boolean pdbAction = false;\r
boolean seqColoursReady = false;\r
jalview.gui.FeatureRenderer fr;\r
+ Color backgroundColour = Color.black;\r
\r
public PDBCanvas(jalview.gui.SeqCanvas seqcanvas, Sequence seq)\r
{\r
\r
public void drawAll(Graphics g, int width, int height)\r
{\r
- g.setColor(Color.black);\r
+ g.setColor(backgroundColour);\r
g.fillRect(0, 0, width, height);\r
drawScene(g);\r
drawLabels(g);\r
fr.transferSettings( seqcanvas.getFeatureRenderer() );\r
}\r
\r
+ Bond tmp;\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
+ tmp = (Bond) chain.bonds.elementAt(i);\r
\r
if(chain!=mainchain)\r
continue;\r
{\r
tmp.startCol = seqcanvas.getSequenceRenderer().\r
getResidueBoxColour( sequence, index);\r
- if(tmp.startCol==null)\r
- tmp.startCol = Color.white;\r
\r
if(showFeatures)\r
tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);\r
+\r
+ if(tmp.startCol==null)\r
+ tmp.startCol = Color.white;\r
}\r
}\r
\r
{\r
tmp.endCol = seqcanvas.getSequenceRenderer().\r
getResidueBoxColour( sequence, index);\r
- if(tmp.endCol==null)\r
- tmp.endCol = Color.white;\r
+\r
if(showFeatures)\r
tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);\r
+\r
+ if(tmp.endCol==null)\r
+ tmp.endCol = Color.white;\r
}\r
}\r
}\r
Zsort zsort;\r
public void drawScene(Graphics g)\r
{\r
- if (zbuffer)\r
- {\r
- if(zsort==null)\r
- zsort = new Zsort();\r
+ if (zbuffer)\r
+ {\r
+ if (zsort == null)\r
+ zsort = new Zsort();\r
\r
- zsort.Zsort(visiblebonds);\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
+ 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
- (getWidth() / 2));\r
- ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +\r
- (getHeight() / 2));\r
+ xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +\r
+ (getWidth() / 2));\r
+ ystart = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +\r
+ (getHeight() / 2));\r
\r
- xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +\r
- (getWidth() / 2));\r
- yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +\r
- (getHeight() / 2));\r
+ xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +\r
+ (getWidth() / 2));\r
+ yend = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +\r
+ (getHeight() / 2));\r
\r
- xmid = (xend + xstart) / 2;\r
- ymid = (yend + ystart) / 2;\r
+ xmid = (xend + xstart) / 2;\r
+ ymid = (yend + ystart) / 2;\r
+ if (depthcue && !bymolecule)\r
+ {\r
+ if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))\r
+ {\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
- g.setColor(tmpBond.endCol.darker().darker());\r
- drawLine(g, xmid, ymid, xend, yend);\r
- } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {\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
- } else {\r
- g.setColor(tmpBond.startCol);\r
- drawLine(g, xstart, ystart, xmid, ymid);\r
+ g.setColor(tmpBond.startCol.darker().darker());\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+ g.setColor(tmpBond.endCol.darker().darker());\r
+ drawLine(g, xmid, ymid, xend, yend);\r
\r
- g.setColor(tmpBond.endCol);\r
- drawLine(g, xmid, ymid, xend, yend);\r
- }\r
- } else if (depthcue && bymolecule) {\r
- if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {\r
- g.setColor(Color.green.darker().darker());\r
- drawLine(g, xstart, ystart, xend, yend);\r
- } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {\r
- g.setColor(Color.green.darker());\r
- drawLine(g, xstart, ystart, xend, yend);\r
- } else {\r
- g.setColor(Color.green);\r
- drawLine(g, xstart, ystart, xend, yend);\r
- }\r
- } else if (!depthcue && !bymolecule) {\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
- } else {\r
- drawLine(g, xstart, ystart, xend, yend);\r
- }\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
- if(highlightBond1!=null && highlightBond1==tmpBond)\r
- {\r
- g.setColor(tmpBond.endCol.brighter().brighter().brighter().brighter());\r
- drawLine(g, xmid, ymid, xend, yend);\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
- if(highlightBond2!=null && highlightBond2==tmpBond)\r
- {\r
- g.setColor(tmpBond.startCol.brighter().brighter().brighter().brighter());\r
- drawLine(g, xstart, ystart, xmid, ymid);\r
- }\r
+ g.setColor(tmpBond.endCol);\r
+ drawLine(g, xmid, ymid, xend, yend);\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(tmpBond.endCol.brighter().brighter().brighter().brighter());\r
+ drawLine(g, xmid, ymid, xend, yend);\r
}\r
\r
+ if (highlightBond2 != null && highlightBond2 == tmpBond)\r
+ {\r
+ g.setColor(tmpBond.startCol.brighter().brighter().brighter().brighter());\r
+ drawLine(g, xstart, ystart, xmid, ymid);\r
+ }\r
+\r
+ }\r
+\r
\r
}\r
\r
-/*
- * 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 javax.swing.*;
-import java.awt.event.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.gui.*;
-import jalview.io.EBIFetchClient;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
-
-public class PDBViewer extends JInternalFrame implements Runnable
-{
- PDBEntry pdb;
- Sequence sequence;
- PDBCanvas pdbcanvas;
-
-
- public PDBViewer(PDBEntry entry,
- Sequence seq,
- SeqCanvas seqcanvas)
- {
- /*Uncomment this to modify in Jbuilder
- try
- {
- jbInit();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }*/
-
- if (entry==null)
- return;
- pdb = entry;
- sequence = seq;
-
- Thread worker = new Thread(this);
- worker.start();
-
- pdbcanvas = new PDBCanvas(seqcanvas, seq);
-
- setContentPane(pdbcanvas);
- StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
- if(pdb.getProperty()!=null)
- {
- if (pdb.getProperty().get("method")!=null)
- {
- title.append(" Method: ");
- title.append(pdb.getProperty().get("method"));
- }
- if (pdb.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdb.getProperty().get("chains"));
- }
- }
- Desktop.addInternalFrame(this,title.toString(),400, 400);
- }
-
- public void run()
- {
- try
- {
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdb.getId();
- String[] result = ebi.fetchData(query, "default","raw");
- if (result!=null) {
- PDBfile pdbfile = new PDBfile(result);
- pdbcanvas.setPDBFile(pdbfile);
- } else {
- throw new Exception("Empty result for WSDbFetch Query: "+query);
- }
-
- try
- {
- jbInit();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- showErrorMessage("Failed to retrieve PDB structure.");
-// this.dispose();
- }
- }
-
- private void jbInit()
- throws Exception
- {
- this.addKeyListener(new KeyAdapter()
- {
- public void keyPressed(KeyEvent evt)
- {
- pdbcanvas.keyPressed(evt);
- }
- });
-
- this.setJMenuBar(jMenuBar1);
- fileMenu.setText("File");
- coloursMenu.setText("Colours");
- saveMenu.setActionCommand("Save Image");
- saveMenu.setText("Save As");
- png.setText("PNG");
- png.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- png_actionPerformed(e);
- }
- });
- eps.setText("EPS");
- eps.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- eps_actionPerformed(e);
- }
- });
- mapping.setText("View Mapping");
- mapping.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- mapping_actionPerformed(e);
- }
- });
- wire.setText("Wireframe");
- wire.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- wire_actionPerformed(e);
- }
- });
- depth.setSelected(true);
- depth.setText("Depthcue");
- depth.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- depth_actionPerformed(e);
- }
- });
- zbuffer.setSelected(true);
- zbuffer.setText("Z Buffering");
- zbuffer.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zbuffer_actionPerformed(e);
- }
- });
- charge.setText("Charge & Cysteine");
- charge.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- charge_actionPerformed(e);
- }
- });
- chain.setText("By Chain");
- chain.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- chain_actionPerformed(e);
- }
- });
- seqButton.setSelected(true);
- seqButton.setText("By Sequence");
- seqButton.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- seqButton_actionPerformed(e);
- }
- });
- allchains.setSelected(true);
- allchains.setText("Show All Chains");
- allchains.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- allchains_itemStateChanged(e);
- }
- });
- zappo.setText("Zappo");
- zappo.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zappo_actionPerformed(e);
- }
- });
- taylor.setText("Taylor");
- taylor.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- taylor_actionPerformed(e);
- }
- });
- hydro.setText("Hydro");
- hydro.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hydro_actionPerformed(e);
- }
- });
- helix.setText("Helix");
- helix.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- helix_actionPerformed(e);
- }
- });
- strand.setText("Strand");
- strand.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- strand_actionPerformed(e);
- }
- });
- turn.setText("Turn");
- turn.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- turn_actionPerformed(e);
- }
- });
- buried.setText("Buried");
- buried.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- buried_actionPerformed(e);
- }
- });
- user.setText("User Defined...");
- user.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- user_actionPerformed(e);
- }
- });
- viewMenu.setText("View");
- jMenuBar1.add(fileMenu);
- jMenuBar1.add(coloursMenu);
- jMenuBar1.add(viewMenu);
- fileMenu.add(saveMenu);
- fileMenu.add(mapping);
- saveMenu.add(png);
- saveMenu.add(eps);
- coloursMenu.add(seqButton);
- coloursMenu.add(chain);
- coloursMenu.add(charge);
- coloursMenu.add(zappo);
- coloursMenu.add(taylor);
- coloursMenu.add(hydro);
- coloursMenu.add(helix);
- coloursMenu.add(strand);
- coloursMenu.add(turn);
- coloursMenu.add(buried);
- coloursMenu.add(user);
- ButtonGroup bg = new ButtonGroup();
- bg.add(seqButton);
- bg.add(chain);
- bg.add(charge);
- bg.add(zappo);
- bg.add(taylor);
- bg.add(hydro);
- bg.add(helix);
- bg.add(strand);
- bg.add(turn);
- bg.add(buried);
- bg.add(user);
-
-
- if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
- getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
- nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
- JOptionPane.YES_NO_OPTION);
- if(option == JOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
- coloursMenu.remove(radioItem);
- }
- else
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- user_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- user_actionPerformed(evt);
- }
- });
- coloursMenu.add(radioItem);
- bg.add(radioItem);
- }
- }
-
- viewMenu.add(wire);
- viewMenu.add(depth);
- viewMenu.add(zbuffer);
- viewMenu.add(allchains);
- }
-
- JMenuBar jMenuBar1 = new JMenuBar();
- JMenu fileMenu = new JMenu();
- JMenu coloursMenu = new JMenu();
- JMenu saveMenu = new JMenu();
- JMenuItem png = new JMenuItem();
- JMenuItem eps = new JMenuItem();
- JMenuItem mapping = new JMenuItem();
- JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
- JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
- JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
- JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
-
- JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
- JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
- JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
- JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
- JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
- JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
- JRadioButtonMenuItem user = new JRadioButtonMenuItem();
- JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
- JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
- JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
- JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
- JMenu viewMenu = new JMenu();
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void eps_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.EPS);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void png_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.PNG);
- }
-
- void makePDBImage(int type)
- {
- int width = pdbcanvas.getWidth();
- int height = pdbcanvas.getHeight();
-
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.PNG)
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.PNG,
- "Make PNG image from view",
- width, height,
- null, null);
- else
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.EPS,
- "Make EPS file from view",
- width, height,
- null, this.getTitle());
-
- if (im.getGraphics() != null)
- {
- pdbcanvas.drawAll(im.getGraphics(), width, height);
- im.writeImage();
- }
- }
- public void charge_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setChargeColours();
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void hydro_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void chain_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setChainColours();
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void zbuffer_actionPerformed(ActionEvent e)
- {
- pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void molecule_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void depth_actionPerformed(ActionEvent e)
- {
- pdbcanvas.depthcue = ! pdbcanvas.depthcue;
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void wire_actionPerformed(ActionEvent e)
- {
- pdbcanvas.wire = ! pdbcanvas.wire;
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void seqButton_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = true;
- pdbcanvas.updateSeqColours();
- }
-
-
- public void mapping_actionPerformed(ActionEvent e)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
- cap.setText(pdbcanvas.mappingDetails.toString());
- }
-
- public void allchains_itemStateChanged(ItemEvent e)
- {
- pdbcanvas.setAllchainsVisible(allchains.getState());
- }
- void showErrorMessage(String error)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);
- }
-
-
- public void zappo_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new ZappoColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void taylor_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new TaylorColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void helix_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new HelixColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void strand_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new StrandColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void turn_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new TurnColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void buried_actionPerformed(ActionEvent e)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setColours(new BuriedColourScheme());
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
-
- public void user_actionPerformed(ActionEvent e)
- {
- if (e.getActionCommand().equals("User Defined..."))
- {
- new UserDefinedColours(pdbcanvas, null);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.
- getUserColourSchemes().get(e.getActionCommand());
-
- pdbcanvas.pdb.setColours(udc);
- pdbcanvas.redrawneeded=true;
- pdbcanvas.repaint();
- }
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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 javax.swing.*;\r
+import java.awt.event.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+import jalview.gui.*;\r
+import jalview.io.EBIFetchClient;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.ActionEvent;\r
+\r
+public class PDBViewer extends JInternalFrame implements Runnable\r
+{\r
+ PDBEntry pdb;\r
+ Sequence sequence;\r
+ PDBCanvas pdbcanvas;\r
+\r
+\r
+ public PDBViewer(PDBEntry entry,\r
+ Sequence seq,\r
+ SeqCanvas seqcanvas)\r
+ {\r
+ /*Uncomment this to modify in Jbuilder\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }*/\r
+\r
+ if (entry==null)\r
+ return;\r
+ pdb = entry;\r
+ sequence = seq;\r
+\r
+ Thread worker = new Thread(this);\r
+ worker.start();\r
+\r
+ pdbcanvas = new PDBCanvas(seqcanvas, seq);\r
+\r
+ setContentPane(pdbcanvas);\r
+ StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());\r
+ if(pdb.getProperty()!=null)\r
+ {\r
+ if (pdb.getProperty().get("method")!=null)\r
+ {\r
+ title.append(" Method: ");\r
+ title.append(pdb.getProperty().get("method"));\r
+ }\r
+ if (pdb.getProperty().get("chains") != null)\r
+ {\r
+ title.append(" Chain:");\r
+ title.append(pdb.getProperty().get("chains"));\r
+ }\r
+ }\r
+ Desktop.addInternalFrame(this,title.toString(),400, 400);\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String query = "pdb:" + pdb.getId();\r
+ String[] result = ebi.fetchData(query, "default","raw");\r
+ if (result!=null) {\r
+ PDBfile pdbfile = new PDBfile(result);\r
+ pdbcanvas.setPDBFile(pdbfile);\r
+ } else {\r
+ throw new Exception("Empty result for WSDbFetch Query: "+query);\r
+ }\r
+\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ showErrorMessage("Failed to retrieve PDB structure.");\r
+// this.dispose();\r
+ }\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ this.addKeyListener(new KeyAdapter()\r
+ {\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ pdbcanvas.keyPressed(evt);\r
+ }\r
+ });\r
+\r
+ this.setJMenuBar(jMenuBar1);\r
+ fileMenu.setText("File");\r
+ coloursMenu.setText("Colours");\r
+ saveMenu.setActionCommand("Save Image");\r
+ saveMenu.setText("Save As");\r
+ png.setText("PNG");\r
+ png.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ png_actionPerformed(e);\r
+ }\r
+ });\r
+ eps.setText("EPS");\r
+ eps.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ eps_actionPerformed(e);\r
+ }\r
+ });\r
+ mapping.setText("View Mapping");\r
+ mapping.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ mapping_actionPerformed(e);\r
+ }\r
+ });\r
+ wire.setText("Wireframe");\r
+ wire.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ wire_actionPerformed(e);\r
+ }\r
+ });\r
+ depth.setSelected(true);\r
+ depth.setText("Depthcue");\r
+ depth.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ depth_actionPerformed(e);\r
+ }\r
+ });\r
+ zbuffer.setSelected(true);\r
+ zbuffer.setText("Z Buffering");\r
+ zbuffer.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ zbuffer_actionPerformed(e);\r
+ }\r
+ });\r
+ charge.setText("Charge & Cysteine");\r
+ charge.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ charge_actionPerformed(e);\r
+ }\r
+ });\r
+ chain.setText("By Chain");\r
+ chain.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ chain_actionPerformed(e);\r
+ }\r
+ });\r
+ seqButton.setSelected(true);\r
+ seqButton.setText("By Sequence");\r
+ seqButton.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ seqButton_actionPerformed(e);\r
+ }\r
+ });\r
+ allchains.setSelected(true);\r
+ allchains.setText("Show All Chains");\r
+ allchains.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ allchains_itemStateChanged(e);\r
+ }\r
+ });\r
+ zappo.setText("Zappo");\r
+ zappo.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ zappo_actionPerformed(e);\r
+ }\r
+ });\r
+ taylor.setText("Taylor");\r
+ taylor.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ taylor_actionPerformed(e);\r
+ }\r
+ });\r
+ hydro.setText("Hydro");\r
+ hydro.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hydro_actionPerformed(e);\r
+ }\r
+ });\r
+ helix.setText("Helix");\r
+ helix.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ helix_actionPerformed(e);\r
+ }\r
+ });\r
+ strand.setText("Strand");\r
+ strand.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ strand_actionPerformed(e);\r
+ }\r
+ });\r
+ turn.setText("Turn");\r
+ turn.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ turn_actionPerformed(e);\r
+ }\r
+ });\r
+ buried.setText("Buried");\r
+ buried.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ buried_actionPerformed(e);\r
+ }\r
+ });\r
+ user.setText("User Defined...");\r
+ user.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ user_actionPerformed(e);\r
+ }\r
+ });\r
+ viewMenu.setText("View");\r
+ background.setText("Background Colour...");\r
+ background.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ background_actionPerformed(e);\r
+ }\r
+ });\r
+ jMenuBar1.add(fileMenu);\r
+ jMenuBar1.add(coloursMenu);\r
+ jMenuBar1.add(viewMenu);\r
+ fileMenu.add(saveMenu);\r
+ fileMenu.add(mapping);\r
+ saveMenu.add(png);\r
+ saveMenu.add(eps);\r
+ coloursMenu.add(seqButton);\r
+ coloursMenu.add(chain);\r
+ coloursMenu.add(charge);\r
+ coloursMenu.add(zappo);\r
+ coloursMenu.add(taylor);\r
+ coloursMenu.add(hydro);\r
+ coloursMenu.add(helix);\r
+ coloursMenu.add(strand);\r
+ coloursMenu.add(turn);\r
+ coloursMenu.add(buried);\r
+ coloursMenu.add(user);\r
+ coloursMenu.add(background);\r
+ ButtonGroup bg = new ButtonGroup();\r
+ bg.add(seqButton);\r
+ bg.add(chain);\r
+ bg.add(charge);\r
+ bg.add(zappo);\r
+ bg.add(taylor);\r
+ bg.add(hydro);\r
+ bg.add(helix);\r
+ bg.add(strand);\r
+ bg.add(turn);\r
+ bg.add(buried);\r
+ bg.add(user);\r
+\r
+\r
+ if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
+ {\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+ getUserColourSchemes().keys();\r
+\r
+ while (userColours.hasMoreElements())\r
+ {\r
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
+ nextElement().toString());\r
+ radioItem.setName("USER_DEFINED");\r
+ radioItem.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
+ "Remove from default list?",\r
+ "Remove user defined colour",\r
+ JOptionPane.YES_NO_OPTION);\r
+ if(option == JOptionPane.YES_OPTION)\r
+ {\r
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
+ coloursMenu.remove(radioItem);\r
+ }\r
+ else\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ user_actionPerformed(evt);\r
+ }\r
+ });\r
+ }\r
+ }\r
+ });\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ user_actionPerformed(evt);\r
+ }\r
+ });\r
+ coloursMenu.add(radioItem);\r
+ bg.add(radioItem);\r
+ }\r
+ }\r
+\r
+ viewMenu.add(wire);\r
+ viewMenu.add(depth);\r
+ viewMenu.add(zbuffer);\r
+ viewMenu.add(allchains);\r
+ }\r
+\r
+ JMenuBar jMenuBar1 = new JMenuBar();\r
+ JMenu fileMenu = new JMenu();\r
+ JMenu coloursMenu = new JMenu();\r
+ JMenu saveMenu = new JMenu();\r
+ JMenuItem png = new JMenuItem();\r
+ JMenuItem eps = new JMenuItem();\r
+ JMenuItem mapping = new JMenuItem();\r
+ JCheckBoxMenuItem wire = new JCheckBoxMenuItem();\r
+ JCheckBoxMenuItem depth = new JCheckBoxMenuItem();\r
+ JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();\r
+ JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();\r
+\r
+ JRadioButtonMenuItem charge = new JRadioButtonMenuItem();\r
+ JRadioButtonMenuItem chain = new JRadioButtonMenuItem();\r
+ JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();\r
+ JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();\r
+ JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();\r
+ JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();\r
+ JRadioButtonMenuItem user = new JRadioButtonMenuItem();\r
+ JRadioButtonMenuItem buried = new JRadioButtonMenuItem();\r
+ JRadioButtonMenuItem turn = new JRadioButtonMenuItem();\r
+ JRadioButtonMenuItem strand = new JRadioButtonMenuItem();\r
+ JRadioButtonMenuItem helix = new JRadioButtonMenuItem();\r
+ JMenu viewMenu = new JMenu();\r
+ JMenuItem background = new JMenuItem();\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void eps_actionPerformed(ActionEvent e)\r
+ {\r
+ makePDBImage(jalview.util.ImageMaker.EPS);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void png_actionPerformed(ActionEvent e)\r
+ {\r
+ makePDBImage(jalview.util.ImageMaker.PNG);\r
+ }\r
+\r
+ void makePDBImage(int type)\r
+ {\r
+ int width = pdbcanvas.getWidth();\r
+ int height = pdbcanvas.getHeight();\r
+\r
+ jalview.util.ImageMaker im;\r
+\r
+ if (type == jalview.util.ImageMaker.PNG)\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.PNG,\r
+ "Make PNG image from view",\r
+ width, height,\r
+ null, null);\r
+ else\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.EPS,\r
+ "Make EPS file from view",\r
+ width, height,\r
+ null, this.getTitle());\r
+\r
+ if (im.getGraphics() != null)\r
+ {\r
+ pdbcanvas.drawAll(im.getGraphics(), width, height);\r
+ im.writeImage();\r
+ }\r
+ }\r
+ public void charge_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setChargeColours();\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void hydro_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setColours(new HydrophobicColourScheme());\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void chain_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setChainColours();\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void zbuffer_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void molecule_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void depth_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void wire_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.wire = ! pdbcanvas.wire;\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void seqButton_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bysequence = true;\r
+ pdbcanvas.updateSeqColours();\r
+ }\r
+\r
+\r
+ public void mapping_actionPerformed(ActionEvent e)\r
+ {\r
+ jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);\r
+ cap.setText(pdbcanvas.mappingDetails.toString());\r
+ }\r
+\r
+ public void allchains_itemStateChanged(ItemEvent e)\r
+ {\r
+ pdbcanvas.setAllchainsVisible(allchains.getState());\r
+ }\r
+ void showErrorMessage(String error)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);\r
+ }\r
+\r
+\r
+ public void zappo_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setColours(new ZappoColourScheme());\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void taylor_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setColours(new TaylorColourScheme());\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void helix_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setColours(new HelixColourScheme());\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void strand_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setColours(new StrandColourScheme());\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void turn_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setColours(new TurnColourScheme());\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void buried_actionPerformed(ActionEvent e)\r
+ {\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setColours(new BuriedColourScheme());\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+\r
+ public void user_actionPerformed(ActionEvent e)\r
+ {\r
+ if (e.getActionCommand().equals("User Defined..."))\r
+ {\r
+ new UserDefinedColours(pdbcanvas, null);\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
+ getUserColourSchemes().get(e.getActionCommand());\r
+\r
+ pdbcanvas.pdb.setColours(udc);\r
+ pdbcanvas.redrawneeded=true;\r
+ pdbcanvas.repaint();\r
+ }\r
+ }\r
+\r
+ public void background_actionPerformed(ActionEvent e)\r
+ {\r
+ java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour",\r
+ pdbcanvas.backgroundColour);\r
+\r
+ if(col!=null)\r
+ {\r
+ pdbcanvas.backgroundColour = col;\r
+ pdbcanvas.redrawneeded = true;\r
+ pdbcanvas.repaint();\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / commitdiff