From 28c093f681b769feb7b69bd4cbe309d580ef6179 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Mon, 14 Nov 2005 18:21:17 +0000 Subject: [PATCH] Applet PDB viewer --- src/MCview/AppletPDBCanvas.java | 782 +++++++++++++++++++++++++++++++++++++++ src/MCview/AppletPDBViewer.java | 236 ++++++++++++ 2 files changed, 1018 insertions(+) create mode 100755 src/MCview/AppletPDBCanvas.java create mode 100755 src/MCview/AppletPDBViewer.java diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java new file mode 100755 index 0000000..478dd45 --- /dev/null +++ b/src/MCview/AppletPDBCanvas.java @@ -0,0 +1,782 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 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.SequenceRenderer sr; + jalview.appletgui.FeatureRenderer fr; + jalview.appletgui.SeqCanvas seqcanvas; + Sequence sequence; + final StringBuffer mappingDetails = new StringBuffer(); + String appletToolTip = null; + int toolx, tooly; + + public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq) + { + this.seqcanvas = seqcanvas; + this.sequence = seq; + sr = seqcanvas.getSequenceRenderer(); + fr = seqcanvas.getFeatureRenderer(); + + seqcanvas.setPDBViewer(this); + addKeyListener(new KeyAdapter() + { + + public void keyPressed(KeyEvent evt) + { + doKeyPressed(evt); + } + }); + + } + + public void setPDBFile(PDBfile pdb) + { + this.sr = sr; + this.fr = fr; + int max = -10; + int maxchain = -1; + int pdbstart = 0; + int pdbend = 0; + int seqstart = 0; + int seqend = 0; + + for (int i = 0; i < pdb.chains.size(); i++) + { + + mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + ((PDBChain) pdb.chains.elementAt(i)).sequence.getSequence()); + 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; + } + + mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend); + mappingDetails.append("\nSEQ start/end "+ seqstart + " " + seqend); + } + + ((PDBChain) pdb.chains.elementAt(maxchain)).pdbstart = pdbstart; + ((PDBChain) pdb.chains.elementAt(maxchain)).pdbend = pdbend; + ((PDBChain) pdb.chains.elementAt(maxchain)).seqstart = seqstart; + ((PDBChain) pdb.chains.elementAt(maxchain)).seqend = seqend; + ((PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true; + ((PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence; + + 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); + + /* + SequenceGroup sg = new SequenceGroup("PDB", + null, true,true,false, + sequence.findIndex(seqstart-1), + sequence.findIndex(seqend-1)); + sg.addSequence(sequence, false); + sg.setOutlineColour(Color.black); + seqcanvas.getViewport().getAlignment().addGroup(sg); + */ + + findCentre(); + findWidth(); + + scale = findScale(); + + updateSeqColours(); + } + + public void deleteBonds() { + scale = 0; + maxwidth = 0; + + width[0] = 0; + width[1] = 0; + width[2] = 0; + + centre[0] = 0; + centre[1] = 0; + centre[2] = 0; + + for (int i = 0; i < pdb.chains.size(); i++) { + ((PDBChain) pdb.chains.elementAt(i)).bonds = null; + } + } + + 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(pdb==null) + { + g.setColor(Color.black); + g.setFont(new Font("Verdana", Font.BOLD, 14)); + g.drawString("Error Parsing Pasted 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)) { + prefsize.width = getSize().width; + prefsize.height = getSize().height; + + scale = findScale(); + img = createImage(prefsize.width, prefsize.height); + ig = img.getGraphics(); + + redrawneeded = true; + } + + + 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); + + + } + + public void drawAll(Graphics g, int width, int height) + { + g.setColor(Color.black); + g.fillRect(0, 0, width, height); + drawScene(g); + drawLabels(g); + } + + + public void updateSeqColours() + { + if(bysequence && pdb!=null) + { + for (int ii = 0; ii < pdb.chains.size(); ii++) + { + colourBySequence((PDBChain) pdb.chains.elementAt(ii)); + } + } + + redrawneeded=true; + repaint(); + } + + // This method has been taken out of PDBChain to allow + // Applet and Application specific sequence renderers to be used + void colourBySequence(PDBChain chain) + { + for (int i = 0; i < chain.bonds.size(); i++) + { + Bond tmp = (Bond) chain.bonds.elementAt(i); + + if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) && + (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1))) + { + int pos = chain.seqstart + + (tmp.at1.resNumber - chain.pdbstart - chain.offset); + + int index = sequence.findIndex(pos); + + tmp.startCol = sr.findSequenceColour(sequence, index); + + // tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index); + + } + else + { + tmp.startCol = Color.gray; + } + + if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) && + (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1))) + { + int pos = chain.seqstart + + (tmp.at2.resNumber - chain.pdbstart - chain.offset); + int index = sequence.findIndex(pos); + + tmp.endCol = sr.findSequenceColour( sequence, index); + // tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index); + } + else + { + tmp.endCol = Color.gray; + } + } + } + + + public void drawScene(Graphics g) { + // Sort the bonds by z coord + Vector bonds = 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++) + { + bonds.addElement(tmp.elementAt(i)); + } + } + } + + if (zbuffer) { + Zsort.Zsort(bonds); + } + + for (int i = 0; i < bonds.size(); i++) { + Bond tmpBond = (Bond) bonds.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); + } + } + } + + 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) { + myAtom fatom = findAtom(e.getX(), e.getY()); + if(fatom!=null) + { + fatom.isSelected = !fatom.isSelected; + redrawneeded = true; + repaint(); + } + mx = e.getX(); + my = e.getY(); + omx = mx; + omy = my; + dragging = false; + } + + public void mouseMoved(MouseEvent e) { + + myAtom fatom = findAtom(e.getX(), e.getY()); + + if(foundchain!=-1) + { + PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain); + int pos = chain.seqstart + + (fatom.resNumber - chain.pdbstart - chain.offset)+1; + + int index = seqcanvas.getViewport().getAlignment().findIndex(sequence); + + seqcanvas.highlightSearchResults(new int[]{index, pos, pos}); + } + else + seqcanvas.highlightSearchResults(null); + + if (fatom != null) { + toolx = e.getX(); + tooly = e.getY(); + appletToolTip = fatom.resNumber+" "+ fatom.resName; + redrawneeded = true; + repaint(); + } else { + appletToolTip = null; + redrawneeded = true; + repaint(); + } + } + + 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 myAtom findAtom(int x, int y) { + myAtom fatom = null; + + foundchain = -1; + + 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); + + int 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; + } + } + } + } + + if (fatom != null) //)&& chain.ds != null) + { + chain = (PDBChain) pdb.chains.elementAt(foundchain); + } + } + + return fatom; + } + + public void update(Graphics g) + { + paint(g); + } +} diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java new file mode 100755 index 0000000..e704f15 --- /dev/null +++ b/src/MCview/AppletPDBViewer.java @@ -0,0 +1,236 @@ +package MCview; + +import java.awt.*; + +import java.awt.event.*; +import jalview.datamodel.*; +import jalview.appletgui.*; +import java.awt.event.ActionListener; +import java.awt.event.ActionEvent; + + +public class AppletPDBViewer extends Frame +{ + PDBEntry pdb; + Sequence sequence; + AppletPDBCanvas pdbcanvas; + + + public AppletPDBViewer(String pdbtext, + Sequence seq, + SeqCanvas seqcanvas) + { + sequence = seq; + + try + { + jbInit(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + + pdbcanvas = new AppletPDBCanvas(seqcanvas, seq); + + add(pdbcanvas, BorderLayout.CENTER); + + StringBuffer title = new StringBuffer(sequence.getName() + ":"); + + jalview.bin.JalviewLite.addFrame(this,title.toString(),400, 400); + + try{ + PDBfile pdbfile = new PDBfile(pdbtext, "Paste"); + pdbcanvas.setPDBFile(pdbfile); + }catch(Exception ex){ex.printStackTrace();} + } + + + private void jbInit() + throws Exception + { + this.setMenuBar(jMenuBar1); + fileMenu.setLabel("File"); + coloursMenu.setLabel("Colours"); + mapping.setLabel("View Mapping"); + mapping.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + mapping_actionPerformed(); + } + }); + wire.setLabel("Wireframe"); + wire.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + wire_actionPerformed(); + } + }); + depth.setState(true); + depth.setLabel("Depthcue"); + depth.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + depth_actionPerformed(); + } + }); + zbuffer.setState(true); + zbuffer.setLabel("Z Buffering"); + zbuffer.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + zbuffer_actionPerformed(); + } + }); + charge.setLabel("Charge & Cysteine"); + charge.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + charge_actionPerformed(); + } + }); + hydro.setLabel("Hydrophobicity"); + hydro.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + hydro_actionPerformed(); + } + }); + chain.setLabel("By Chain"); + chain.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + chain_actionPerformed(); + } + }); + seqButton.setState(true); + seqButton.setLabel("By Sequence"); + seqButton.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + seqButton_actionPerformed(); + } + }); + molecule.setLabel("By Molecule"); + molecule.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + molecule_actionPerformed(); + } + }); + jMenuBar1.add(fileMenu); + jMenuBar1.add(coloursMenu); + fileMenu.add(mapping);; + + coloursMenu.add(seqButton); + coloursMenu.add(chain); + coloursMenu.add(hydro); + coloursMenu.add(charge); + coloursMenu.addSeparator(); + coloursMenu.add(wire); + coloursMenu.add(depth); + coloursMenu.add(zbuffer); + coloursMenu.add(molecule); + + } + + MenuBar jMenuBar1 = new MenuBar(); + Menu fileMenu = new Menu(); + Menu coloursMenu = new Menu(); + MenuItem mapping = new MenuItem(); + CheckboxGroup bg = new CheckboxGroup(); + CheckboxMenuItem wire = new CheckboxMenuItem(); + CheckboxMenuItem depth = new CheckboxMenuItem(); + CheckboxMenuItem zbuffer = new CheckboxMenuItem(); + CheckboxMenuItem charge = new CheckboxMenuItem(); + + + CheckboxMenuItem hydro = new CheckboxMenuItem(); + CheckboxMenuItem chain = new CheckboxMenuItem(); + CheckboxMenuItem seqButton = new CheckboxMenuItem(); + CheckboxMenuItem molecule = new CheckboxMenuItem(); + + public void charge_actionPerformed() + { + clearButtonGroup(); + pdbcanvas.pdb.setChargeColours(); + pdbcanvas.redrawneeded=true; + pdbcanvas.repaint(); + } + + public void hydro_actionPerformed() + { + clearButtonGroup(); + pdbcanvas.pdb.setHydrophobicityColours(); + pdbcanvas.redrawneeded=true; + pdbcanvas.repaint(); + } + + public void chain_actionPerformed() + { + clearButtonGroup(); + pdbcanvas.pdb.setChainColours(); + pdbcanvas.redrawneeded=true; + pdbcanvas.repaint(); + } + + public void zbuffer_actionPerformed() + { + pdbcanvas.zbuffer = ! pdbcanvas.zbuffer; + pdbcanvas.redrawneeded=true; + pdbcanvas.repaint(); + } + + public void molecule_actionPerformed() + { + pdbcanvas.bymolecule = ! pdbcanvas.bymolecule; + pdbcanvas.redrawneeded=true; + pdbcanvas.repaint(); + } + + public void depth_actionPerformed() + { + pdbcanvas.depthcue = ! pdbcanvas.depthcue; + pdbcanvas.redrawneeded=true; + pdbcanvas.repaint(); + } + + public void wire_actionPerformed() + { + pdbcanvas.wire = ! pdbcanvas.wire; + pdbcanvas.redrawneeded=true; + pdbcanvas.repaint(); + } + + public void seqButton_actionPerformed() + { + clearButtonGroup(); + pdbcanvas.bysequence = seqButton.getState(); + pdbcanvas.updateSeqColours(); + } + + void clearButtonGroup() + { + pdbcanvas.bysequence = false; + pdbcanvas.bymolecule = false; + } + + public void mapping_actionPerformed() + { + jalview.appletgui.CutAndPasteTransfer cap + = new jalview.appletgui.CutAndPasteTransfer(false, null); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600); + cap.setText(pdbcanvas.mappingDetails.toString()); + } + } -- 1.7.10.2