+++ /dev/null
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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 jalview.analysis.AlignSeq;
-
-import jalview.datamodel.*;
-
-// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
-import java.awt.*;
-import java.awt.event.*;
-
-import java.io.*;
-
-import java.util.*;
-
-
-
-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();
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff