/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.appletgui;
import java.util.*;
import org.jmol.popup.*;
import jalview.schemes.*;
-
-public class AppletJmol extends Frame
- implements StructureListener, JmolStatusListener,
- KeyListener, ActionListener, ItemListener
+public class AppletJmol extends EmbmenuFrame implements StructureListener,
+ JmolStatusListener, KeyListener, ActionListener, ItemListener
{
Menu fileMenu = new Menu("File");
+
Menu viewMenu = new Menu("View");
+
Menu coloursMenu = new Menu("Colours");
+
Menu chainMenu = new Menu("Show Chain");
+
Menu helpMenu = new Menu("Help");
+
MenuItem mappingMenuItem = new MenuItem("View Mapping");
CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
+
MenuItem chain = new MenuItem("By Chain");
+
MenuItem charge = new MenuItem("Charge & Cysteine");
+
MenuItem zappo = new MenuItem("Zappo");
+
MenuItem taylor = new MenuItem("Taylor");
+
MenuItem hydro = new MenuItem("Hydrophobicity");
+
MenuItem helix = new MenuItem("Helix Propensity");
+
MenuItem strand = new MenuItem("Strand Propensity");
+
MenuItem turn = new MenuItem("Turn Propensity");
+
MenuItem buried = new MenuItem("Buried Index");
+
MenuItem user = new MenuItem("User Defined Colours");
MenuItem jmolHelp = new MenuItem("Jmol Help");
JmolViewer viewer;
+
JmolPopup jmolpopup;
Panel scriptWindow;
+
TextField inputLine;
+
TextArea history;
+
SequenceI[] sequence;
- String [] chains;
+
+ String[] chains;
+
StructureSelectionManager ssm;
+
RenderPanel renderPanel;
+
AlignmentPanel ap;
+
String fileLoadingError;
+
boolean loadedInline;
+
PDBEntry pdbentry;
+
boolean colourBySequence = true;
+
Vector atomsPicked = new Vector();
- public AppletJmol(PDBEntry pdbentry,
- SequenceI[] seq,
- String[] chains,
- AlignmentPanel ap,
- String protocol)
+ /**
+ * datasource protocol for access to PDBEntry
+ */
+ String protocol = null;
+
+ public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ AlignmentPanel ap, String protocol)
{
this.ap = ap;
this.sequence = seq;
this.chains = chains;
this.pdbentry = pdbentry;
+ this.protocol = protocol;
+ if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
+ {
+ if (jalview.bin.JalviewLite.debug)
+ {
+ System.err.println("Setting PDB id for file " + pdbentry.getFile());
+ if (protocol.equals(AppletFormatAdapter.PASTE))
+ {
+ pdbentry.setId("PASTED PDB"
+ + (chains == null ? "_" : chains.toString()));
+ }
+ else
+ {
+ pdbentry.setId(pdbentry.getFile());
+ }
+ }
+ }
+ if (jalview.bin.JalviewLite.debug)
+ {
+ System.err
+ .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
+ }
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager()
- .alreadyMappedToFile(pdbentry.getId());
-
+ String alreadyMapped = StructureSelectionManager
+ .getStructureSelectionManager().alreadyMappedToFile(
+ pdbentry.getId());
+ MCview.PDBfile reader = null;
if (alreadyMapped != null)
{
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, pdbentry.getFile(), protocol);
- //PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
- //FOR NOW, LETS JUST OPEN A NEW WINDOW
+ reader = StructureSelectionManager.getStructureSelectionManager()
+ .setMapping(seq, chains, pdbentry.getFile(), protocol);
+ // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
+ // FOR NOW, LETS JUST OPEN A NEW WINDOW
}
-
- renderPanel = new RenderPanel();
-
- this.add(renderPanel, BorderLayout.CENTER);
- viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());
-
- viewer.setAppletContext("jalview",
- ap.av.applet.getDocumentBase(),
- ap.av.applet.getCodeBase(),
- null);
-
- viewer.setJmolStatusListener(this);
-
- jmolpopup = JmolPopup.newJmolPopup(viewer);
-
- this.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- closeViewer();
- }
- });
-
MenuBar menuBar = new MenuBar();
menuBar.add(fileMenu);
fileMenu.add(mappingMenuItem);
helpMenu.add(jmolHelp);
- this.setMenuBar(menuBar);
+ setMenuBar(menuBar);
+
+ renderPanel = new RenderPanel();
+ embedMenuIfNeeded(renderPanel);
+ this.add(renderPanel, BorderLayout.CENTER);
+ viewer = JmolViewer.allocateViewer(renderPanel,
+ new SmarterJmolAdapter());
+
+ viewer.setAppletContext("jalview", ap.av.applet.getDocumentBase(),
+ ap.av.applet.getCodeBase(), null);
+
+ viewer.setJmolStatusListener(this);
+
+ jmolpopup = JmolPopup.newJmolPopup(viewer);
- if(pdbentry.getFile()!=null)
+ this.addWindowListener(new WindowAdapter()
{
+ public void windowClosing(WindowEvent evt)
+ {
+ closeViewer();
+ }
+ });
+
+ if (pdbentry.getFile() != null)
+ {
+ // import structure data from pdbentry.getFile based on given protocol
if (protocol.equals(AppletFormatAdapter.PASTE))
+ {
loadInline(pdbentry.getFile());
+ }
+ else if (protocol.equals(AppletFormatAdapter.FILE)
+ || protocol.equals(AppletFormatAdapter.URL))
+ {
+ viewer.openFile(pdbentry.getFile());
+ }
else
- viewer.openFile(pdbentry.getFile());
+ {
+ // probably CLASSLOADER based datasource..
+ // Try and get a reader on the datasource, and pass that to Jmol
+ try
+ {
+ java.io.Reader freader = null;
+ if (reader != null)
+ {
+ if (jalview.bin.JalviewLite.debug)
+ {
+ System.err
+ .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
+ }
+ // re-use the one we opened earlier
+ freader = reader.getReader();
+ }
+ if (freader == null)
+ {
+ if (jalview.bin.JalviewLite.debug)
+ {
+ System.err
+ .println("AppletJmol:Creating new PDBfile IO parser.");
+ }
+ FileParse fp = new FileParse(pdbentry.getFile(), protocol);
+ fp.mark();
+ // reader = new MCview.PDBfile(fp);
+ // could set ID, etc.
+ // if (!reader.isValid())
+ // {
+ // throw new Exception("Invalid datasource.
+ // "+reader.getWarningMessage());
+ // }
+ // fp.reset();
+ freader = fp.getReader();
+ }
+ if (freader == null)
+ {
+ throw new Exception(
+ "Invalid datasource. Could not obtain Reader.");
+ }
+ viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader);
+ } catch (Exception e)
+ {
+ // give up!
+ System.err.println("Couldn't access pdbentry id="
+ + pdbentry.getId() + " and file=" + pdbentry.getFile()
+ + " using protocol=" + protocol);
+ e.printStackTrace();
+ }
+ }
}
- jalview.bin.JalviewLite.addFrame(this, "Jmol", 400,400);
+ jalview.bin.JalviewLite.addFrame(this, "Jmol", 400, 400);
}
public void loadInline(String string)
viewer.openStringInline(string);
}
-
void setChainMenuItems(Vector chains)
{
chainMenu.removeAll();
CheckboxMenuItem menuItemCB;
for (int c = 0; c < chains.size(); c++)
{
- menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(), true);
+ menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
+ true);
menuItemCB.addItemListener(this);
chainMenu.add(menuItemCB);
}
}
boolean allChainsSelected = false;
+
void centerViewer()
{
StringBuffer cmd = new StringBuffer();
if (cmd.length() > 0)
cmd.setLength(cmd.length() - 4);
- viewer.evalString("select *;restrict "
- + cmd + ";cartoon;center " + cmd);
+ viewer
+ .evalString("select *;restrict " + cmd + ";cartoon;center "
+ + cmd);
}
-
void closeViewer()
{
viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
viewer.setJmolStatusListener(null);
viewer = null;
- //We'll need to find out what other
+ // We'll need to find out what other
// listeners need to be shut down in Jmol
- StructureSelectionManager
- .getStructureSelectionManager()
- .removeStructureViewerListener(this, pdbentry.getId());
+ StructureSelectionManager.getStructureSelectionManager()
+ .removeStructureViewerListener(this, pdbentry.getId());
this.setVisible(false);
}
public void actionPerformed(ActionEvent evt)
{
- if(evt.getSource()==mappingMenuItem)
+ if (evt.getSource() == mappingMenuItem)
{
- jalview.appletgui.CutAndPasteTransfer cap
- = new jalview.appletgui.CutAndPasteTransfer(false, null);
+ jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
+ false, null);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 550,
- 600);
- cap.setText(
- StructureSelectionManager.getStructureSelectionManager().printMapping(
- pdbentry.getFile())
- );
+ jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
+ 550, 600);
+ cap.setText(StructureSelectionManager.getStructureSelectionManager()
+ .printMapping(pdbentry.getFile()));
}
else if (evt.getSource() == charge)
{
colourBySequence = false;
seqColour.setState(false);
- viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
- +"select LYS,ARG;color blue;select CYS;color yellow");
+ viewer
+ .evalStringQuiet("select *;color white;select ASP,GLU;color red;"
+ + "select LYS,ARG;color blue;select CYS;color yellow");
}
else if (evt.getSource() == chain)
}
else if (evt.getSource() == taylor)
{
- setJalviewColourScheme(new TaylorColourScheme());
+ setJalviewColourScheme(new TaylorColourScheme());
}
else if (evt.getSource() == hydro)
{
{
new UserDefinedColours(this);
}
- else if(evt.getSource() == jmolHelp)
+ else if (evt.getSource() == jmolHelp)
{
- try{
+ try
+ {
ap.av.applet.getAppletContext().showDocument(
- new java.net.URL("http://jmol.sourceforge.net/docs/JmolUserGuide/"),
- "jmolHelp");
- }catch(java.net.MalformedURLException ex){}
+ new java.net.URL(
+ "http://jmol.sourceforge.net/docs/JmolUserGuide/"),
+ "jmolHelp");
+ } catch (java.net.MalformedURLException ex)
+ {
+ }
}
else
{
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
- ( (CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
+ ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
}
centerViewer();
allChainsSelected = false;
colourBySequence = false;
seqColour.setState(false);
- if(cs==null)
+ if (cs == null)
return;
String res;
Enumeration en = ResidueProperties.aa3Hash.keys();
StringBuffer command = new StringBuffer("select *;color white;");
- while(en.hasMoreElements())
+ while (en.hasMoreElements())
{
res = en.nextElement().toString();
index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if(index>20)
+ if (index > 20)
continue;
col = cs.findColour(ResidueProperties.aa[index].charAt(0));
- command.append("select "+res+";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];");
+ command.append("select " + res + ";color[" + col.getRed() + ","
+ + col.getGreen() + "," + col.getBlue() + "];");
}
viewer.evalStringQuiet(command.toString());
public void keyPressed(KeyEvent evt)
{
- if (evt.getKeyCode() == KeyEvent.VK_ENTER
- && scriptWindow.isVisible())
+ if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
{
viewer.evalString(inputLine.getText());
- history.append("\n$ "+inputLine.getText());
+ history.append("\n$ " + inputLine.getText());
inputLine.setText("");
}
}
public void keyTyped(KeyEvent evt)
- { }
+ {
+ }
- public void keyReleased(KeyEvent evt){}
+ public void keyReleased(KeyEvent evt)
+ {
+ }
- //////////////////////////////////
- ///StructureListener
+ // ////////////////////////////////
+ // /StructureListener
public String getPdbFile()
{
return "???";
}
-
-
String lastMessage;
+
public void mouseOverStructure(int atomIndex, String strInfo)
{
- int pdbResNum;
+ int pdbResNum;
- int chainSeparator = strInfo.indexOf(":");
+ int chainSeparator = strInfo.indexOf(":");
- if(chainSeparator==-1)
- chainSeparator = strInfo.indexOf(".");
+ if (chainSeparator == -1)
+ chainSeparator = strInfo.indexOf(".");
- pdbResNum = Integer.parseInt(
- strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator));
+ pdbResNum = Integer.parseInt(strInfo.substring(
+ strInfo.indexOf("]") + 1, chainSeparator));
- String chainId;
+ String chainId;
- if (strInfo.indexOf(":") > -1)
- chainId = strInfo.substring
- (strInfo.indexOf(":")+1, strInfo.indexOf("."));
- else
- {
- chainId = " ";
- }
+ if (strInfo.indexOf(":") > -1)
+ chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
+ .indexOf("."));
+ else
+ {
+ chainId = " ";
+ }
- if (lastMessage == null || !lastMessage.equals(strInfo))
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
+ if (lastMessage == null || !lastMessage.equals(strInfo))
+ ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
- lastMessage = strInfo;
+ lastMessage = strInfo;
}
StringBuffer resetLastRes = new StringBuffer();
+
StringBuffer eval = new StringBuffer();
- public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
{
if (!pdbfile.equals(pdbentry.getFile()))
return;
resetLastRes.append(":" + chain);
}
- eval.append(";wireframe 100;"+eval.toString()+".CA;");
+ eval.append(";wireframe 100;" + eval.toString() + ".CA;");
- resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
+ resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
+ + ".CA;spacefill 0;");
eval.append("spacefill 200;select none");
public void updateColours(Object source)
{
- colourBySequence( (AlignmentPanel) source);
+ colourBySequence((AlignmentPanel) source);
}
-//End StructureListener
-////////////////////////////
+ // End StructureListener
+ // //////////////////////////
- public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+ public Color getColour(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
{
if (!pdbfile.equals(pdbentry.getFile()))
return null;
}
String lastCommand;
- FeatureRenderer fr=null;
+
+ FeatureRenderer fr = null;
+
public void colourBySequence(AlignmentPanel sourceap)
{
this.ap = sourceap;
int lastPos = -1;
for (int s = 0; s < sequence.length; s++)
{
- for (int m = 0; m < mapping.length; m++)
+ for (int sp, m = 0; m < mapping.length; m++)
{
if (mapping[m].getSequence() == sequence[s]
- && ap.av.alignment.findIndex(sequence[s]) > -1)
+ && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
{
- for (int r = 0; r < sequence[s].getLength(); r++)
+ SequenceI asp = ap.av.alignment.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
{
- int pos = mapping[m].getPDBResNum(
- sequence[s].findPosition(r));
+ // no mapping to gaps in sequence
+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
+ int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
continue;
if (showFeatures)
col = fr.findFeatureColour(col, sequence[s], r);
- if (command.toString().endsWith(":" + mapping[m].getChain() +
- ";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "]"))
+ if (command.toString().endsWith(
+ ":" + mapping[m].getChain() + ";color[" + col.getRed()
+ + "," + col.getGreen() + "," + col.getBlue()
+ + "]"))
{
command = condenseCommand(command.toString(), pos);
continue;
command.append(":" + mapping[m].getChain());
}
- command.append(";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "]");
+ command.append(";color[" + col.getRed() + "," + col.getGreen()
+ + "," + col.getBlue() + "]");
}
break;
}
lastCommand = command.toString();
}
-
StringBuffer condenseCommand(String command, int pos)
{
- StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
+ StringBuffer sb = new StringBuffer(command.substring(0, command
+ .lastIndexOf("select") + 7));
command = command.substring(sb.length());
if (command.indexOf("-") > -1)
{
- start = command.substring(0,command.indexOf("-"));
+ start = command.substring(0, command.indexOf("-"));
}
else
{
start = command.substring(0, command.indexOf(":"));
}
- sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
+ sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
return sb;
}
- /////////////////////////////////
- //JmolStatusListener
+ // ///////////////////////////////
+ // JmolStatusListener
public String eval(String strEval)
{
- // System.out.println(strEval);
- //"# 'eval' is implemented only for the applet.";
+ // System.out.println(strEval);
+ // "# 'eval' is implemented only for the applet.";
return null;
}
public void createImage(String file, String type, int quality)
- {}
+ {
+ }
public void setCallbackFunction(String callbackType,
- String callbackFunction)
- {}
+ String callbackFunction)
+ {
+ }
public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile,
- String errorMsg)
+ String modelName, Object clientFile, String errorMsg)
{
- if(errorMsg!=null)
+ if (errorMsg != null)
{
fileLoadingError = errorMsg;
repaint();
if (fileName != null)
{
- //FILE LOADED OK
+ // FILE LOADED OK
jmolpopup.updateComputedMenus();
- viewer.evalStringQuiet(
- "select backbone;restrict;cartoon;wireframe off;spacefill off");
+ viewer
+ .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
ssm = StructureSelectionManager.getStructureSelectionManager();
-
MCview.PDBfile pdb;
if (loadedInline)
{
- pdb = ssm.setMapping(sequence,chains,
- pdbentry.getFile(),
- AppletFormatAdapter.PASTE);
- pdbentry.setFile("INLINE"+pdb.id);
+ pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
+ AppletFormatAdapter.PASTE);
+ pdbentry.setFile("INLINE" + pdb.id);
}
else
{
- pdb = ssm.setMapping(sequence,chains,
- pdbentry.getFile(),
- AppletFormatAdapter.URL);
+ // TODO: Jmol can in principle retrieve from CLASSLOADER but this needs
+ // to be tested. See mantis bug
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+
+ pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
+ AppletFormatAdapter.URL);
+
}
pdbentry.setId(pdb.id);
Vector chains = new Vector();
for (int i = 0; i < pdb.chains.size(); i++)
{
- chains.addElement( ( (MCview.PDBChain) pdb.chains.elementAt(i)).id);
+ chains.addElement(((MCview.PDBChain) pdb.chains.elementAt(i)).id);
}
setChainMenuItems(chains);
colourBySequence(ap);
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
- pdbentry.getId());
+ StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+ + pdbentry.getId());
if (pdbentry.getProperty() != null)
{
}
}
-
- viewer.evalStringQuiet("set picking label");
-
this.setTitle(title.toString());
}
}
public void notifyScriptStart(String statusMessage, String additionalInfo)
- {}
+ {
+ }
public void sendConsoleEcho(String strEcho)
{
if (scriptWindow == null)
showConsole(true);
- history.append("\n"+strEcho);
+ history.append("\n" + strEcho);
}
public void sendConsoleMessage(String strStatus)
{
- if(history!=null && strStatus!=null
- && !strStatus.equals("Script completed"))
+ if (history != null && strStatus != null
+ && !strStatus.equals("Script completed"))
{
- history.append("\n"+strStatus);
+ history.append("\n" + strStatus);
}
}
public void notifyScriptTermination(String strStatus, int msWalltime)
- { }
+ {
+ }
public void handlePopupMenu(int x, int y)
{
}
public void notifyNewDefaultModeMeasurement(int count, String strInfo)
- {}
+ {
+ }
public void notifyAtomPicked(int atomIndex, String strInfo)
{
int chainSeparator = strInfo.indexOf(":");
- if(chainSeparator==-1)
+ if (chainSeparator == -1)
chainSeparator = strInfo.indexOf(".");
- String picked =
- strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator);
-
+ String picked = strInfo.substring(strInfo.indexOf("]") + 1,
+ chainSeparator);
if (strInfo.indexOf(":") > -1)
- picked+=strInfo.substring(strInfo.indexOf(":")+1,
- strInfo.indexOf("."));
+ picked += strInfo.substring(strInfo.indexOf(":") + 1, strInfo
+ .indexOf("."));
- picked+=".CA";
+ picked += ".CA";
if (!atomsPicked.contains(picked))
{
- viewer.evalString("select "+picked+";label %n %r:%c");
+ viewer.evalString("select " + picked + ";label %n %r:%c");
atomsPicked.addElement(picked);
}
else
{
- viewer.evalString("select "+picked+";label off");
+ viewer.evalString("select " + picked + ";label off");
atomsPicked.removeElement(picked);
}
}
}
public void sendSyncScript(String script, String appletName)
- {}
+ {
+ }
public void showUrl(String url)
{
- try{
+ try
+ {
ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
- "jmolOutput");
- }catch(java.net.MalformedURLException ex)
- {}
+ "jmolOutput");
+ } catch (java.net.MalformedURLException ex)
+ {
+ }
}
public void showConsole(boolean showConsole)
return 0;
}
- ///End JmolStatusListener
- ///////////////////////////////
+ // /End JmolStatusListener
+ // /////////////////////////////
-
- class RenderPanel
- extends Panel
+ class RenderPanel extends Panel
{
Dimension currentSize = new Dimension();
+
Rectangle rectClip = new Rectangle();
- public void update(Graphics g) {
+ public void update(Graphics g)
+ {
paint(g);
}
+
public void paint(Graphics g)
{
currentSize = this.getSize();