--- /dev/null
+/*
+ * 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<sequence.length; i++)
+ v.addElement(sequence[i]);
+
+ for(int i=0; i<seq.length; i++)
+ if(!v.contains(seq[i]))
+ v.addElement(seq[i]);
+
+ SequenceI [] tmp = new SequenceI[v.size()];
+ v.copyInto(tmp);
+ sequence = tmp;
+ }
+
+ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String [] chains, AlignmentPanel ap)
+ {
+ //////////////////////////////////
+ //Is the pdb file already loaded?
+ String alreadyMapped = StructureSelectionManager
+ .getStructureSelectionManager()
+ .alreadyMappedToFile(pdbentry.getId());
+
+ if (alreadyMapped != null)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ pdbentry.getId() + " is already displayed."
+ + "\nDo you want to map sequences to the visible structure?",
+ "Map Sequences to Visible Window: " + pdbentry.getId(),
+ JOptionPane.YES_NO_OPTION);
+
+ if (option == JOptionPane.YES_OPTION)
+ {
+ StructureSelectionManager.getStructureSelectionManager()
+ .setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE);
+ if (ap.seqPanel.seqCanvas.fr!=null) {
+ ap.seqPanel.seqCanvas.fr.featuresAdded();
+ ap.paintAlignment(true);
+ }
+
+ //Now this AppJmol is mapped to new sequences. We must add them to
+ // the exisiting array
+ JInternalFrame [] frames = Desktop.instance.getAllFrames();
+
+ for(int i=0; i<frames.length; i++)
+ {
+ if(frames[i] instanceof AppJmol)
+ {
+ AppJmol topJmol = ((AppJmol)frames[i]);
+ if(topJmol.pdbentry.getFile().equals(alreadyMapped))
+ {
+ topJmol.addSequence(seq);
+ break;
+ }
+ }
+ }
+
+ return;
+ }
+ }
+ ///////////////////////////////////
+
+ this.ap = ap;
+ this.pdbentry = pdbentry;
+ this.sequence = seq;
+
+ jalview.gui.Desktop.addInternalFrame(this, "Loading File", 400, 400);
+
+ if (pdbentry.getFile() != null)
+ {
+ initJmol("load \""+pdbentry.getFile()+"\"");
+ }
+ else
+ {
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ this.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ {
+ closeViewer();
+ }
+ });
+ }
+
+
+ void initJmol(String command)
+ {
+ renderPanel = new RenderPanel();
+
+ this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+
+ StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
+ pdbentry.getId());
+
+ if (pdbentry.getProperty() != null)
+ {
+ if (pdbentry.getProperty().get("method") != null)
+ {
+ title.append(" Method: ");
+ title.append(pdbentry.getProperty().get("method"));
+ }
+ if (pdbentry.getProperty().get("chains") != null)
+ {
+ title.append(" Chain:");
+ title.append(pdbentry.getProperty().get("chains"));
+ }
+ }
+
+ this.setTitle(title.toString());
+
+ viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
+ new SmarterJmolAdapter());
+
+
+ viewer.setAppletContext("", null, null, "");
+
+ viewer.setJmolStatusListener(this);
+
+ jmolpopup = JmolPopup.newJmolPopup(viewer);
+
+ viewer.evalStringQuiet(command);
+ }
+
+
+ void setChainMenuItems(Vector chains)
+ {
+ chainMenu.removeAll();
+
+ JMenuItem menuItem = new JMenuItem("All");
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ allChainsSelected = true;
+ for(int i=0; i<chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ ( (JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
+ centerViewer();
+ allChainsSelected = false;
+ }
+ });
+
+ chainMenu.add(menuItem);
+
+ for (int c = 0; c < chains.size(); c++)
+ {
+ menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
+ menuItem.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (!allChainsSelected)
+ centerViewer();
+ }
+ });
+
+ chainMenu.add(menuItem);
+ }
+ }
+
+ boolean allChainsSelected = false;
+ void centerViewer()
+ {
+ StringBuffer cmd = new StringBuffer();
+ for(int i=0; i<chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+ if(item.isSelected())
+ cmd.append(":"+item.getText()+" or ");
+ }
+ }
+
+ if (cmd.length() > 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("<PRE>") > -1 || data.indexOf("</PRE>") > -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<pdbFile.chains.size(); i++)
+ {
+ chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);
+ }
+ setChainMenuItems(chains);
+
+ jmolpopup.updateComputedMenus();
+
+ if(!loadingFromArchive)
+ {
+ viewer.evalStringQuiet(
+ "select backbone;restrict;cartoon;wireframe off;spacefill off");
+
+ colourBySequence(ap);
+ }
+ if (fr!=null)
+ fr.featuresAdded();
+
+ loadingFromArchive = false;
+ }
+ else
+ return;
+ }
+
+ public void notifyFrameChanged(int frameNo)
+ {
+ boolean isAnimationRunning = (frameNo <= -2);
+ }
+
+ public void notifyScriptStart(String statusMessage, String additionalInfo)
+ {}
+
+ public void sendConsoleEcho(String strEcho)
+ {
+ if (scriptWindow != null)
+ scriptWindow.sendConsoleEcho(strEcho);
+ }
+
+ public void sendConsoleMessage(String strStatus)
+ {
+ if (scriptWindow != null)
+ scriptWindow.sendConsoleMessage(strStatus);
+ }
+
+ public void notifyScriptTermination(String strStatus, int msWalltime)
+ {
+ if (scriptWindow != null)
+ scriptWindow.notifyScriptTermination(strStatus, msWalltime);
+ }
+
+ public void handlePopupMenu(int x, int y)
+ {
+ jmolpopup.show(x, y);
+ }
+
+ public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
+ {
+ notifyAtomPicked(iatom, strMeasure);
+ }
+
+ public void notifyNewDefaultModeMeasurement(int count, String strInfo)
+ {}
+
+ public void notifyAtomPicked(int atomIndex, String strInfo)
+ {
+ Matcher matcher = pattern.matcher(strInfo);
+ matcher.find();
+
+ matcher.group(1);
+ String resnum = new String(matcher.group(2));
+ String chainId = matcher.group(3);
+
+ String picked = resnum;
+
+ if (chainId != null)
+ picked+=(":"+chainId.substring(1, chainId.length()));
+
+ picked+=".C";
+
+ if (!atomsPicked.contains(picked))
+ {
+ if(chainId!=null)
+ viewer.evalString("select "+picked+";label %n %r:%c");
+ else
+ viewer.evalString("select "+picked+";label %n %r");
+ atomsPicked.addElement(picked);
+ }
+ else
+ {
+ viewer.evalString("select "+picked+";label off");
+ atomsPicked.removeElement(picked);
+ }
+
+ if (scriptWindow != null)
+ {
+ scriptWindow.sendConsoleMessage(strInfo);
+ scriptWindow.sendConsoleMessage("\n");
+ }
+ }
+
+ public void notifyAtomHovered(int atomIndex, String strInfo)
+ {
+ mouseOverStructure(atomIndex, strInfo);
+ }
+
+ public void sendSyncScript(String script, String appletName)
+ {}
+
+ public void showUrl(String url)
+ {}
+
+ public void showConsole(boolean showConsole)
+ {
+ if (scriptWindow == null)
+ scriptWindow = new ScriptWindow(this);
+
+ if(showConsole)
+ {
+ if(splitPane==null)
+ {
+ splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
+ splitPane.setTopComponent(renderPanel);
+ splitPane.setBottomComponent(scriptWindow);
+ this.getContentPane().add(splitPane, BorderLayout.CENTER);
+ }
+
+ splitPane.setDividerLocation(getHeight()-200);
+ splitPane.validate();
+ }
+ else
+ {
+ if (splitPane != null)
+ splitPane.setVisible(false);
+
+ splitPane = null;
+
+ this.getContentPane().add(renderPanel, BorderLayout.CENTER);
+ }
+
+ validate();
+ }
+
+ public float functionXY(String functionName, int x, int y)
+ {
+ return 0;
+ }
+
+ ///End JmolStatusListener
+ ///////////////////////////////
+
+
+ class RenderPanel
+ extends JPanel
+ {
+ final Dimension currentSize = new Dimension();
+ final Rectangle rectClip = new Rectangle();
+
+ public void paintComponent(Graphics g)
+ {
+ getSize(currentSize);
+ g.getClipBounds(rectClip);
+
+ if (viewer == null)
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, 0, currentSize.width, currentSize.height);
+ g.setColor(Color.white);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+ }
+ else if(fileLoadingError!=null)
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, 0, currentSize.width, currentSize.height);
+ g.setColor(Color.white);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString("Error loading file..." + pdbentry.getId(), 20,
+ currentSize.height / 2);
+ }
+ else
+ {
+ viewer.renderScreenImage(g, currentSize, rectClip);
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff