/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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 javax.swing.*;
+import java.io.*;
+
import java.awt.event.*;
+import javax.swing.*;
+
import jalview.datamodel.*;
-import jalview.schemes.*;
import jalview.gui.*;
-import jalview.io.EBIFetchClient;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
public class PDBViewer extends JInternalFrame implements Runnable
{
- PDBEntry pdb;
- Sequence sequence;
+
+ /**
+ * The associated sequence in an alignment
+ */
PDBCanvas pdbcanvas;
+ PDBEntry pdbentry;
- public PDBViewer(PDBEntry entry,
- Sequence seq,
- SeqCanvas seqcanvas)
+ SequenceI[] seq;
+
+ String[] chains;
+
+ AlignmentPanel ap;
+
+ String protocol;
+
+ String tmpPDBFile;
+
+ public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ AlignmentPanel ap, String protocol)
{
- /*Uncomment this to modify in Jbuilder
+ 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;
+ }
- Thread worker = new Thread(this);
- worker.start();
+ StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+ + pdbentry.getFile());
- pdbcanvas = new PDBCanvas(seqcanvas, seq);
+ pdbcanvas = new PDBCanvas();
setContentPane(pdbcanvas);
- StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
- if(pdb.getProperty()!=null)
+
+ if (pdbentry.getFile() != null)
+ {
+ try
+ {
+ tmpPDBFile = pdbentry.getFile();
+ PDBfile pdbfile = new PDBfile(tmpPDBFile,
+ jalview.io.AppletFormatAdapter.FILE);
+
+ pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+
+ } catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ else
{
- if (pdb.getProperty().get("method")!=null)
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ if (pdbentry.getProperty() != 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"));
+ title.append(pdbentry.getProperty().get("chains"));
}
}
- Desktop.addInternalFrame(this,title.toString(),400, 400);
+ Desktop.addInternalFrame(this, title.toString(), 400, 400);
}
public void run()
try
{
EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdb.getId();
- String[] result = ebi.fetchData(query, "default","raw");
- if (result!=null) {
- PDBfile pdbfile = new PDBfile(result);
- pdbcanvas.setPDBFile(pdbfile);
- } else {
- throw new Exception("Empty result for WSDbFetch Query: "+query);
- }
+ String query = "pdb:" + pdbentry.getId();
+ pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+ .getAbsolutePath());
- try
- {
- jbInit();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- catch (Exception ex)
+ 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()
- {
- public void keyPressed(KeyEvent evt)
- {
- pdbcanvas.keyPressed(evt);
- }
- });
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ pdbcanvas.keyPressed(evt);
+ }
+ });
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");
+ 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(MessageManager.getString("label.pdb_file"));
+ savePDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ savePDB_actionPerformed(e);
+ }
+ });
jMenuBar1.add(fileMenu);
jMenuBar1.add(coloursMenu);
jMenuBar1.add(viewMenu);
fileMenu.add(saveMenu);
fileMenu.add(mapping);
+ saveMenu.add(savePDB);
saveMenu.add(png);
saveMenu.add(eps);
coloursMenu.add(seqButton);
coloursMenu.add(turn);
coloursMenu.add(buried);
coloursMenu.add(user);
+ coloursMenu.add(background);
ButtonGroup bg = new ButtonGroup();
bg.add(seqButton);
bg.add(chain);
bg.add(buried);
bg.add(user);
-
- if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+ 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());
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+ userColours.nextElement().toString());
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isControlDown()
+ || SwingUtilities.isRightMouseButton(evt))
{
- public void mousePressed(MouseEvent evt)
- {
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
+ 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)
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
+ coloursMenu.remove(radioItem);
+ }
+ else
+ {
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
{
- jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
- coloursMenu.remove(radioItem);
+ user_actionPerformed(evt);
}
- else
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- user_actionPerformed(evt);
- }
- });
- }
+ });
}
- });
+ }
+ }
+ });
radioItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
}
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 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)
{
- makePDBImage(jalview.util.ImageMaker.PNG);
+ makePDBImage(jalview.util.ImageMaker.PNG);
}
void makePDBImage(int type)
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);
+ {
+ 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)
{
im.writeImage();
}
}
+
public void charge_actionPerformed(ActionEvent e)
{
pdbcanvas.bysequence = false;
pdbcanvas.pdb.setChargeColours();
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
{
pdbcanvas.bysequence = false;
pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
{
pdbcanvas.bysequence = false;
pdbcanvas.pdb.setChainColours();
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
public void zbuffer_actionPerformed(ActionEvent e)
{
- pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
public void molecule_actionPerformed(ActionEvent e)
{
- pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
public void depth_actionPerformed(ActionEvent e)
{
- pdbcanvas.depthcue = ! pdbcanvas.depthcue;
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.depthcue = !pdbcanvas.depthcue;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
public void wire_actionPerformed(ActionEvent e)
{
- pdbcanvas.wire = ! pdbcanvas.wire;
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.wire = !pdbcanvas.wire;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
pdbcanvas.updateSeqColours();
}
-
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;
pdbcanvas.pdb.setColours(new ZappoColourScheme());
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
{
pdbcanvas.bysequence = false;
pdbcanvas.pdb.setColours(new TaylorColourScheme());
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
{
pdbcanvas.bysequence = false;
pdbcanvas.pdb.setColours(new HelixColourScheme());
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
{
pdbcanvas.bysequence = false;
pdbcanvas.pdb.setColours(new StrandColourScheme());
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
{
pdbcanvas.bysequence = false;
pdbcanvas.pdb.setColours(new TurnColourScheme());
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
{
pdbcanvas.bysequence = false;
pdbcanvas.pdb.setColours(new BuriedColourScheme());
- pdbcanvas.redrawneeded=true;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
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;
+ pdbcanvas.redrawneeded = true;
pdbcanvas.repaint();
}
}
+
+ public void background_actionPerformed(ActionEvent e)
+ {
+ java.awt.Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_backgroud_colour"), pdbcanvas.backgroundColour);
+
+ if (col != null)
+ {
+ pdbcanvas.backgroundColour = col;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+ }
+
+ public void savePDB_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save PDB File");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ try
+ {
+ BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
+ 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();
+ in.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff