resNumber, chain.id);
}
}
if (fatom != null)
{
this.setToolTipText(
chain.id + ":" + fatom.resNumber + " " + fatom.resName);
}
else
{
mouseOverStructure(-1, chain != null ? chain.id : null);
this.setToolTipText(null);
}
}
@Override
public void mouseClicked(MouseEvent e)
{
}
@Override
public void mouseEntered(MouseEvent e)
{
}
@Override
public void mouseExited(MouseEvent e)
{
}
@Override
public void mouseDragged(MouseEvent evt)
{
int x = evt.getX();
int y = evt.getY();
mx = x;
my = y;
MCMatrix objmat = new MCMatrix(3, 3);
objmat.setIdentity();
if ((evt.getModifiers() & Event.META_MASK) != 0)
{
objmat.rotatez(((mx - omx)));
}
else
{
objmat.rotatex(((my - omy)));
objmat.rotatey(((omx - mx)));
}
// Alter the bonds
for (PDBChain chain : pdb.getChains())
{
for (Bond tmpBond : chain.bonds)
{
// Translate the bond so the centre is 0,0,0
tmpBond.translate(-centre[0], -centre[1], -centre[2]);
// Now apply the rotation matrix
tmpBond.start = objmat.vectorMultiply(tmpBond.start);
tmpBond.end = objmat.vectorMultiply(tmpBond.end);
// Now translate back again
tmpBond.translate(centre[0], centre[1], centre[2]);
}
}
objmat = null;
omx = mx;
omy = my;
dragging = true;
redrawneeded = true;
repaint();
}
@Override
public void mouseReleased(MouseEvent evt)
{
dragging = false;
return;
}
void drawLabels(Graphics g)
{
for (PDBChain chain : pdb.getChains())
{
if (chain.isVisible)
{
for (Bond tmpBond : chain.bonds)
{
if (tmpBond.at1.isSelected)
{
labelAtom(g, tmpBond, 1);
}
if (tmpBond.at2.isSelected)
{
labelAtom(g, tmpBond, 2);
}
}
}
}
}
public void labelAtom(Graphics g, Bond b, int n)
{
g.setFont(font);
g.setColor(Color.red);
if (n == 1)
{
int xstart = (int) (((b.start[0] - centre[0]) * scale)
+ (getWidth() / 2));
int ystart = (int) (((centre[1] - b.start[1]) * scale)
+ (getHeight() / 2));
g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
}
if (n == 2)
{
int xstart = (int) (((b.end[0] - centre[0]) * scale)
+ (getWidth() / 2));
int ystart = (int) (((centre[1] - b.end[1]) * scale)
+ (getHeight() / 2));
g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
}
}
int foundchain = -1;
public Atom findAtom(int x, int y)
{
Atom fatom = null;
foundchain = -1;
for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
PDBChain chain = pdb.getChains().elementAt(ii);
int truex;
Bond tmpBond = null;
if (chain.isVisible)
{
for (Bond bond : chain.bonds)
{
tmpBond = bond;
truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
+ (getWidth() / 2));
if (Math.abs(truex - x) <= 2)
{
int truey = (int) (((centre[1] - tmpBond.start[1]) * scale)
+ (getHeight() / 2));
if (Math.abs(truey - y) <= 2)
{
fatom = tmpBond.at1;
foundchain = ii;
break;
}
}
}
// Still here? Maybe its the last bond
truex = (int) (((tmpBond.end[0] - centre[0]) * scale)
+ (getWidth() / 2));
if (Math.abs(truex - x) <= 2)
{
int truey = (int) (((tmpBond.end[1] - centre[1]) * scale)
+ (getHeight() / 2));
if (Math.abs(truey - y) <= 2)
{
fatom = tmpBond.at2;
foundchain = ii;
break;
}
}
}
if (fatom != null) // )&& chain.ds != null)
{ // dead code? value of chain is either overwritten or discarded
chain = pdb.getChains().elementAt(foundchain);
}
}
return fatom;
}
Bond highlightBond1, highlightBond2;
public void highlightRes(int ii)
{
if (!seqColoursReady)
{
return;
}
if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
{
return;
}
int index = -1;
Bond tmpBond;
for (index = 0; index < mainchain.bonds.size(); index++)
{
tmpBond = mainchain.bonds.elementAt(index);
if (tmpBond.at1.alignmentMapping == ii - 1)
{
if (highlightBond1 != null)
{
highlightBond1.at2.isSelected = false;
}
if (highlightBond2 != null)
{
highlightBond2.at1.isSelected = false;
}
highlightBond1 = null;
highlightBond2 = null;
if (index > 0)
{
highlightBond1 = mainchain.bonds.elementAt(index - 1);
highlightBond1.at2.isSelected = true;
}
if (index != mainchain.bonds.size())
{
highlightBond2 = mainchain.bonds.elementAt(index);
highlightBond2.at1.isSelected = true;
}
break;
}
}
redrawneeded = true;
repaint();
}
public void setAllchainsVisible(boolean b)
{
for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
PDBChain chain = pdb.getChains().elementAt(ii);
chain.isVisible = b;
}
mainchain.isVisible = true;
findCentre();
setupBonds();
}
// ////////////////////////////////
// /StructureListener
@Override
public String[] getStructureFiles()
{
return new String[] { pdbentry.getFile() };
}
String lastMessage;
public void mouseOverStructure(int pdbResNum, String chain)
{
if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
{
ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
}
lastMessage = pdbResNum + chain;
}
StringBuffer resetLastRes = new StringBuffer();
StringBuffer eval = new StringBuffer();
/**
* Highlight the specified atoms in the structure.
*
* @param atoms
*/
@Override
public void highlightAtoms(List atoms)
{
if (!seqColoursReady)
{
return;
}
for (AtomSpec atom : atoms)
{
int atomIndex = atom.getAtomIndex();
if (highlightRes != null
&& highlightRes.contains((atomIndex - 1) + ""))
{
continue;
}
highlightAtom(atomIndex);
}
redrawneeded = true;
repaint();
}
/**
* Highlight the atom at the specified index.
*
* @param atomIndex
*/
protected void highlightAtom(int atomIndex)
{
int index = -1;
Bond tmpBond;
for (index = 0; index < mainchain.bonds.size(); index++)
{
tmpBond = mainchain.bonds.elementAt(index);
if (tmpBond.at1.atomIndex == atomIndex)
{
if (highlightBond1 != null)
{
highlightBond1.at2.isSelected = false;
}
if (highlightBond2 != null)
{
highlightBond2.at1.isSelected = false;
}
highlightBond1 = null;
highlightBond2 = null;
if (index > 0)
{
highlightBond1 = mainchain.bonds.elementAt(index - 1);
highlightBond1.at2.isSelected = true;
}
if (index != mainchain.bonds.size())
{
highlightBond2 = mainchain.bonds.elementAt(index);
highlightBond2.at1.isSelected = true;
}
break;
}
}
}
public Color getColour(int atomIndex, int pdbResNum, String chain,
String pdbfile)
{
return Color.white;
// if (!pdbfile.equals(pdbentry.getFile()))
// return null;
// return new Color(viewer.getAtomArgb(atomIndex));
}
@Override
public void updateColours(Object source)
{
colourBySequence();
redrawneeded = true;
repaint();
}
@Override
public void releaseReferences(Object svl)
{
// TODO Auto-generated method stub
}
@Override
public boolean isListeningFor(SequenceI seq)
{
if (sequence != null)
{
for (SequenceI s : sequence)
{
if (s == seq)
{
return true;
}
}
}
return false;
}
}