/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
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 java.io.*;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.ws.ebi.EBIFetchClient;
public class PDBViewer extends JInternalFrame implements Runnable
{
- PDBEntry pdb;
+
/**
* The associated sequence in an alignment
*/
- Sequence sequence;
PDBCanvas pdbcanvas;
- String tmpPDBFile;
+ PDBEntry pdbentry;
+
+ SequenceI[] seq;
+
+ String[] chains;
+
+ AlignmentPanel ap;
- public PDBViewer(PDBEntry entry,
- Sequence seq,
- SeqCanvas seqcanvas)
+ String protocol;
+
+ String tmpPDBFile;
+
+ public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ AlignmentPanel ap, String protocol)
{
+ 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();
}
+ StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+ + pdbentry.getFile());
+
+ pdbcanvas = new PDBCanvas();
- if (entry==null)
- return;
- pdb = entry;
- sequence = seq;
- pdbcanvas = new PDBCanvas(seqcanvas, sequence);
+ setContentPane(pdbcanvas);
- if(pdb.getFile()!=null)
+ if (pdbentry.getFile() != null)
{
- try{
- tmpPDBFile = pdb.getFile();
- PDBfile pdbfile = new PDBfile(tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
- pdbcanvas.setPDBFile(pdbfile);
+ try
+ {
+ tmpPDBFile = pdbentry.getFile();
+ PDBfile pdbfile = new PDBfile(tmpPDBFile,
+ jalview.io.AppletFormatAdapter.FILE);
- }catch(java.io.IOException ex)
- {
- ex.printStackTrace();
- }
+ pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+
+ } catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
}
else
{
worker.start();
}
-
-
- 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"));
+ 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();
- 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)
+ EBIFetchClient ebi = new EBIFetchClient();
+ 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()
- {
- public void keyPressed(KeyEvent evt)
- {
- pdbcanvas.keyPressed(evt);
- }
- });
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ pdbcanvas.keyPressed(evt);
+ }
+ });
this.setJMenuBar(jMenuBar1);
fileMenu.setText("File");
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,
+ int option = JOptionPane.showInternalConfirmDialog(
+ jalview.gui.Desktop.desktop,
"Remove from default list?",
"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, "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();
}
{
if (e.getActionCommand().equals("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, "Select Background Colour",
- pdbcanvas.backgroundColour);
-
- if(col!=null)
- {
- pdbcanvas.backgroundColour = col;
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
+ java.awt.Color col = JColorChooser.showDialog(this,
+ "Select Background 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"));
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- try
- {
- BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
- File outFile = chooser.getSelectedFile();
+ 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)
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+ 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.println(data);
}
- out.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
}
+ out.close();
+ in.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff