/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
* 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.
- *
+ *
+ * Jalview 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
import java.io.*;
-import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
-import java.util.BitSet;
import jalview.datamodel.*;
import jalview.gui.*;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
-import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-import org.jmol.util.Logger;
-import org.jmol.popup.*;
-
-public class PDBViewer
- extends JInternalFrame implements Runnable
+public class PDBViewer extends JInternalFrame implements Runnable
{
- PDBEntry pdb;
+
/**
* The associated sequence in an alignment
*/
- Sequence sequence;
PDBCanvas pdbcanvas;
+
+ PDBEntry pdbentry;
+
+ SequenceI[] seq;
+
+ String[] chains;
+
+ AlignmentPanel ap;
+
+ String protocol;
+
String tmpPDBFile;
- public PDBViewer(PDBEntry entry,
- Sequence seq,
- SeqCanvas seqcanvas)
+ public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ AlignmentPanel ap, String protocol)
{
- /* try
+ this.pdbentry = pdbentry;
+ this.seq = seq;
+ this.chains = chains;
+ this.ap = ap;
+ this.protocol = protocol;
+
+ try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
- if (entry == null)
- {
- return;
- }
- pdb = entry;
- sequence = seq;
- pdbcanvas = new PDBCanvas(seqcanvas, sequence);
+ StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+ + pdbentry.getFile());
+
+ pdbcanvas = new PDBCanvas();
- if (pdb.getFile() != null)
+ setContentPane(pdbcanvas);
+
+ if (pdbentry.getFile() != null)
{
try
{
- tmpPDBFile = pdb.getFile();
+ tmpPDBFile = pdbentry.getFile();
PDBfile pdbfile = new PDBfile(tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
- pdbcanvas.setPDBFile(pdbfile);
+ jalview.io.AppletFormatAdapter.FILE);
- }
- catch (java.io.IOException ex)
+ pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+
+ } catch (java.io.IOException ex)
{
ex.printStackTrace();
}
worker.start();
}
- public void run()
- {
- try
- {
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdb.getId();
- tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
- if (tmpPDBFile != null)
- {
- PDBfile pdbfile = new PDBfile(tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
- pdbcanvas.setPDBFile(pdbfile);
- }
- else
- {
- throw new Exception("Empty result for WSDbFetch Query: " + query);
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- showErrorMessage("Failed to retrieve PDB structure.");
-// this.dispose();
- }
- }
-
-
- setContentPane(pdbcanvas);
- StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
- if (pdb.getProperty() != null)
+ if (pdbentry.getProperty() != null)
{
- if (pdb.getProperty().get("method") != null)
+ if (pdbentry.getProperty().get("method") != null)
{
title.append(" Method: ");
- title.append(pdb.getProperty().get("method"));
+ title.append(pdbentry.getProperty().get("method"));
}
- if (pdb.getProperty().get("chains") != null)
+ if (pdbentry.getProperty().get("chains") != null)
{
title.append(" Chain:");
- title.append(pdb.getProperty().get("chains"));
- }
- }
- */
-
- Container contentPane = getContentPane();
- JmolPanel jmolPanel = new JmolPanel();
- contentPane.add(jmolPanel);
-
- JmolViewer viewer = jmolPanel.viewer;
-
-
- System.out.println(entry.getFile()+" "+entry.getId());
- viewer.openFile(entry.getFile());
-
-
- StringBuffer string = new StringBuffer();
-
- for(int i=0; i<seq.getLength(); i++)
- {
- Color col = seqcanvas.getSequenceRenderer().getResidueBoxColour(seq, i);
-
- string.append("select " + i + "B; color [" +
- col.getRed()+","
- +col.getGreen()+","
- +col.getBlue()+"]; ");
- }
- System.out.println(string);
-
- viewer.evalString(string.toString());
-
-
- String strError = viewer.getOpenFileError();
- if (strError != null)
- Logger.error(strError);
-
-
- // Desktop.addInternalFrame(this,
- // seq.getName() + ":1GAQ"
- // , 400, 400);
-
- }
-
-
-
-
- static class JmolPanel
- extends JPanel implements JmolSelectionListener
- {
- JmolViewer viewer;
- JmolAdapter adapter;
- JmolPanel()
- {
- adapter = new SmarterJmolAdapter(null);
- viewer = org.jmol.viewer.Viewer.allocateViewer(this, adapter);
- viewer.addSelectionListener(this);
-
- MyStatusListener myStatusListener;
- myStatusListener = new MyStatusListener();
- viewer.setJmolStatusListener(myStatusListener);
-
- JFrame frame = new JFrame("script window");
- // scriptWindow = new ScriptWindow(viewer, frame);
-
- myStatusListener.jmolpopup = JmolPopup.newJmolPopup(viewer);
- }
- public ScriptWindow scriptWindow;
- class MyStatusListener implements JmolStatusListener
- {
-
- JmolPopup jmolpopup ;
-
-
- public String eval(String strEval) {
- return "# 'eval' is implemented only for the applet.";
- }
-
- public void createImage(String file, String type, int quality) {
- System.out.println("CREATE IMAGE");
- // ImageCreator c = new ImageCreator(viewer, status);
- // c.createImage(file, type, quality);
- }
-
- public void setCallbackFunction(String callbackType, String callbackFunction) {
- // applet only?
- }
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile,
- String errorMsg) {
-
- }
-
- public void notifyFrameChanged(int frameNo) {
- // Note: twos-complement. To get actual frame number, use
- // Math.max(frameNo, -2 - frameNo)
- // -1 means all frames are now displayed
-
- boolean isAnimationRunning = (frameNo <= -2);
-
- }
-
- public void notifyScriptStart(String statusMessage, String additionalInfo) {
- //System.out.println("notifyScriptStart:" + statusMessage + (additionalInfo == "" ? "" : 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) {
- // measurementTable.updateTables();
- }
-
- public void notifyAtomPicked(int atomIndex, String strInfo) {
-
- System.out.println("ATOM PICKED "+atomIndex+" "+strInfo);
- if (scriptWindow != null) {
- scriptWindow.sendConsoleMessage(strInfo);
- scriptWindow.sendConsoleMessage("\n");
- }
- }
-
- public void notifyAtomHovered(int atomIndex, String strInfo) {
-System.out.println("HOVER "+atomIndex+" "+strInfo);
- }
-
- public void sendSyncScript(String script, String appletName) {
- }
-
- public void showUrl(String url) {
- }
-
- public void showConsole(boolean showConsole) {
- System.out.println("SHOW CONSOLE" +(scriptWindow==null));
- if (scriptWindow == null)
- return;
- if (showConsole)
- scriptWindow.show();
- else
- scriptWindow.hide();
- }
-
- public float functionXY(String functionName, int x, int y) {
- return 0; // for user-defined isosurface functions (testing only -- bob hanson)
- }
-
- }
-
-
- class ScriptWindowAction extends AbstractAction {
-
- public ScriptWindowAction() {
- super("BLAH");
- }
-
- public void actionPerformed(ActionEvent e) {
- if (scriptWindow != null)
- scriptWindow.show();
+ title.append(pdbentry.getProperty().get("chains"));
}
}
-
- /**
- * Called when the selected atoms change
- * @param selection bit set giving selection of atom indexes
- */
- public void selectionChanged(BitSet selection)
- {
- System.out.println("SELECTION: "+selection);
- }
-
-
- public JmolSimpleViewer getViewer()
- {
- return viewer;
- }
-
- final Dimension currentSize = new Dimension();
- final Rectangle rectClip = new Rectangle();
-
- public void paint(Graphics g)
- {
-
- getSize(currentSize);
- g.getClipBounds(rectClip);
- viewer.renderScreenImage(g, currentSize, rectClip);
- }
+ Desktop.addInternalFrame(this, title.toString(), 400, 400);
}
-
public void run()
{
try
{
EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdb.getId();
- tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
- if (tmpPDBFile != null)
- {
- PDBfile pdbfile = new PDBfile(tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
- pdbcanvas.setPDBFile(pdbfile);
- }
- else
- {
- throw new Exception("Empty result for WSDbFetch Query: " + query);
- }
- }
- catch (Exception ex)
+ String query = "pdb:" + pdbentry.getId();
+ pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+ .getAbsolutePath());
+
+ if (pdbentry.getFile() != null)
+ pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+ } catch (Exception ex)
{
+ pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
ex.printStackTrace();
- showErrorMessage("Failed to retrieve PDB structure.");
-// this.dispose();
}
}
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
this.addKeyListener(new KeyAdapter()
{
});
this.setJMenuBar(jMenuBar1);
- fileMenu.setText("File");
- coloursMenu.setText("Colours");
- saveMenu.setActionCommand("Save Image");
- saveMenu.setText("Save As");
+ fileMenu.setText(MessageManager.getString("action.file"));
+ coloursMenu.setText(MessageManager.getString("label.colours"));
+ saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
+ saveMenu.setText(MessageManager.getString("action.save_as"));
png.setText("PNG");
png.addActionListener(new ActionListener()
{
eps_actionPerformed(e);
}
});
- mapping.setText("View Mapping");
+ mapping.setText(MessageManager.getString("label.view_mapping"));
mapping.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
mapping_actionPerformed(e);
}
});
- wire.setText("Wireframe");
+ wire.setText(MessageManager.getString("label.wireframe"));
wire.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
depth.setSelected(true);
- depth.setText("Depthcue");
+ depth.setText(MessageManager.getString("label.depthcue"));
depth.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
zbuffer.setSelected(true);
- zbuffer.setText("Z Buffering");
+ zbuffer.setText(MessageManager.getString("label.z_buffering"));
zbuffer.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
zbuffer_actionPerformed(e);
}
});
- charge.setText("Charge & Cysteine");
+ charge.setText(MessageManager.getString("label.charge_cysteine"));
charge.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
charge_actionPerformed(e);
}
});
- chain.setText("By Chain");
+ chain.setText(MessageManager.getString("action.by_chain"));
chain.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
seqButton.setSelected(true);
- seqButton.setText("By Sequence");
+ seqButton.setText(MessageManager.getString("action.by_sequence"));
seqButton.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
allchains.setSelected(true);
- allchains.setText("Show All Chains");
+ allchains.setText(MessageManager.getString("label.show_all_chains"));
allchains.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
allchains_itemStateChanged(e);
}
});
- zappo.setText("Zappo");
+ zappo.setText(MessageManager.getString("label.zappo"));
zappo.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
zappo_actionPerformed(e);
}
});
- taylor.setText("Taylor");
+ taylor.setText(MessageManager.getString("label.taylor"));
taylor.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
taylor_actionPerformed(e);
}
});
- hydro.setText("Hydro");
+ hydro.setText(MessageManager.getString("label.hydrophobicity"));
hydro.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
hydro_actionPerformed(e);
}
});
- helix.setText("Helix");
+ helix.setText(MessageManager.getString("label.helix_propensity"));
helix.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
helix_actionPerformed(e);
}
});
- strand.setText("Strand");
+ strand.setText(MessageManager.getString("label.strand_propensity"));
strand.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
strand_actionPerformed(e);
}
});
- turn.setText("Turn");
+ turn.setText(MessageManager.getString("label.turn_propensity"));
turn.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
turn_actionPerformed(e);
}
});
- buried.setText("Buried");
+ buried.setText(MessageManager.getString("label.buried_index"));
buried.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
buried_actionPerformed(e);
}
});
- user.setText("User Defined...");
+ user.setText(MessageManager.getString("action.user_defined"));
user.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
user_actionPerformed(e);
}
});
- viewMenu.setText("View");
- background.setText("Background Colour...");
+ viewMenu.setText(MessageManager.getString("action.view"));
+ background.setText(MessageManager.getString("label.background_colour") + "...");
background.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
background_actionPerformed(e);
}
});
- savePDB.setText("PDB File");
+ savePDB.setText(MessageManager.getString("label.pdb_file"));
savePDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
- getUserColourSchemes().keys();
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
while (userColours.hasMoreElements())
{
final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.
- nextElement().toString());
+ userColours.nextElement().toString());
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
public void mousePressed(MouseEvent evt)
{
- if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ if (evt.isControlDown()
+ || SwingUtilities.isRightMouseButton(evt))
{
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
- Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
- JOptionPane.YES_NO_OPTION);
+ int option = JOptionPane.showInternalConfirmDialog(
+ jalview.gui.Desktop.desktop,
+ MessageManager.getString("label.remove_from_default_list"),
+ MessageManager.getString("label.remove_user_defined_colour"),
+ JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
- jalview.gui.UserDefinedColours.removeColourFromDefaults(
- radioItem.getText());
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
coloursMenu.remove(radioItem);
}
else
}
JMenuBar jMenuBar1 = new JMenuBar();
+
JMenu fileMenu = new JMenu();
+
JMenu coloursMenu = new JMenu();
+
JMenu saveMenu = new JMenu();
+
JMenuItem png = new JMenuItem();
+
JMenuItem eps = new JMenuItem();
+
JMenuItem mapping = new JMenuItem();
+
JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
+
JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
+
JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
+
JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem user = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
+
JMenu viewMenu = new JMenu();
+
JMenuItem background = new JMenuItem();
+
JMenuItem savePDB = new JMenuItem();
/**
* 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)
public void mapping_actionPerformed(ActionEvent e)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- // Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
- cap.setText(pdbcanvas.mappingDetails.toString());
+ try
+ {
+ cap.setText(pdbcanvas.mappingDetails.toString());
+ Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"), 550, 600);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Opening sequence to structure mapping report", oom);
+ cap.dispose();
+ }
}
public void allchains_itemStateChanged(ItemEvent e)
pdbcanvas.setAllchainsVisible(allchains.getState());
}
- void showErrorMessage(String error)
- {
- // JOptionPane.showInternalMessageDialog(Desktop.desktop,
- // error, "PDB Viewer Error",
- // JOptionPane.WARNING_MESSAGE);
- }
-
public void zappo_actionPerformed(ActionEvent e)
{
pdbcanvas.bysequence = false;
public void user_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))
{
- new UserDefinedColours(pdbcanvas, null);
+ // new UserDefinedColours(pdbcanvas, null);
}
else
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.
- getUserColourSchemes().get(e.getActionCommand());
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ .getUserColourSchemes().get(e.getActionCommand());
pdbcanvas.pdb.setColours(udc);
pdbcanvas.redrawneeded = true;
public void background_actionPerformed(ActionEvent e)
{
java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour",
- pdbcanvas.backgroundColour);
+ MessageManager.getString("label.select_backgroud_colour"), pdbcanvas.backgroundColour);
if (col != null)
{
public void savePDB_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"));
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
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)
+ in.close();
+ } catch (Exception ex)
{
ex.printStackTrace();
}
git://source.jalview.org / jalview.git / blobdiff