-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package MCview;
-
-import java.io.*;
-import java.util.*;
-
-// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-
-public class AppletPDBCanvas
- extends Panel implements MouseListener, MouseMotionListener
-{
-
- MCMatrix idmat = new MCMatrix(3, 3);
- MCMatrix objmat = new MCMatrix(3, 3);
- boolean redrawneeded = true;
- int omx = 0;
- int mx = 0;
- int omy = 0;
- int my = 0;
- public PDBfile pdb;
- 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.appletgui.SeqCanvas seqcanvas;
- public Sequence sequence;
- final StringBuffer mappingDetails = new StringBuffer();
- String appletToolTip = null;
- int toolx, tooly;
- PDBChain mainchain;
- Vector highlightRes;
- boolean pdbAction = false;
- Bond highlightBond1, highlightBond2;
- boolean errorLoading = false;
- boolean seqColoursReady = false;
- jalview.appletgui.FeatureRenderer fr;
-
- public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)
- {
- this.seqcanvas = seqcanvas;
- this.sequence = seq;
-
- seqcanvas.setPDBCanvas(this);
- addKeyListener(new KeyAdapter()
- {
-
- public void keyPressed(KeyEvent evt)
- {
- doKeyPressed(evt);
- }
- });
- }
-
- public void setPDBFile(PDBfile pdb)
- {
- int max = -10;
- int maxchain = -1;
- int pdbstart = 0;
- int pdbend = 0;
- int seqstart = 0;
- int seqend = 0;
- AlignSeq maxAlignseq = null; ;
-
- for (int i = 0; i < pdb.chains.size(); i++)
- {
-
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +
- ( (PDBChain) pdb.chains.elementAt(i)).sequence.
- getSequenceAsString());
- mappingDetails.append("\nNo of residues = " +
- ( (PDBChain) pdb.chains.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,
- ( (PDBChain) pdb.chains.elementAt(i)).sequence,
- "pep");
- as.calcScoreMatrix();
- as.traceAlignment();
- PrintStream ps = new PrintStream(System.out)
- {
- public void print(String x)
- {
- mappingDetails.append(x);
- }
-
- 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;
- maxAlignseq = as;
- }
-
- mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
- mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
- }
-
- mainchain = (PDBChain) pdb.chains.elementAt(maxchain);
-
- mainchain.pdbstart = pdbstart;
- mainchain.pdbend = pdbend;
- mainchain.seqstart = seqstart;
- mainchain.seqend = seqend;
- mainchain.isVisible = true;
- mainchain.makeExactMapping(maxAlignseq, sequence);
- mainchain.transferRESNUMFeatures(sequence, null);
- this.pdb = pdb;
- this.prefsize = new Dimension(getSize().width, getSize().height);
-
- //Initialize the matrices to identity
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- }
- else
- {
- idmat.addElement(i, j, 1);
- objmat.addElement(i, j, 1);
- }
- }
- }
-
- addMouseMotionListener(this);
- addMouseListener(this);
-
- findCentre();
- findWidth();
-
- setupBonds();
-
- scale = findScale();
- }
-
- Vector visiblebonds;
- void setupBonds()
- {
- seqColoursReady = false;
- // Sort the bonds by z coord
- visiblebonds = new Vector();
-
- for (int ii = 0; ii < pdb.chains.size(); ii++)
- {
- if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
- {
- Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
-
- for (int i = 0; i < tmp.size(); i++)
- {
- visiblebonds.addElement(tmp.elementAt(i));
- }
- }
- }
- 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 (int ii = 0; ii < pdb.chains.size(); ii++)
- {
- if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
- {
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
-
- for (int i = 0; i < bonds.size(); i++)
- {
- Bond tmp = (Bond) bonds.elementAt(i);
-
- 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];
- }
- }
- }
- }
-
- width[0] = (float) Math.abs(max[0] - min[0]);
- width[1] = (float) Math.abs(max[1] - min[1]);
- width[2] = (float) 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 (getSize().width != 0)
- {
- width = getSize().width;
- height = getSize().height;
- }
- 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 (int ii = 0; ii < pdb.chains.size(); ii++)
- {
- if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
- {
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
-
- bsize += bonds.size();
-
- for (int i = 0; i < bonds.size(); i++)
- {
- xtot = xtot + ( (Bond) bonds.elementAt(i)).start[0] +
- ( (Bond) bonds.elementAt(i)).end[0];
-
- ytot = ytot + ( (Bond) bonds.elementAt(i)).start[1] +
- ( (Bond) bonds.elementAt(i)).end[1];
-
- ztot = ztot + ( (Bond) bonds.elementAt(i)).start[2] +
- ( (Bond) bonds.elementAt(i)).end[2];
- }
- }
- }
-
- centre[0] = xtot / (2 * (float) bsize);
- centre[1] = ytot / (2 * (float) bsize);
- centre[2] = ztot / (2 * (float) bsize);
- }
-
- public void paint(Graphics g)
- {
-
- if (errorLoading)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, getSize().width, getSize().height);
- g.setColor(Color.black);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading PDB data!!", 50, getSize().height / 2);
- return;
- }
-
- if (!seqColoursReady)
- {
- g.setColor(Color.black);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Fetching PDB data...", 50, getSize().height / 2);
- return;
- }
-
- //Only create the image at the beginning -
- //this saves much memory usage
- if ( (img == null) || (prefsize.width != getSize().width) ||
- (prefsize.height != getSize().height))
- {
-
- try
- {
- prefsize.width = getSize().width;
- prefsize.height = getSize().height;
-
- scale = findScale();
- img = createImage(prefsize.width, prefsize.height);
- ig = img.getGraphics();
-
- redrawneeded = true;
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- if (redrawneeded)
- {
- drawAll(ig, prefsize.width, prefsize.height);
- redrawneeded = false;
- }
- if (appletToolTip != null)
- {
- ig.setColor(Color.red);
- ig.drawString(appletToolTip, toolx, tooly);
- }
-
- g.drawImage(img, 0, 0, this);
-
- pdbAction = false;
- }
-
- public void drawAll(Graphics g, int width, int height)
- {
- ig.setColor(Color.black);
- ig.fillRect(0, 0, width, height);
- drawScene(ig);
- drawLabels(ig);
- }
-
- void setColours(jalview.schemes.ColourSchemeI cs)
- {
- bysequence = false;
- pdb.setColours(cs);
- redrawneeded = true;
- repaint();
- }
-
- public void updateSeqColours()
- {
- if (pdbAction)
- {
- return;
- }
-
- if (bysequence && pdb != null)
- {
- for (int ii = 0; ii < pdb.chains.size(); ii++)
- {
- colourBySequence( (PDBChain) pdb.chains.elementAt(ii));
- }
- }
-
- redrawneeded = true;
- repaint();
- }
-
- int findTrueIndex(int pos)
- {
- // returns the alignment position for a residue
- int j = sequence.getStart();
- int i = 0;
-
- while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) &&
- (j <= pos + 1))
- {
- if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
- {
- j++;
- }
-
- i++;
- }
-
- if (i > 1)
- {
- i--;
- }
-
- if ( (j == sequence.getEnd()) && (j < pos))
- {
- return sequence.getEnd() + 1;
- }
- else
- {
- return i;
- }
- }
-
- // This method has been taken out of PDBChain to allow
- // Applet and Application specific sequence renderers to be used
- void colourBySequence(PDBChain chain)
- {
- boolean showFeatures = false;
-
- if (seqcanvas.getViewport().getShowSequenceFeatures())
- {
- if (fr == null)
- {
- fr = new jalview.appletgui.FeatureRenderer(seqcanvas.getViewport());
- }
- fr.transferSettings(seqcanvas.getFeatureRenderer());
- showFeatures = true;
- }
-
- for (int i = 0; i < chain.bonds.size(); i++)
- {
- Bond tmp = (Bond) chain.bonds.elementAt(i);
- tmp.startCol = Color.lightGray;
- tmp.endCol = Color.lightGray;
- if (chain != mainchain)
- {
- continue;
- }
-
- if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
- (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
- {
-
- int index = findTrueIndex(tmp.at1.alignmentMapping);
- //sequence.findIndex(tmp.at1.alignmentMapping);
- if (index != -1)
- {
- tmp.startCol = seqcanvas.getSequenceRenderer().
- getResidueBoxColour(sequence, index);
-
- if (showFeatures)
- {
- tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
- }
- }
- }
-
- int index = findTrueIndex(tmp.at2.alignmentMapping);
- //sequence.findIndex( tmp.at2.alignmentMapping );
- if (index != -1)
- {
- tmp.endCol = seqcanvas.getSequenceRenderer().
- getResidueBoxColour(sequence, index);
-
- if (showFeatures)
- {
- tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);
- }
- }
- }
- }
-
- Zsort zsort;
- public void drawScene(Graphics g)
- {
- if (zbuffer)
- {
- if (zsort == null)
- {
- zsort = new Zsort();
- }
-
- zsort.Zsort(visiblebonds);
- }
-
- Bond tmpBond = null;
- for (int i = 0; i < visiblebonds.size(); i++)
- {
- tmpBond = (Bond) visiblebonds.elementAt(i);
-
- xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
- (getSize().width / 2));
- ystart = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
- (getSize().height / 2));
-
- xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
- (getSize().width / 2));
- yend = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
- (getSize().height / 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(Color.white);
- drawLine(g, xmid, ymid, xend, yend);
- }
-
- if (highlightBond2 != null && highlightBond2 == tmpBond)
- {
- g.setColor(Color.white);
- 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 doKeyPressed(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();
- }
- }
-
- 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 = (PDBChain) pdb.chains.elementAt(foundchain);
- if (chain == mainchain)
- {
- if (fatom.alignmentMapping != -1)
- {
- if (highlightRes == null)
- {
- highlightRes = new Vector();
- }
-
- if (highlightRes.contains(fatom.alignmentMapping + "" + ""))
- {
- highlightRes.removeElement(fatom.alignmentMapping + "");
- }
- else
- {
- highlightRes.addElement(fatom.alignmentMapping + "");
- }
- }
- }
- }
-
- }
- mx = e.getX();
- my = e.getY();
- omx = mx;
- omy = my;
- dragging = false;
- }
-
- 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 = (PDBChain) pdb.chains.elementAt(foundchain);
- if (chain == mainchain)
- {
- highlightSeqcanvas(fatom.alignmentMapping);
- }
- }
-
- if (fatom != null)
- {
- toolx = e.getX();
- tooly = e.getY();
-
- appletToolTip = chain.id + ":" + fatom.resNumber + " " + fatom.resName;
- redrawneeded = true;
- repaint();
- }
- else
- {
- highlightSeqcanvas( -1);
- appletToolTip = null;
- redrawneeded = true;
- repaint();
- }
- }
-
- void highlightSeqcanvas(int pos)
- {
- SearchResults searchResults = new SearchResults();
- if (highlightRes != null)
- {
- for (int i = 0; i < highlightRes.size(); i++)
- {
- int a = Integer.parseInt(highlightRes.elementAt(
- i).toString()) + 1;
-
- searchResults.addResult(sequence, a, a);
- }
- }
-
- if (pos != -1)
- {
- searchResults.addResult(sequence, pos + 1, pos + 1);
- }
-
- seqcanvas.highlightSearchResults(searchResults);
- }
-
- public void mouseClicked(MouseEvent e)
- {
- }
-
- public void mouseEntered(MouseEvent e)
- {
- }
-
- public void mouseExited(MouseEvent e)
- {
- }
-
- 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( (float) ( (mx - omx)));
- }
- else
- {
- objmat.rotatex( (float) ( (my - omy)));
- objmat.rotatey( (float) ( (omx - mx)));
- }
-
- //Alter the bonds
- for (int ii = 0; ii < pdb.chains.size(); ii++)
- {
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
-
- for (int i = 0; i < bonds.size(); i++)
- {
- Bond tmpBond = (Bond) bonds.elementAt(i);
-
- //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();
- }
-
- public void mouseReleased(MouseEvent evt)
- {
- dragging = false;
- return;
- }
-
- void drawLabels(Graphics g)
- {
-
- for (int ii = 0; ii < pdb.chains.size(); ii++)
- {
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
-
- if (chain.isVisible)
- {
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
-
- for (int i = 0; i < bonds.size(); i++)
- {
- Bond tmpBond = (Bond) bonds.elementAt(i);
-
- 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);
-
- if (n == 1)
- {
- int xstart = (int) ( ( (b.start[0] - centre[0]) * scale) +
- (getSize().width / 2));
- int ystart = (int) ( ( (b.start[1] - centre[1]) * scale) +
- (getSize().height / 2));
-
- g.setColor(Color.red);
- g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
- }
-
- if (n == 2)
- {
- int xstart = (int) ( ( (b.end[0] - centre[0]) * scale) +
- (getSize().width / 2));
- int ystart = (int) ( ( (b.end[1] - centre[1]) * scale) +
- (getSize().height / 2));
-
- g.setColor(Color.red);
- 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.chains.size(); ii++)
- {
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
- int truex;
- Bond tmpBond = null;
-
- if (chain.isVisible)
- {
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
-
- for (int i = 0; i < bonds.size(); i++)
- {
- tmpBond = (Bond) bonds.elementAt(i);
-
- truex = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
- (getSize().width / 2));
-
- if (Math.abs(truex - x) <= 2)
- {
- int truey = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
- (getSize().height / 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) +
- (getSize().width / 2));
-
- if (Math.abs(truex - x) <= 2)
- {
- int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
- (getSize().height / 2));
-
- if (Math.abs(truey - y) <= 2)
- {
- fatom = tmpBond.at2;
- foundchain = ii;
- break;
- }
- }
-
- }
-
- if (fatom != null) //)&& chain.ds != null)
- {
- chain = (PDBChain) pdb.chains.elementAt(foundchain);
- }
- }
-
- return fatom;
- }
-
- public void update(Graphics g)
- {
- paint(g);
- }
-
- 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 = (Bond) 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 = (Bond) mainchain.bonds.elementAt(index - 1);
- highlightBond1.at2.isSelected = true;
- }
-
- if (index != mainchain.bonds.size())
- {
- highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
- highlightBond2.at1.isSelected = true;
- }
-
- break;
- }
- }
-
- redrawneeded = true;
- repaint();
- }
-
- public void setAllchainsVisible(boolean b)
- {
- for (int ii = 0; ii < pdb.chains.size(); ii++)
- {
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
- chain.isVisible = b;
- }
- mainchain.isVisible = true;
- findCentre();
- setupBonds();
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package MCview;\r
+\r
+import java.io.*;\r
+import java.util.*;\r
+\r
+// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+\r
+import jalview.appletgui.*;\r
+import jalview.structure.*;\r
+\r
+public class AppletPDBCanvas\r
+ extends Panel implements MouseListener, MouseMotionListener, StructureListener\r
+{\r
+\r
+ MCMatrix idmat = new MCMatrix(3, 3);\r
+ MCMatrix objmat = new MCMatrix(3, 3);\r
+ boolean redrawneeded = true;\r
+ int omx = 0;\r
+ int mx = 0;\r
+ int omy = 0;\r
+ int my = 0;\r
+ public PDBfile pdb;\r
+ PDBEntry pdbentry;\r
+ int bsize;\r
+ Image img;\r
+ Graphics ig;\r
+ Dimension prefsize;\r
+ float[] centre = new float[3];\r
+ float[] width = new float[3];\r
+ float maxwidth;\r
+ float scale;\r
+ String inStr;\r
+ String inType;\r
+ boolean bysequence = true;\r
+ boolean depthcue = true;\r
+ boolean wire = false;\r
+ boolean bymolecule = false;\r
+ boolean zbuffer = true;\r
+ boolean dragging;\r
+ int xstart;\r
+ int xend;\r
+ int ystart;\r
+ int yend;\r
+ int xmid;\r
+ int ymid;\r
+ Font font = new Font("Helvetica", Font.PLAIN, 10);\r
+ public SequenceI [] sequence;\r
+ final StringBuffer mappingDetails = new StringBuffer();\r
+ String appletToolTip = null;\r
+ int toolx, tooly;\r
+ PDBChain mainchain;\r
+ Vector highlightRes;\r
+ boolean pdbAction = false;\r
+ Bond highlightBond1, highlightBond2;\r
+ boolean errorLoading = false;\r
+ boolean seqColoursReady = false;\r
+ FeatureRenderer fr;\r
+ AlignmentPanel ap;\r
+ StructureSelectionManager ssm;\r
+\r
+ public AppletPDBCanvas(PDBEntry pdbentry,\r
+ SequenceI[] seq,\r
+ AlignmentPanel ap,\r
+ String protocol)\r
+\r
+ {\r
+ this.ap = ap;\r
+ this.pdbentry = pdbentry;\r
+ this.sequence = seq;\r
+\r
+ ssm = StructureSelectionManager.getStructureSelectionManager();\r
+\r
+ try{\r
+ pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ return;\r
+ }\r
+\r
+ pdbentry.setId(pdb.id);\r
+\r
+ ssm.addStructureViewerListener(this);\r
+\r
+ colourBySequence(ap.getSequenceRenderer(),\r
+ ap.av.getShowSequenceFeatures() ?\r
+ ap.getFeatureRenderer() : null);\r
+\r
+ int max = -10;\r
+ int maxchain = -1;\r
+ int pdbstart = 0;\r
+ int pdbend = 0;\r
+ int seqstart = 0;\r
+ int seqend = 0;\r
+ AlignSeq maxAlignseq = null;\r
+\r
+ //JUST DEAL WITH ONE SEQUENCE FOR NOW\r
+ SequenceI sequence = seq[0];\r
+\r
+ for (int i = 0; i < pdb.chains.size(); i++)\r
+ {\r
+\r
+ mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +\r
+ ( (PDBChain) pdb.chains.elementAt(i)).sequence.\r
+ getSequenceAsString());\r
+ mappingDetails.append("\nNo of residues = " +\r
+ ( (PDBChain) pdb.chains.elementAt(i)).residues.size() +\r
+ "\n\n");\r
+\r
+ // Now lets compare the sequences to get\r
+ // the start and end points.\r
+ // Align the sequence to the pdb\r
+ AlignSeq as = new AlignSeq(sequence,\r
+ ( (PDBChain) pdb.chains.elementAt(i)).sequence,\r
+ "pep");\r
+ as.calcScoreMatrix();\r
+ as.traceAlignment();\r
+ PrintStream ps = new PrintStream(System.out)\r
+ {\r
+ public void print(String x)\r
+ {\r
+ mappingDetails.append(x);\r
+ }\r
+\r
+ public void println()\r
+ {\r
+ mappingDetails.append("\n");\r
+ }\r
+ };\r
+\r
+ as.printAlignment(ps);\r
+\r
+ if (as.maxscore > max)\r
+ {\r
+ max = as.maxscore;\r
+ maxchain = i;\r
+\r
+ pdbstart = as.seq2start;\r
+ pdbend = as.seq2end;\r
+ seqstart = as.seq1start + sequence.getStart() - 1;\r
+ seqend = as.seq1end + sequence.getEnd() - 1;\r
+ maxAlignseq = as;\r
+ }\r
+\r
+ mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);\r
+ mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);\r
+ }\r
+\r
+ mainchain = (PDBChain) pdb.chains.elementAt(maxchain);\r
+\r
+ mainchain.pdbstart = pdbstart;\r
+ mainchain.pdbend = pdbend;\r
+ mainchain.seqstart = seqstart;\r
+ mainchain.seqend = seqend;\r
+ mainchain.isVisible = true;\r
+ // mainchain.makeExactMapping(maxAlignseq, sequence);\r
+ // mainchain.transferRESNUMFeatures(sequence, null);\r
+ this.pdb = pdb;\r
+ this.prefsize = new Dimension(getSize().width, getSize().height);\r
+\r
+ //Initialize the matrices to identity\r
+ for (int i = 0; i < 3; i++)\r
+ {\r
+ for (int j = 0; j < 3; j++)\r
+ {\r
+ if (i != j)\r
+ {\r
+ idmat.addElement(i, j, 0);\r
+ objmat.addElement(i, j, 0);\r
+ }\r
+ else\r
+ {\r
+ idmat.addElement(i, j, 1);\r
+ objmat.addElement(i, j, 1);\r
+ }\r
+ }\r
+ }\r
+\r
+ addMouseMotionListener(this);\r
+ addMouseListener(this);\r
+\r
+ addKeyListener(new KeyAdapter()\r
+ {\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ doKeyPressed(evt);\r
+ }\r
+ });\r
+\r
+ findCentre();\r
+ findWidth();\r
+\r
+ setupBonds();\r
+\r
+ scale = findScale();\r
+ }\r
+\r
+ Vector visiblebonds;\r
+ void setupBonds()\r
+ {\r
+ seqColoursReady = false;\r
+ // Sort the bonds by z coord\r
+ visiblebonds = new Vector();\r
+\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+ {\r
+ if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)\r
+ {\r
+ Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i = 0; i < tmp.size(); i++)\r
+ {\r
+ visiblebonds.addElement(tmp.elementAt(i));\r
+ }\r
+ }\r
+ }\r
+ seqColoursReady = true;\r
+ colourBySequence(ap.getSequenceRenderer(),\r
+ ap.av.getShowSequenceFeatures() ?\r
+ ap.getFeatureRenderer() : null);\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
+\r
+ public void findWidth()\r
+ {\r
+ float[] max = new float[3];\r
+ float[] min = new float[3];\r
+\r
+ max[0] = (float) - 1e30;\r
+ max[1] = (float) - 1e30;\r
+ max[2] = (float) - 1e30;\r
+\r
+ min[0] = (float) 1e30;\r
+ min[1] = (float) 1e30;\r
+ min[2] = (float) 1e30;\r
+\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+ {\r
+ if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)\r
+ {\r
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i = 0; i < bonds.size(); i++)\r
+ {\r
+ Bond tmp = (Bond) bonds.elementAt(i);\r
+\r
+ if (tmp.start[0] >= max[0])\r
+ {\r
+ max[0] = tmp.start[0];\r
+ }\r
+\r
+ if (tmp.start[1] >= max[1])\r
+ {\r
+ max[1] = tmp.start[1];\r
+ }\r
+\r
+ if (tmp.start[2] >= max[2])\r
+ {\r
+ max[2] = tmp.start[2];\r
+ }\r
+\r
+ if (tmp.start[0] <= min[0])\r
+ {\r
+ min[0] = tmp.start[0];\r
+ }\r
+\r
+ if (tmp.start[1] <= min[1])\r
+ {\r
+ min[1] = tmp.start[1];\r
+ }\r
+\r
+ if (tmp.start[2] <= min[2])\r
+ {\r
+ min[2] = tmp.start[2];\r
+ }\r
+\r
+ if (tmp.end[0] >= max[0])\r
+ {\r
+ max[0] = tmp.end[0];\r
+ }\r
+\r
+ if (tmp.end[1] >= max[1])\r
+ {\r
+ max[1] = tmp.end[1];\r
+ }\r
+\r
+ if (tmp.end[2] >= max[2])\r
+ {\r
+ max[2] = tmp.end[2];\r
+ }\r
+\r
+ if (tmp.end[0] <= min[0])\r
+ {\r
+ min[0] = tmp.end[0];\r
+ }\r
+\r
+ if (tmp.end[1] <= min[1])\r
+ {\r
+ min[1] = tmp.end[1];\r
+ }\r
+\r
+ if (tmp.end[2] <= min[2])\r
+ {\r
+ min[2] = tmp.end[2];\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ width[0] = (float) Math.abs(max[0] - min[0]);\r
+ width[1] = (float) Math.abs(max[1] - min[1]);\r
+ width[2] = (float) Math.abs(max[2] - min[2]);\r
+\r
+ maxwidth = width[0];\r
+\r
+ if (width[1] > width[0])\r
+ {\r
+ maxwidth = width[1];\r
+ }\r
+\r
+ if (width[2] > width[1])\r
+ {\r
+ maxwidth = width[2];\r
+ }\r
+\r
+ // System.out.println("Maxwidth = " + maxwidth);\r
+ }\r
+\r
+ public float findScale()\r
+ {\r
+ int dim;\r
+ int width;\r
+ int height;\r
+\r
+ if (getSize().width != 0)\r
+ {\r
+ width = getSize().width;\r
+ height = getSize().height;\r
+ }\r
+ else\r
+ {\r
+ width = prefsize.width;\r
+ height = prefsize.height;\r
+ }\r
+\r
+ if (width < height)\r
+ {\r
+ dim = width;\r
+ }\r
+ else\r
+ {\r
+ dim = height;\r
+ }\r
+\r
+ return (float) (dim / (1.5d * maxwidth));\r
+ }\r
+\r
+ public void findCentre()\r
+ {\r
+ float xtot = 0;\r
+ float ytot = 0;\r
+ float ztot = 0;\r
+\r
+ int bsize = 0;\r
+\r
+ //Find centre coordinate\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+ {\r
+ if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)\r
+ {\r
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
+\r
+ bsize += bonds.size();\r
+\r
+ for (int i = 0; i < bonds.size(); i++)\r
+ {\r
+ xtot = xtot + ( (Bond) bonds.elementAt(i)).start[0] +\r
+ ( (Bond) bonds.elementAt(i)).end[0];\r
+\r
+ ytot = ytot + ( (Bond) bonds.elementAt(i)).start[1] +\r
+ ( (Bond) bonds.elementAt(i)).end[1];\r
+\r
+ ztot = ztot + ( (Bond) bonds.elementAt(i)).start[2] +\r
+ ( (Bond) bonds.elementAt(i)).end[2];\r
+ }\r
+ }\r
+ }\r
+\r
+ centre[0] = xtot / (2 * (float) bsize);\r
+ centre[1] = ytot / (2 * (float) bsize);\r
+ centre[2] = ztot / (2 * (float) bsize);\r
+ }\r
+\r
+ public void paint(Graphics g)\r
+ {\r
+\r
+ if (errorLoading)\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setColor(Color.black);\r
+ g.setFont(new Font("Verdana", Font.BOLD, 14));\r
+ g.drawString("Error loading PDB data!!", 50, getSize().height / 2);\r
+ return;\r
+ }\r
+\r
+ if (!seqColoursReady)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.setFont(new Font("Verdana", Font.BOLD, 14));\r
+ g.drawString("Fetching PDB data...", 50, getSize().height / 2);\r
+ return;\r
+ }\r
+\r
+ //Only create the image at the beginning -\r
+ //this saves much memory usage\r
+ if ( (img == null) || (prefsize.width != getSize().width) ||\r
+ (prefsize.height != getSize().height))\r
+ {\r
+\r
+ try\r
+ {\r
+ prefsize.width = getSize().width;\r
+ prefsize.height = getSize().height;\r
+\r
+ scale = findScale();\r
+ img = createImage(prefsize.width, prefsize.height);\r
+ ig = img.getGraphics();\r
+\r
+ redrawneeded = true;\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ if (redrawneeded)\r
+ {\r
+ drawAll(ig, prefsize.width, prefsize.height);\r
+ redrawneeded = false;\r
+ }\r
+ if (appletToolTip != null)\r
+ {\r
+ ig.setColor(Color.red);\r
+ ig.drawString(appletToolTip, toolx, tooly);\r
+ }\r
+\r
+ g.drawImage(img, 0, 0, this);\r
+\r
+ pdbAction = false;\r
+ }\r
+\r
+ public void drawAll(Graphics g, int width, int height)\r
+ {\r
+ ig.setColor(Color.black);\r
+ ig.fillRect(0, 0, width, height);\r
+ drawScene(ig);\r
+ drawLabels(ig);\r
+ }\r
+\r
+ public void setColours(jalview.schemes.ColourSchemeI cs)\r
+ {\r
+ bysequence = false;\r
+ pdb.setColours(cs);\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
+\r
+\r
+\r
+ // This method has been taken out of PDBChain to allow\r
+ // Applet and Application specific sequence renderers to be used\r
+ void colourBySequence(SequenceRenderer sr, FeatureRenderer fr)\r
+ {\r
+ StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());\r
+\r
+ boolean showFeatures = false;\r
+ if (fr!=null)\r
+ {\r
+ if (fr == null)\r
+ {\r
+ fr = new jalview.appletgui.FeatureRenderer(ap.av);\r
+ }\r
+ fr.transferSettings(fr);\r
+ showFeatures = true;\r
+ }\r
+\r
+ PDBChain chain;\r
+ if (bysequence && pdb != null)\r
+ {\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+ {\r
+ chain = (PDBChain) pdb.chains.elementAt(ii);\r
+\r
+ for (int i = 0; i < chain.bonds.size(); i++)\r
+ {\r
+ Bond tmp = (Bond) chain.bonds.elementAt(i);\r
+ tmp.startCol = Color.lightGray;\r
+ tmp.endCol = Color.lightGray;\r
+ if (chain != mainchain)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ for (int s = 0; s < sequence.length; s++)\r
+ {\r
+ for (int m = 0; m < mapping.length; m++)\r
+ {\r
+ if (mapping[m].getSequence() == sequence[s])\r
+ {\r
+ int pos = mapping[m].getSeqPos(tmp.at1.resNumber)-1;\r
+ if (pos > 0)\r
+ {\r
+ pos = sequence[s].findIndex(pos);\r
+ tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);\r
+ if (showFeatures)\r
+ {\r
+ tmp.startCol = fr.findFeatureColour(tmp.startCol,\r
+ sequence[s],\r
+ pos);\r
+ }\r
+ }\r
+ pos = mapping[m].getSeqPos(tmp.at2.resNumber)-1;\r
+ if (pos > 0)\r
+ {\r
+ pos = sequence[s].findIndex(pos);\r
+ tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);\r
+ if (showFeatures)\r
+ {\r
+ tmp.endCol = fr.findFeatureColour(tmp.endCol,\r
+ sequence[s],\r
+ pos);\r
+ }\r
+ }\r
+\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ Zsort zsort;\r
+ public void drawScene(Graphics g)\r
+ {\r
+ if (zbuffer)\r
+ {\r
+ if (zsort == null)\r
+ {\r
+ zsort = new Zsort();\r
+ }\r
+\r
+ zsort.Zsort(visiblebonds);\r
+ }\r
+\r
+ Bond tmpBond = null;\r
+ for (int i = 0; i < visiblebonds.size(); i++)\r
+ {\r
+ tmpBond = (Bond) visiblebonds.elementAt(i);\r
+\r
+ xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +\r
+ (getSize().width / 2));\r
+ ystart = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +\r
+ (getSize().height / 2));\r
+\r
+ xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +\r
+ (getSize().width / 2));\r
+ yend = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +\r
+ (getSize().height / 2));\r
+\r
+ xmid = (xend + xstart) / 2;\r
+ ymid = (yend + ystart) / 2;\r
+\r
+ if (depthcue && !bymolecule)\r
+ {\r
+ if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))\r
+ {\r
+ g.setColor(tmpBond.startCol.darker().darker());\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+\r
+ g.setColor(tmpBond.endCol.darker().darker());\r
+ drawLine(g, xmid, ymid, xend, yend);\r
+ }\r
+ else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))\r
+ {\r
+ g.setColor(tmpBond.startCol.darker());\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+\r
+ g.setColor(tmpBond.endCol.darker());\r
+ drawLine(g, xmid, ymid, xend, yend);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(tmpBond.startCol);\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+\r
+ g.setColor(tmpBond.endCol);\r
+ drawLine(g, xmid, ymid, xend, yend);\r
+ }\r
+\r
+ }\r
+ else if (depthcue && bymolecule)\r
+ {\r
+ if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))\r
+ {\r
+ g.setColor(Color.green.darker().darker());\r
+ drawLine(g, xstart, ystart, xend, yend);\r
+ }\r
+ else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))\r
+ {\r
+ g.setColor(Color.green.darker());\r
+ drawLine(g, xstart, ystart, xend, yend);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(Color.green);\r
+ drawLine(g, xstart, ystart, xend, yend);\r
+ }\r
+ }\r
+ else if (!depthcue && !bymolecule)\r
+ {\r
+ g.setColor(tmpBond.startCol);\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+ g.setColor(tmpBond.endCol);\r
+ drawLine(g, xmid, ymid, xend, yend);\r
+ }\r
+ else\r
+ {\r
+ drawLine(g, xstart, ystart, xend, yend);\r
+ }\r
+\r
+ if (highlightBond1 != null && highlightBond1 == tmpBond)\r
+ {\r
+ g.setColor(Color.white);\r
+ drawLine(g, xmid, ymid, xend, yend);\r
+ }\r
+\r
+ if (highlightBond2 != null && highlightBond2 == tmpBond)\r
+ {\r
+ g.setColor(Color.white);\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ public void drawLine(Graphics g, int x1, int y1, int x2, int y2)\r
+ {\r
+ if (!wire)\r
+ {\r
+ if ( ( (float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)\r
+ {\r
+ g.drawLine(x1, y1, x2, y2);\r
+ g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);\r
+ g.drawLine(x1, y1 - 1, x2, y2 - 1);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(g.getColor().brighter());\r
+ g.drawLine(x1, y1, x2, y2);\r
+ g.drawLine(x1 + 1, y1, x2 + 1, y2);\r
+ g.drawLine(x1 - 1, y1, x2 - 1, y2);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ g.drawLine(x1, y1, x2, y2);\r
+ }\r
+ }\r
+\r
+ public Dimension minimumsize()\r
+ {\r
+ return prefsize;\r
+ }\r
+\r
+ public Dimension preferredsize()\r
+ {\r
+ return prefsize;\r
+ }\r
+\r
+ public void doKeyPressed(KeyEvent evt)\r
+ {\r
+ if (evt.getKeyCode() == KeyEvent.VK_UP)\r
+ {\r
+ scale = (float) (scale * 1.1);\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
+ else if (evt.getKeyCode() == KeyEvent.VK_DOWN)\r
+ {\r
+ scale = (float) (scale * 0.9);\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
+ }\r
+\r
+ public void mousePressed(MouseEvent e)\r
+ {\r
+ pdbAction = true;\r
+ Atom fatom = findAtom(e.getX(), e.getY());\r
+ if (fatom != null)\r
+ {\r
+ fatom.isSelected = !fatom.isSelected;\r
+\r
+ redrawneeded = true;\r
+ repaint();\r
+ if (foundchain != -1)\r
+ {\r
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
+ if (chain == mainchain)\r
+ {\r
+ if (fatom.alignmentMapping != -1)\r
+ {\r
+ if (highlightRes == null)\r
+ {\r
+ highlightRes = new Vector();\r
+ }\r
+\r
+ if (highlightRes.contains(fatom.alignmentMapping + "" + ""))\r
+ {\r
+ highlightRes.removeElement(fatom.alignmentMapping + "");\r
+ }\r
+ else\r
+ {\r
+ highlightRes.addElement(fatom.alignmentMapping + "");\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+ mx = e.getX();\r
+ my = e.getY();\r
+ omx = mx;\r
+ omy = my;\r
+ dragging = false;\r
+ }\r
+\r
+ public void mouseMoved(MouseEvent e)\r
+ {\r
+ pdbAction = true;\r
+ if (highlightBond1 != null)\r
+ {\r
+ highlightBond1.at2.isSelected = false;\r
+ highlightBond2.at1.isSelected = false;\r
+ highlightBond1 = null;\r
+ highlightBond2 = null;\r
+ }\r
+\r
+ Atom fatom = findAtom(e.getX(), e.getY());\r
+\r
+ PDBChain chain = null;\r
+ if (foundchain != -1)\r
+ {\r
+ chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
+ if (chain == mainchain)\r
+ {\r
+ mouseOverStructure(fatom.resNumber, chain.id);\r
+ }\r
+ }\r
+\r
+ if (fatom != null)\r
+ {\r
+ toolx = e.getX();\r
+ tooly = e.getY();\r
+\r
+ appletToolTip = chain.id + ":" + fatom.resNumber + " " + fatom.resName;\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
+ else\r
+ {\r
+ mouseOverStructure(-1, chain!=null?chain.id:null);\r
+ appletToolTip = null;\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent e)\r
+ {\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent e)\r
+ {\r
+ }\r
+\r
+ public void mouseExited(MouseEvent e)\r
+ {\r
+ }\r
+\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ int x = evt.getX();\r
+ int y = evt.getY();\r
+ mx = x;\r
+ my = y;\r
+\r
+ MCMatrix objmat = new MCMatrix(3, 3);\r
+ objmat.setIdentity();\r
+\r
+ if ( (evt.getModifiers() & Event.META_MASK) != 0)\r
+ {\r
+ objmat.rotatez( (float) ( (mx - omx)));\r
+ }\r
+ else\r
+ {\r
+ objmat.rotatex( (float) ( (my - omy)));\r
+ objmat.rotatey( (float) ( (omx - mx)));\r
+ }\r
+\r
+ //Alter the bonds\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+ {\r
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i = 0; i < bonds.size(); i++)\r
+ {\r
+ Bond tmpBond = (Bond) bonds.elementAt(i);\r
+\r
+ //Translate the bond so the centre is 0,0,0\r
+ tmpBond.translate( -centre[0], -centre[1], -centre[2]);\r
+\r
+ //Now apply the rotation matrix\r
+ tmpBond.start = objmat.vectorMultiply(tmpBond.start);\r
+ tmpBond.end = objmat.vectorMultiply(tmpBond.end);\r
+\r
+ //Now translate back again\r
+ tmpBond.translate(centre[0], centre[1], centre[2]);\r
+ }\r
+ }\r
+\r
+ objmat = null;\r
+\r
+ omx = mx;\r
+ omy = my;\r
+\r
+ dragging = true;\r
+\r
+ redrawneeded = true;\r
+\r
+ repaint();\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ dragging = false;\r
+ return;\r
+ }\r
+\r
+ void drawLabels(Graphics g)\r
+ {\r
+\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+ {\r
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
+\r
+ if (chain.isVisible)\r
+ {\r
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i = 0; i < bonds.size(); i++)\r
+ {\r
+ Bond tmpBond = (Bond) bonds.elementAt(i);\r
+\r
+ if (tmpBond.at1.isSelected)\r
+ {\r
+ labelAtom(g, tmpBond, 1);\r
+ }\r
+\r
+ if (tmpBond.at2.isSelected)\r
+ {\r
+\r
+ labelAtom(g, tmpBond, 2);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ public void labelAtom(Graphics g, Bond b, int n)\r
+ {\r
+ g.setFont(font);\r
+\r
+ if (n == 1)\r
+ {\r
+ int xstart = (int) ( ( (b.start[0] - centre[0]) * scale) +\r
+ (getSize().width / 2));\r
+ int ystart = (int) ( ( (b.start[1] - centre[1]) * scale) +\r
+ (getSize().height / 2));\r
+\r
+ g.setColor(Color.red);\r
+ g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);\r
+ }\r
+\r
+ if (n == 2)\r
+ {\r
+ int xstart = (int) ( ( (b.end[0] - centre[0]) * scale) +\r
+ (getSize().width / 2));\r
+ int ystart = (int) ( ( (b.end[1] - centre[1]) * scale) +\r
+ (getSize().height / 2));\r
+\r
+ g.setColor(Color.red);\r
+ g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);\r
+ }\r
+ }\r
+\r
+ int foundchain = -1;\r
+ public Atom findAtom(int x, int y)\r
+ {\r
+ Atom fatom = null;\r
+\r
+ foundchain = -1;\r
+\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+ {\r
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
+ int truex;\r
+ Bond tmpBond = null;\r
+\r
+ if (chain.isVisible)\r
+ {\r
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i = 0; i < bonds.size(); i++)\r
+ {\r
+ tmpBond = (Bond) bonds.elementAt(i);\r
+\r
+ truex = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +\r
+ (getSize().width / 2));\r
+\r
+ if (Math.abs(truex - x) <= 2)\r
+ {\r
+ int truey = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +\r
+ (getSize().height / 2));\r
+\r
+ if (Math.abs(truey - y) <= 2)\r
+ {\r
+ fatom = tmpBond.at1;\r
+ foundchain = ii;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ // Still here? Maybe its the last bond\r
+\r
+ truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +\r
+ (getSize().width / 2));\r
+\r
+ if (Math.abs(truex - x) <= 2)\r
+ {\r
+ int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +\r
+ (getSize().height / 2));\r
+\r
+ if (Math.abs(truey - y) <= 2)\r
+ {\r
+ fatom = tmpBond.at2;\r
+ foundchain = ii;\r
+ break;\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ if (fatom != null) //)&& chain.ds != null)\r
+ {\r
+ chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
+ }\r
+ }\r
+\r
+ return fatom;\r
+ }\r
+\r
+ public void update(Graphics g)\r
+ {\r
+ paint(g);\r
+ }\r
+\r
+ public void highlightRes(int ii)\r
+ {\r
+ if (!seqColoursReady)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (highlightRes != null\r
+ && highlightRes.contains( (ii - 1) + ""))\r
+ {\r
+ return;\r
+ }\r
+\r
+ int index = -1;\r
+ Bond tmpBond;\r
+ for (index = 0; index < mainchain.bonds.size(); index++)\r
+ {\r
+ tmpBond = (Bond) mainchain.bonds.elementAt(index);\r
+ if (tmpBond.at1.alignmentMapping == ii - 1)\r
+ {\r
+ if (highlightBond1 != null)\r
+ {\r
+ highlightBond1.at2.isSelected = false;\r
+ }\r
+\r
+ if (highlightBond2 != null)\r
+ {\r
+ highlightBond2.at1.isSelected = false;\r
+ }\r
+\r
+ highlightBond1 = null;\r
+ highlightBond2 = null;\r
+\r
+ if (index > 0)\r
+ {\r
+ highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);\r
+ highlightBond1.at2.isSelected = true;\r
+ }\r
+\r
+ if (index != mainchain.bonds.size())\r
+ {\r
+ highlightBond2 = (Bond) mainchain.bonds.elementAt(index);\r
+ highlightBond2.at1.isSelected = true;\r
+ }\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
+\r
+ public void setAllchainsVisible(boolean b)\r
+ {\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+ {\r
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
+ chain.isVisible = b;\r
+ }\r
+ mainchain.isVisible = true;\r
+ findCentre();\r
+ setupBonds();\r
+ }\r
+\r
+\r
+ //////////////////////////////////\r
+ ///StructureListener\r
+ public String getPdbFile()\r
+ {\r
+ return "???";\r
+ }\r
+\r
+\r
+ String lastMessage;\r
+ public void mouseOverStructure(int pdbResNum, String chain)\r
+ {\r
+ if (lastMessage == null || !lastMessage.equals(pdbResNum+chain))\r
+ ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());\r
+\r
+ lastMessage = pdbResNum+chain;\r
+ }\r
+\r
+ StringBuffer resetLastRes = new StringBuffer();\r
+ StringBuffer eval = new StringBuffer();\r
+\r
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)\r
+ {\r
+ if (!seqColoursReady)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (highlightRes != null\r
+ && highlightRes.contains( (atomIndex - 1) + ""))\r
+ {\r
+ return;\r
+ }\r
+\r
+ int index = -1;\r
+ Bond tmpBond;\r
+ for (index = 0; index < mainchain.bonds.size(); index++)\r
+ {\r
+ tmpBond = (Bond) mainchain.bonds.elementAt(index);\r
+ if (tmpBond.at1.atomIndex == atomIndex)\r
+ {\r
+ if (highlightBond1 != null)\r
+ {\r
+ highlightBond1.at2.isSelected = false;\r
+ }\r
+\r
+ if (highlightBond2 != null)\r
+ {\r
+ highlightBond2.at1.isSelected = false;\r
+ }\r
+\r
+ highlightBond1 = null;\r
+ highlightBond2 = null;\r
+\r
+ if (index > 0)\r
+ {\r
+ highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);\r
+ highlightBond1.at2.isSelected = true;\r
+ }\r
+\r
+ if (index != mainchain.bonds.size())\r
+ {\r
+ highlightBond2 = (Bond) mainchain.bonds.elementAt(index);\r
+ highlightBond2.at1.isSelected = true;\r
+ }\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
+\r
+ public void updateColours(Object source)\r
+ {\r
+ AlignmentPanel ap = (AlignmentPanel) source;\r
+ colourBySequence(ap.getSequenceRenderer(),\r
+ ap.av.getShowSequenceFeatures() ?\r
+ ap.getFeatureRenderer() : null);\r
+ redrawneeded = true;\r
+ repaint();\r
+ }\r
+\r
+\r
+}\r
git://source.jalview.org / jalview.git / commitdiff