/*
- * 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
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.popup.*;
-
-public class AppJmol
- extends GStructureViewer
- implements StructureListener, JmolStatusListener, Runnable
+public class AppJmol extends GStructureViewer implements StructureListener,
+ JmolStatusListener, Runnable
{
JmolViewer viewer;
+
JmolPopup jmolpopup;
+
ScriptWindow scriptWindow;
+
PDBEntry pdbentry;
+
SequenceI[] sequence;
- String [] chains;
+
+ 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)
+ public AppJmol(String file, String id, SequenceI[] seq,
+ AlignmentPanel ap, String loadStatus, Rectangle bounds)
{
loadingFromArchive = true;
pdbentry = new PDBEntry();
colourBySequence = false;
seqColour.setSelected(false);
- //jalview.gui.Desktop.addInternalFrame(this, "Loading File",
- // bounds.width,bounds.height);
+ // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
+ // bounds.width,bounds.height);
initJmol(loadStatus);
});
}
-public synchronized void addSequence(SequenceI [] seq)
- {
+ 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 < sequence.length; i++)
+ v.addElement(sequence[i]);
- for(int i=0; i<seq.length; i++)
- if(!v.contains(seq[i]))
- v.addElement(seq[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;
- }
+ SequenceI[] tmp = new SequenceI[v.size()];
+ v.copyInto(tmp);
+ sequence = tmp;
+ }
- public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String [] chains, AlignmentPanel ap)
+ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ AlignmentPanel ap)
{
- //////////////////////////////////
- //Is the pdb file already loaded?
+ // ////////////////////////////////
+ // Is the pdb file already loaded?
String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager()
- .alreadyMappedToFile(pdbentry.getId());
+ .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);
+ 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) {
+ .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
+ // Now this AppJmol is mapped to new sequences. We must add them to
// the exisiting array
- JInternalFrame [] frames = Desktop.instance.getAllFrames();
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
- for(int i=0; i<frames.length; i++)
+ for (int i = 0; i < frames.length; i++)
{
- if(frames[i] instanceof AppJmol)
+ if (frames[i] instanceof AppJmol)
{
- AppJmol topJmol = ((AppJmol)frames[i]);
- if(topJmol.pdbentry.getFile().equals(alreadyMapped))
- {
- topJmol.addSequence(seq);
- break;
- }
+ 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;
- this.setSize(400,400);
- //jalview.gui.Desktop.addInternalFrame(this, "Jmol View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
- // : ""), 400, 400);
+ this.setSize(400, 400);
+ // jalview.gui.Desktop.addInternalFrame(this, "Jmol
+ // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
+ // : ""), 400, 400);
if (pdbentry.getFile() != null)
{
- initJmol("load \""+pdbentry.getFile()+"\"");
+ initJmol("load \"" + pdbentry.getFile() + "\"");
}
else
{
});
}
-
void initJmol(String command)
{
renderPanel = new RenderPanel();
this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
- pdbentry.getId());
+ StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+ + pdbentry.getId());
if (pdbentry.getProperty() != null)
{
}
this.setTitle(title.toString());
- jalview.gui.Desktop.addInternalFrame(this, title.toString(),
- getBounds().width,getBounds().height);
+ jalview.gui.Desktop.addInternalFrame(this, title.toString(),
+ getBounds().width, getBounds().height);
viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter());
-
+ new SmarterJmolAdapter());
viewer.setAppletContext("", null, null, "");
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++)
{
- 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;
- }
- });
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
+ centerViewer();
+ allChainsSelected = false;
+ }
+ });
chainMenu.add(menuItem);
}
boolean allChainsSelected = false;
+
void centerViewer()
{
StringBuffer cmd = new StringBuffer();
- for(int i=0; i<chainMenu.getItemCount(); i++)
+ 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 ");
+ 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);
+ viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
+ + cmd);
}
void closeViewer()
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.getFile());
+ StructureSelectionManager.getStructureSelectionManager()
+ .removeStructureViewerListener(this, pdbentry.getFile());
}
public void run()
EBIFetchClient ebi = new EBIFetchClient();
String query = "pdb:" + pdbentry.getId();
pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
- .getAbsolutePath());
- initJmol("load "+pdbentry.getFile());
- }
- catch (Exception ex)
+ .getAbsolutePath());
+ initJmol("load " + pdbentry.getFile());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
+ oomerror);
+ } catch (Exception ex)
{
ex.printStackTrace();
}
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
{
try
{
- BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));
+ 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)
+ while ((data = in.readLine()) != null)
{
- if (
- ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
- )
+ if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
{
out.println(data);
}
}
out.close();
- }
- catch (Exception ex)
+ } 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())
- );
+ jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
+ 550, 600);
+ cap.setText(StructureSelectionManager.getStructureSelectionManager()
+ .printMapping(pdbentry.getFile()));
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void eps_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void png_actionPerformed(ActionEvent e)
{
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);
+ 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());
+ 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);
+ viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
im.writeImage();
}
}
-
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
lastCommand = null;
colourBySequence = false;
seqColour.setSelected(false);
viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
- +"select LYS,ARG;color blue;select CYS;color yellow");
+ + "select LYS,ARG;color blue;select CYS;color yellow");
}
public void zappoColour_actionPerformed(ActionEvent actionEvent)
colourBySequence = false;
seqColour.setSelected(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 backGround_actionPerformed(ActionEvent actionEvent)
{
java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour",
- null);
+ "Select Background Colour", null);
if (col != null)
{
- viewer.evalStringQuiet("background ["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];");
+ 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){}
- }
-
+ try
+ {
+ jalview.util.BrowserLauncher
+ .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ } catch (Exception ex)
+ {
+ }
+ }
- //////////////////////////////////
- ///StructureListener
+ // ////////////////////////////////
+ // /StructureListener
public String getPdbFile()
{
return pdbentry.getFile();
}
- Pattern pattern = Pattern.compile(
- "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"
- );
+ 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);
}
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");
viewer.evalStringQuiet(eval.toString());
}
- 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;
public void updateColours(Object source)
{
- colourBySequence( (AlignmentPanel) source);
+ colourBySequence((AlignmentPanel) source);
}
-
-//End StructureListener
-////////////////////////////
+ // End StructureListener
+ // //////////////////////////
String lastCommand;
- FeatureRenderer fr=null;
+
+ FeatureRenderer fr = null;
+
public void colourBySequence(AlignmentPanel sourceap)
{
this.ap = sourceap;
- if(!colourBySequence || ap.alignFrame.getCurrentView()!=ap.av)
+ if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
return;
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
if (mapping.length < 1)
- return;
-
+ return;
SequenceRenderer sr = new SequenceRenderer(ap.av);
StringBuffer command = new StringBuffer();
int lastPos = -1;
- for (int sp,s = 0; s < sequence.length; s++)
+ for (int sp, s = 0; s < sequence.length; s++)
{
for (int m = 0; m < mapping.length; m++)
{
if (mapping[m].getSequence() == sequence[s]
- && (sp=ap.av.alignment.findIndex(sequence[s]))>-1)
+ && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
{
SequenceI asp = ap.av.alignment.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
continue;
}
- int pos = mapping[m].getPDBResNum(
- asp.findPosition(r));
+ int pos = mapping[m].getPDBResNum(asp.findPosition(r));
- if (pos < 1 || pos==lastPos)
+ if (pos < 1 || pos == lastPos)
continue;
lastPos = pos;
if (showFeatures)
col = fr.findFeatureColour(col, asp, 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, 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;
StringBuffer condenseCommand(StringBuffer 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.delete(0, 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 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
ssm = StructureSelectionManager.getStructureSelectionManager();
- MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE);
+ 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++)
+ for (int i = 0; i < pdbFile.chains.size(); i++)
{
- chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);
+ chains
+ .addElement(((MCview.PDBChain) pdbFile.chains.elementAt(i)).id);
}
setChainMenuItems(chains);
jmolpopup.updateComputedMenus();
- if(!loadingFromArchive)
+ if (!loadingFromArchive)
{
- viewer.evalStringQuiet(
- "select backbone;restrict;cartoon;wireframe off;spacefill off");
+ viewer
+ .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
colourBySequence(ap);
}
- if (fr!=null)
+ if (fr != null)
fr.featuresAdded();
loadingFromArchive = false;
}
public void notifyScriptStart(String statusMessage, String additionalInfo)
- {}
+ {
+ }
public void sendConsoleEcho(String strEcho)
{
}
public void notifyNewDefaultModeMeasurement(int count, String strInfo)
- {}
+ {
+ }
public void notifyAtomPicked(int atomIndex, String strInfo)
{
String picked = resnum;
if (chainId != null)
- picked+=(":"+chainId.substring(1, chainId.length()));
-
- picked+=".CA";
+ picked += (":" + chainId.substring(1, chainId.length()));
+ picked += ".CA";
if (!atomsPicked.contains(picked))
{
- if(chainId!=null)
- viewer.evalString("select "+picked+";label %n %r:%c");
- else
- viewer.evalString("select "+picked+";label %n %r");
+ 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");
+ viewer.evalString("select " + picked + ";label off");
atomsPicked.removeElement(picked);
}
}
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 (showConsole)
{
- if(splitPane==null)
+ if (splitPane == null)
{
splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
splitPane.setTopComponent(renderPanel);
this.getContentPane().add(splitPane, BorderLayout.CENTER);
}
- splitPane.setDividerLocation(getHeight()-200);
+ splitPane.setDividerLocation(getHeight() - 200);
splitPane.validate();
}
else
return 0;
}
- ///End JmolStatusListener
- ///////////////////////////////
+ // /End JmolStatusListener
+ // /////////////////////////////
-
- class RenderPanel
- extends JPanel
+ class RenderPanel extends JPanel
{
final Dimension currentSize = new Dimension();
+
final Rectangle rectClip = new Rectangle();
public void paintComponent(Graphics g)
g.setFont(new Font("Verdana", Font.BOLD, 14));
g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
}
- else if(fileLoadingError!=null)
+ 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);
+ currentSize.height / 2);
}
else
{
git://source.jalview.org / jalview.git / blobdiff