From 31b00a6d85b8a1b4032f11f448911938004a5f6b Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Fri, 4 May 2007 13:34:04 +0000 Subject: [PATCH] added --- src/jalview/gui/AppJmol.java | 963 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 963 insertions(+) create mode 100644 src/jalview/gui/AppJmol.java diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java new file mode 100644 index 0000000..4a091b2 --- /dev/null +++ b/src/jalview/gui/AppJmol.java @@ -0,0 +1,963 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.gui; + +import java.util.regex.*; +import java.util.*; +import java.awt.*; +import javax.swing.*; +import javax.swing.event.*; +import java.awt.event.*; +import java.io.*; + +import jalview.jbgui.GStructureViewer; +import jalview.datamodel.*; +import jalview.gui.*; +import jalview.structure.*; +import jalview.datamodel.PDBEntry; +import jalview.io.*; +import jalview.schemes.*; + +import org.jmol.api.*; +import org.jmol.adapter.smarter.SmarterJmolAdapter; +import org.jmol.popup.*; + + +public class AppJmol + extends GStructureViewer + implements StructureListener, JmolStatusListener, Runnable + +{ + JmolViewer viewer; + JmolPopup jmolpopup; + ScriptWindow scriptWindow; + PDBEntry pdbentry; + SequenceI[] sequence; + String [] chains; + StructureSelectionManager ssm; + JSplitPane splitPane; + RenderPanel renderPanel; + AlignmentPanel ap; + String fileLoadingError; + boolean colourBySequence = true; + boolean loadingFromArchive = false; + Vector atomsPicked = new Vector(); + + public AppJmol(String file, String id, + SequenceI[] seq, + AlignmentPanel ap, + String loadStatus, + Rectangle bounds) + { + loadingFromArchive = true; + pdbentry = new PDBEntry(); + pdbentry.setFile(file); + pdbentry.setId(id); + this.chains = chains; + this.sequence = seq; + this.ap = ap; + this.setBounds(bounds); + + colourBySequence = false; + seqColour.setSelected(false); + + jalview.gui.Desktop.addInternalFrame(this, "Loading File", + bounds.width,bounds.height); + + initJmol(loadStatus); + + this.addInternalFrameListener(new InternalFrameAdapter() + { + public void internalFrameClosing(InternalFrameEvent internalFrameEvent) + { + closeViewer(); + } + }); + } + +public synchronized void addSequence(SequenceI [] seq) + { + Vector v = new Vector(); + for(int i=0; i 0) + cmd.setLength(cmd.length() - 4); + + viewer.evalStringQuiet("select *;restrict " + +cmd+";cartoon;center "+cmd); + } + + void closeViewer() + { + viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE); + viewer.evalStringQuiet("zap"); + viewer.setJmolStatusListener(null); + viewer = null; + + //We'll need to find out what other + // listeners need to be shut down in Jmol + StructureSelectionManager + .getStructureSelectionManager() + .removeStructureViewerListener(this, pdbentry.getFile()); + } + + public void run() + { + try + { + EBIFetchClient ebi = new EBIFetchClient(); + String query = "pdb:" + pdbentry.getId(); + pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw") + .getAbsolutePath()); + initJmol("load "+pdbentry.getFile()); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + public void pdbFile_actionPerformed(ActionEvent actionEvent) + { + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty( + "LAST_DIRECTORY")); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Save PDB File"); + chooser.setToolTipText("Save"); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + try + { + BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile())); + File outFile = chooser.getSelectedFile(); + + PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); + String data; + while ( (data = in.readLine()) != null) + { + if ( + ! (data.indexOf("
") > -1 || data.indexOf("
") > -1) + ) + { + out.println(data); + } + } + out.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + public void viewMapping_actionPerformed(ActionEvent actionEvent) + { + jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); + jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, + 600); + cap.setText( + StructureSelectionManager.getStructureSelectionManager().printMapping( + pdbentry.getFile()) + ); + } + + /** + * 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 = getWidth(); + int height = 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) + { + Rectangle rect = new Rectangle(width, height); + viewer.renderScreenImage(im.getGraphics(), + rect.getSize(), rect); + im.writeImage(); + } + } + + + public void seqColour_actionPerformed(ActionEvent actionEvent) + { + colourBySequence = seqColour.isSelected(); + colourBySequence(ap.alignFrame.alignPanel); + } + + public void chainColour_actionPerformed(ActionEvent actionEvent) + { + colourBySequence = false; + seqColour.setSelected(false); + viewer.evalStringQuiet("select *;color chain"); + } + + public void chargeColour_actionPerformed(ActionEvent actionEvent) + { + colourBySequence = false; + seqColour.setSelected(false); + viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;" + +"select LYS,ARG;color blue;select CYS;color yellow"); + } + + public void zappoColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new ZappoColourScheme()); + } + + public void taylorColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new TaylorColourScheme()); + } + + public void hydroColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new HydrophobicColourScheme()); + } + + public void helixColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new HelixColourScheme()); + } + + public void strandColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new StrandColourScheme()); + } + + public void turnColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new TurnColourScheme()); + } + + public void buriedColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new BuriedColourScheme()); + } + + public void setJalviewColourScheme(ColourSchemeI cs) + { + colourBySequence = false; + seqColour.setSelected(false); + + if(cs==null) + return; + + String res; + int index; + Color col; + + Enumeration en = ResidueProperties.aa3Hash.keys(); + StringBuffer command = new StringBuffer("select *;color white;"); + while(en.hasMoreElements()) + { + res = en.nextElement().toString(); + index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue(); + if(index>20) + continue; + + col = cs.findColour(ResidueProperties.aa[index].charAt(0)); + + command.append("select "+res+";color[" + + col.getRed() + "," + + col.getGreen() + "," + + col.getBlue() + "];"); + } + + viewer.evalStringQuiet(command.toString()); + } + + public void userColour_actionPerformed(ActionEvent actionEvent) + { + new UserDefinedColours(this, null); + } + + public void backGround_actionPerformed(ActionEvent actionEvent) + { + java.awt.Color col = JColorChooser.showDialog(this, + "Select Background Colour", + null); + + if (col != null) + { + viewer.evalStringQuiet("background [" + + col.getRed() + "," + + col.getGreen() + "," + + col.getBlue() + "];"); + } + } + + + public void jmolHelp_actionPerformed(ActionEvent actionEvent) + { + try{ + jalview.util.BrowserLauncher.openURL( + "http://jmol.sourceforge.net/docs/JmolUserGuide/"); + }catch(Exception ex){} + } + + + ////////////////////////////////// + ///StructureListener + public String getPdbFile() + { + return pdbentry.getFile(); + } + + Pattern pattern = Pattern.compile( + "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?" + ); + + String lastMessage; + public void mouseOverStructure(int atomIndex, String strInfo) + { + Matcher matcher = pattern.matcher(strInfo); + matcher.find(); + matcher.group(1); + int pdbResNum = Integer.parseInt(matcher.group(2)); + String chainId = matcher.group(3); + + if (chainId != null) + chainId = chainId.substring(1, chainId.length()); + else + { + chainId = " "; + } + + if (lastMessage == null || !lastMessage.equals(strInfo)) + { + ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile()); + } + lastMessage = strInfo; + } + + StringBuffer resetLastRes = new StringBuffer(); + StringBuffer eval = new StringBuffer(); + + public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile) + { + if (!pdbfile.equals(pdbentry.getFile())) + return; + + if (resetLastRes.length() > 0) + { + viewer.evalStringQuiet(resetLastRes.toString()); + } + + eval.setLength(0); + eval.append("select " + pdbResNum); + + resetLastRes.setLength(0); + resetLastRes.append("select " + pdbResNum); + + if (!chain.equals(" ")) + { + eval.append(":" + chain); + resetLastRes.append(":" + chain); + } + + eval.append(";color gold;wireframe 100"); + + Color col = new Color(viewer.getAtomArgb(atomIndex)); + + resetLastRes.append(";color[" + + col.getRed() + "," + + col.getGreen() + "," + + col.getBlue() + "];wireframe 0"); + + viewer.evalStringQuiet(eval.toString()); + + } + + public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile) + { + if (!pdbfile.equals(pdbentry.getFile())) + return null; + + return new Color(viewer.getAtomArgb(atomIndex)); + } + + public void updateColours(Object source) + { + colourBySequence( (AlignmentPanel) source); + } + + +//End StructureListener +//////////////////////////// + + String lastCommand; + FeatureRenderer fr=null; + public void colourBySequence(AlignmentPanel sourceap) + { + this.ap = sourceap; + + if(!colourBySequence || ap.alignFrame.getCurrentView()!=ap.av) + return; + + StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile()); + + if (mapping.length < 1) + return; + + + SequenceRenderer sr = new SequenceRenderer(ap.av); + + boolean showFeatures = false; + + if (ap.av.showSequenceFeatures) + { + showFeatures = true; + if (fr == null) + { + fr = new jalview.gui.FeatureRenderer(ap); + } + + fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); + } + + StringBuffer command = new StringBuffer(); + + int lastPos = -1; + for (int s = 0; s < sequence.length; s++) + { + for (int m = 0; m < mapping.length; m++) + { + System.out.println(mapping[m].getSequence().getName()+" "+sequence[s].getName()+" " + +((mapping[m].getSequence() == sequence[s]) + +" "+(ap.av.alignment.findIndex(sequence[s])))); + + if (mapping[m].getSequence() == sequence[s] + && ap.av.alignment.findIndex(sequence[s])>-1) + { + for (int r = 0; r < sequence[s].getLength(); r++) + { + int pos = mapping[m].getPDBResNum( + sequence[s].findPosition(r)); + + if (pos < 1 || pos==lastPos) + continue; + + lastPos = pos; + + Color col = sr.getResidueBoxColour(sequence[s], r); + + if (showFeatures) + col = fr.findFeatureColour(col, sequence[s], r); + + if (command.toString().endsWith(":" + mapping[m].getChain()+ + ";color[" + + col.getRed() + "," + + col.getGreen() + "," + + col.getBlue() + "]")) + { + command = condenseCommand(command, pos); + continue; + } + + command.append(";select " + pos); + + if (!mapping[m].getChain().equals(" ")) + { + command.append(":" + mapping[m].getChain()); + } + + command.append(";color[" + + col.getRed() + "," + + col.getGreen() + "," + + col.getBlue() + "]"); + + } + break; + } + } + } + + if (lastCommand == null || !lastCommand.equals(command.toString())) + { + viewer.evalStringQuiet(command.toString()); + } + lastCommand = command.toString(); + } + + StringBuffer condenseCommand(StringBuffer command, int pos) + { + StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7)); + + command.delete(0, sb.length()); + + String start; + + if (command.indexOf("-") > -1) + { + start = command.substring(0,command.indexOf("-")); + } + else + { + start = command.substring(0, command.indexOf(":")); + } + + sb.append(start+"-"+pos+command.substring(command.indexOf(":"))); + + return sb; + } + + ///////////////////////////////// + //JmolStatusListener + + public String eval(String strEval) + { + // System.out.println(strEval); + //"# 'eval' is implemented only for the applet."; + return null; + } + + public void createImage(String file, String type, int quality) + { + System.out.println("JMOL CREATE IMAGE"); + } + + public void setCallbackFunction(String callbackType, + String callbackFunction) + {} + + public void notifyFileLoaded(String fullPathName, String fileName, + String modelName, Object clientFile, + String errorMsg) + { + if(errorMsg!=null) + { + fileLoadingError = errorMsg; + repaint(); + return; + } + + fileLoadingError = null; + + if (fileName != null) + { + + //FILE LOADED OK + ssm = StructureSelectionManager.getStructureSelectionManager(); + MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE); + ssm.addStructureViewerListener(this); + Vector chains = new Vector(); + for(int i=0; i