--- /dev/null
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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<String> 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<Bond> visiblebonds;
+
+ void setupBonds()
+ {
+ seqColoursReady = false;
+ // Sort the bonds by z coord
+ visiblebonds = new Vector<Bond>();
+
+ 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<String>();
+ }
+
+ 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<AtomSpec> 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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff