2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import java.util.regex.*;
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24 import javax.swing.*;
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25 import javax.swing.event.*;
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26 import java.awt.event.*;
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29 import jalview.jbgui.GStructureViewer;
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30 import jalview.datamodel.*;
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31 import jalview.gui.*;
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32 import jalview.structure.*;
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33 import jalview.datamodel.PDBEntry;
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34 import jalview.io.*;
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35 import jalview.schemes.*;
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37 import org.jmol.api.*;
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38 import org.jmol.adapter.smarter.SmarterJmolAdapter;
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39 import org.jmol.popup.*;
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42 public class AppJMol
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43 extends GStructureViewer
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44 implements StructureListener, JmolStatusListener, Runnable
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48 JmolPopup jmolpopup;
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49 ScriptWindow scriptWindow;
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51 SequenceI[] sequence;
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52 StructureSelectionManager ssm;
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53 JSplitPane splitPane;
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54 RenderPanel renderPanel;
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56 String fileLoadingError;
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57 boolean colourBySequence = true;
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58 boolean loadingFromArchive = false;
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60 public AppJMol(String file, String id,
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66 loadingFromArchive = true;
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67 pdbentry = new PDBEntry();
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68 pdbentry.setFile(file);
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70 this.sequence = seq;
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72 this.setBounds(bounds);
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74 colourBySequence = false;
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75 seqColour.setSelected(false);
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77 jalview.gui.Desktop.addInternalFrame(this, "Loading File",
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78 bounds.width,bounds.height);
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80 initJmol(loadStatus);
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82 this.addInternalFrameListener(new InternalFrameAdapter()
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84 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
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91 public AppJMol(PDBEntry pdbentry, SequenceI[] seq, AlignmentPanel ap)
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93 //////////////////////////////////
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94 //Is the pdb file already loaded?
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95 String alreadyMapped = StructureSelectionManager
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96 .getStructureSelectionManager()
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97 .alreadyMappedToFile(pdbentry.getId());
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99 if (alreadyMapped != null)
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101 int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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102 pdbentry.getId() + " is already displayed."
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103 + "\nDo you want to map sequences to the visible structure?",
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104 "Map Sequences to Visible Window: " + pdbentry.getId(),
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105 JOptionPane.YES_NO_OPTION);
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107 if (option == JOptionPane.YES_OPTION)
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109 StructureSelectionManager.getStructureSelectionManager()
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110 .setMapping(seq, alreadyMapped, AppletFormatAdapter.FILE);
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114 ///////////////////////////////////
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117 this.pdbentry = pdbentry;
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118 this.sequence = seq;
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120 jalview.gui.Desktop.addInternalFrame(this, "Loading File", 400, 400);
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122 if (pdbentry.getFile() != null)
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124 initJmol("load \""+pdbentry.getFile()+"\"");
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128 Thread worker = new Thread(this);
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132 this.addInternalFrameListener(new InternalFrameAdapter()
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134 public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
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141 void initJmol(String command)
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143 renderPanel = new RenderPanel();
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145 this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
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147 StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
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150 if (pdbentry.getProperty() != null)
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152 if (pdbentry.getProperty().get("method") != null)
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154 title.append(" Method: ");
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155 title.append(pdbentry.getProperty().get("method"));
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157 if (pdbentry.getProperty().get("chains") != null)
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159 title.append(" Chain:");
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160 title.append(pdbentry.getProperty().get("chains"));
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164 this.setTitle(title.toString());
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166 viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
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167 new SmarterJmolAdapter());
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170 viewer.setAppletContext("", null, null, "");
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172 viewer.setJmolStatusListener(this);
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174 jmolpopup = JmolPopup.newJmolPopup(viewer);
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176 viewer.evalStringQuiet(command);
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180 void setChainMenuItems(Vector chains)
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182 chainMenu.removeAll();
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184 JMenuItem menuItem = new JMenuItem("All");
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185 menuItem.addActionListener(new ActionListener()
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187 public void actionPerformed(ActionEvent evt)
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189 allChainsSelected = true;
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190 for(int i=0; i<chainMenu.getItemCount(); i++)
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192 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
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193 ( (JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
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196 allChainsSelected = false;
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200 chainMenu.add(menuItem);
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202 for (int c = 0; c < chains.size(); c++)
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204 menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
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205 menuItem.addItemListener(new ItemListener()
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207 public void itemStateChanged(ItemEvent evt)
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209 if (!allChainsSelected)
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214 chainMenu.add(menuItem);
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218 boolean allChainsSelected = false;
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219 void centerViewer()
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221 StringBuffer cmd = new StringBuffer();
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222 for(int i=0; i<chainMenu.getItemCount(); i++)
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224 if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
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226 JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
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227 if(item.isSelected())
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228 cmd.append(":"+item.getText()+" or ");
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232 if (cmd.length() > 0)
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233 cmd.setLength(cmd.length() - 4);
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235 viewer.evalStringQuiet("select *;restrict "
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236 +cmd+";cartoon;center "+cmd);
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241 viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
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242 viewer.evalStringQuiet("zap");
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243 viewer.setJmolStatusListener(null);
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246 //We'll need to find out what other
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247 // listeners need to be shut down in Jmol
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248 StructureSelectionManager
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249 .getStructureSelectionManager()
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250 .removeStructureViewerListener(this, pdbentry.getFile());
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257 EBIFetchClient ebi = new EBIFetchClient();
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258 String query = "pdb:" + pdbentry.getId();
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259 pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
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260 .getAbsolutePath());
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261 initJmol("load "+pdbentry.getFile());
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263 catch (Exception ex)
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265 ex.printStackTrace();
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269 public void pdbFile_actionPerformed(ActionEvent actionEvent)
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271 JalviewFileChooser chooser = new JalviewFileChooser(
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272 jalview.bin.Cache.getProperty(
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273 "LAST_DIRECTORY"));
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275 chooser.setFileView(new JalviewFileView());
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276 chooser.setDialogTitle("Save PDB File");
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277 chooser.setToolTipText("Save");
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279 int value = chooser.showSaveDialog(this);
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281 if (value == JalviewFileChooser.APPROVE_OPTION)
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285 BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));
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286 File outFile = chooser.getSelectedFile();
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288 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
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290 while ( (data = in.readLine()) != null)
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293 ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
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301 catch (Exception ex)
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303 ex.printStackTrace();
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308 public void viewMapping_actionPerformed(ActionEvent actionEvent)
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310 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
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311 jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550,
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314 StructureSelectionManager.getStructureSelectionManager().printMapping(
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315 pdbentry.getFile())
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322 * @param e DOCUMENT ME!
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324 public void eps_actionPerformed(ActionEvent e)
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326 makePDBImage(jalview.util.ImageMaker.EPS);
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332 * @param e DOCUMENT ME!
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334 public void png_actionPerformed(ActionEvent e)
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336 makePDBImage(jalview.util.ImageMaker.PNG);
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339 void makePDBImage(int type)
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341 int width = getWidth();
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342 int height = getHeight();
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344 jalview.util.ImageMaker im;
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346 if (type == jalview.util.ImageMaker.PNG)
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348 im = new jalview.util.ImageMaker(this,
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349 jalview.util.ImageMaker.PNG,
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350 "Make PNG image from view",
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356 im = new jalview.util.ImageMaker(this,
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357 jalview.util.ImageMaker.EPS,
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358 "Make EPS file from view",
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360 null, this.getTitle());
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363 if (im.getGraphics() != null)
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365 Rectangle rect = new Rectangle(width, height);
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366 viewer.renderScreenImage(im.getGraphics(),
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367 rect.getSize(), rect);
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373 public void seqColour_actionPerformed(ActionEvent actionEvent)
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375 colourBySequence = seqColour.isSelected();
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376 colourBySequence(ap);
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379 public void chainColour_actionPerformed(ActionEvent actionEvent)
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381 colourBySequence = false;
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382 seqColour.setSelected(false);
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383 viewer.evalStringQuiet("select *;color chain");
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386 public void chargeColour_actionPerformed(ActionEvent actionEvent)
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388 colourBySequence = false;
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389 seqColour.setSelected(false);
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390 viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
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391 +"select LYS,ARG;color blue;select CYS;color yellow");
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394 public void zappoColour_actionPerformed(ActionEvent actionEvent)
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396 setJalviewColourScheme(new ZappoColourScheme());
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399 public void taylorColour_actionPerformed(ActionEvent actionEvent)
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401 setJalviewColourScheme(new TaylorColourScheme());
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404 public void hydroColour_actionPerformed(ActionEvent actionEvent)
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406 setJalviewColourScheme(new HydrophobicColourScheme());
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409 public void helixColour_actionPerformed(ActionEvent actionEvent)
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411 setJalviewColourScheme(new HelixColourScheme());
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414 public void strandColour_actionPerformed(ActionEvent actionEvent)
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416 setJalviewColourScheme(new StrandColourScheme());
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419 public void turnColour_actionPerformed(ActionEvent actionEvent)
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421 setJalviewColourScheme(new TurnColourScheme());
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424 public void buriedColour_actionPerformed(ActionEvent actionEvent)
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426 setJalviewColourScheme(new BuriedColourScheme());
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429 public void setJalviewColourScheme(ColourSchemeI cs)
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431 colourBySequence = false;
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432 seqColour.setSelected(false);
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441 Enumeration en = ResidueProperties.aa3Hash.keys();
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442 StringBuffer command = new StringBuffer("select *;color white;");
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443 while(en.hasMoreElements())
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445 res = en.nextElement().toString();
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446 index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
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450 col = cs.findColour(ResidueProperties.aa[index].charAt(0));
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452 command.append("select "+res+";color["
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453 + col.getRed() + ","
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454 + col.getGreen() + ","
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455 + col.getBlue() + "];");
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458 viewer.evalStringQuiet(command.toString());
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461 public void userColour_actionPerformed(ActionEvent actionEvent)
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463 new UserDefinedColours(this, null);
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466 public void backGround_actionPerformed(ActionEvent actionEvent)
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468 java.awt.Color col = JColorChooser.showDialog(this,
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469 "Select Background Colour",
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474 viewer.evalStringQuiet("background ["
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475 + col.getRed() + ","
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476 + col.getGreen() + ","
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477 + col.getBlue() + "];");
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482 public void jmolHelp_actionPerformed(ActionEvent actionEvent)
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485 jalview.util.BrowserLauncher.openURL(
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486 "http://jmol.sourceforge.net/docs/JmolUserGuide/");
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487 }catch(Exception ex){}
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491 //////////////////////////////////
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492 ///StructureListener
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493 public String getPdbFile()
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495 return pdbentry.getFile();
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498 Pattern pattern = Pattern.compile(
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499 "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"
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502 String lastMessage;
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503 public void mouseOverStructure(int atomIndex, String strInfo)
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505 Matcher matcher = pattern.matcher(strInfo);
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508 int pdbResNum = Integer.parseInt(matcher.group(2));
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509 String chainId = matcher.group(3);
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511 if (chainId != null)
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512 chainId = chainId.substring(1, chainId.length());
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518 if (lastMessage == null || !lastMessage.equals(strInfo))
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519 ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
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521 lastMessage = strInfo;
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524 StringBuffer resetLastRes = new StringBuffer();
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525 StringBuffer eval = new StringBuffer();
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527 public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
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529 if (!pdbfile.equals(pdbentry.getFile()))
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532 if (resetLastRes.length() > 0)
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534 viewer.evalStringQuiet(resetLastRes.toString());
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538 eval.append("select " + pdbResNum);
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540 resetLastRes.setLength(0);
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541 resetLastRes.append("select " + pdbResNum);
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543 if (!chain.equals(" "))
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545 eval.append(":" + chain);
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546 resetLastRes.append(":" + chain);
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549 eval.append(";color gold;wireframe 100");
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551 Color col = new Color(viewer.getAtomArgb(atomIndex));
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553 resetLastRes.append(";color["
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554 + col.getRed() + ","
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555 + col.getGreen() + ","
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556 + col.getBlue() + "];wireframe 0");
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558 viewer.evalStringQuiet(eval.toString());
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562 public void updateColours(Object source)
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564 colourBySequence( (AlignmentPanel) source);
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568 //End StructureListener
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569 ////////////////////////////
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571 FeatureRenderer fr;
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572 public void colourBySequence(AlignmentPanel ap)
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574 if(!colourBySequence)
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578 StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
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580 if (mapping.length < 1)
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583 SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
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585 boolean showFeatures = false;
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586 if (ap.av.showSequenceFeatures)
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588 showFeatures = true;
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591 fr = new jalview.gui.FeatureRenderer(ap.av);
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594 fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
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597 StringBuffer command = new StringBuffer();
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600 for (int s = 0; s < sequence.length; s++)
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602 for (int m = 0; m < mapping.length; m++)
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604 if (mapping[m].getSequence() == sequence[s])
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606 for (int r = 0; r < sequence[s].getLength(); r++)
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608 int pos = mapping[m].getPDBResNum(
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609 sequence[s].findPosition(r));
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611 if (pos < 1 || pos==lastPos)
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616 Color col = sr.getResidueBoxColour(sequence[s], r);
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619 col = fr.findFeatureColour(col, sequence[s], r);
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621 if (command.toString().endsWith(":" + mapping[m].getChain()+
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623 + col.getRed() + ","
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624 + col.getGreen() + ","
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625 + col.getBlue() + "]"))
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627 command = condenseCommand(command, pos);
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631 command.append(";select " + pos);
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633 if (!mapping[m].getChain().equals(" "))
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635 command.append(":" + mapping[m].getChain());
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638 command.append(";color["
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639 + col.getRed() + ","
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640 + col.getGreen() + ","
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641 + col.getBlue() + "]");
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649 viewer.evalStringQuiet(command.toString());
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652 StringBuffer condenseCommand(StringBuffer command, int pos)
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654 StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
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656 command.delete(0, sb.length());
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660 if (command.indexOf("-") > -1)
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662 start = command.substring(0,command.indexOf("-"));
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666 start = command.substring(0, command.indexOf(":"));
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669 sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
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674 /////////////////////////////////
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675 //JmolStatusListener
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677 public String eval(String strEval)
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679 // System.out.println(strEval);
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680 //"# 'eval' is implemented only for the applet.";
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684 public void createImage(String file, String type, int quality)
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686 System.out.println("JMOL CREATE IMAGE");
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689 public void setCallbackFunction(String callbackType,
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690 String callbackFunction)
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693 public void notifyFileLoaded(String fullPathName, String fileName,
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694 String modelName, Object clientFile,
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699 fileLoadingError = errorMsg;
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704 fileLoadingError = null;
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706 if (fileName != null)
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710 ssm = StructureSelectionManager.getStructureSelectionManager();
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711 MCview.PDBfile pdbFile = ssm.setMapping(sequence, pdbentry.getFile(), AppletFormatAdapter.FILE);
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712 ssm.addStructureViewerListener(this);
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714 Vector chains = new Vector();
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715 for(int i=0; i<pdbFile.chains.size(); i++)
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717 chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);
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719 setChainMenuItems(chains);
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721 jmolpopup.updateComputedMenus();
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723 if(!loadingFromArchive)
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725 viewer.evalStringQuiet(
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726 "select backbone;restrict;cartoon;wireframe off;spacefill off");
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728 colourBySequence(ap);
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731 loadingFromArchive = false;
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737 public void notifyFrameChanged(int frameNo)
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739 boolean isAnimationRunning = (frameNo <= -2);
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742 public void notifyScriptStart(String statusMessage, String additionalInfo)
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745 public void sendConsoleEcho(String strEcho)
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747 if (scriptWindow != null)
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748 scriptWindow.sendConsoleEcho(strEcho);
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751 public void sendConsoleMessage(String strStatus)
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753 if (scriptWindow != null)
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754 scriptWindow.sendConsoleMessage(strStatus);
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757 public void notifyScriptTermination(String strStatus, int msWalltime)
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759 if (scriptWindow != null)
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760 scriptWindow.notifyScriptTermination(strStatus, msWalltime);
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763 public void handlePopupMenu(int x, int y)
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765 jmolpopup.show(x, y);
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768 public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
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770 notifyAtomPicked(iatom, strMeasure);
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773 public void notifyNewDefaultModeMeasurement(int count, String strInfo)
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776 public void notifyAtomPicked(int atomIndex, String strInfo)
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778 if (scriptWindow != null)
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780 scriptWindow.sendConsoleMessage(strInfo);
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781 scriptWindow.sendConsoleMessage("\n");
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785 public void notifyAtomHovered(int atomIndex, String strInfo)
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787 mouseOverStructure(atomIndex, strInfo);
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790 public void sendSyncScript(String script, String appletName)
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793 public void showUrl(String url)
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796 public void showConsole(boolean showConsole)
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798 if (scriptWindow == null)
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799 scriptWindow = new ScriptWindow(this);
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803 if(splitPane==null)
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805 splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
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806 splitPane.setTopComponent(renderPanel);
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807 splitPane.setBottomComponent(scriptWindow);
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808 this.getContentPane().add(splitPane, BorderLayout.CENTER);
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811 splitPane.setDividerLocation(getHeight()-200);
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812 splitPane.validate();
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816 if (splitPane != null)
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817 splitPane.setVisible(false);
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821 this.getContentPane().add(renderPanel, BorderLayout.CENTER);
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827 public float functionXY(String functionName, int x, int y)
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832 ///End JmolStatusListener
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833 ///////////////////////////////
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839 final Dimension currentSize = new Dimension();
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840 final Rectangle rectClip = new Rectangle();
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842 public void paintComponent(Graphics g)
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844 getSize(currentSize);
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845 g.getClipBounds(rectClip);
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847 if (viewer == null)
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849 g.setColor(Color.black);
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850 g.fillRect(0, 0, currentSize.width, currentSize.height);
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851 g.setColor(Color.white);
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852 g.setFont(new Font("Verdana", Font.BOLD, 14));
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853 g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
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855 else if(fileLoadingError!=null)
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857 g.setColor(Color.black);
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858 g.fillRect(0, 0, currentSize.width, currentSize.height);
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859 g.setColor(Color.white);
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860 g.setFont(new Font("Verdana", Font.BOLD, 14));
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861 g.drawString("Error loading file..." + pdbentry.getId(), 20,
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862 currentSize.height / 2);
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866 viewer.renderScreenImage(g, currentSize, rectClip);
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