/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
*/
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.ws.EBIFetchClient;
+
+import java.awt.BorderLayout;
-public class PDBViewer extends JInternalFrame implements Runnable
+public class PDBViewer
+ extends JInternalFrame implements Runnable
{
- PDBEntry pdb;
- Sequence sequence;
+
+ /**
+ * The associated sequence in an alignment
+ */
PDBCanvas pdbcanvas;
+ PDBEntry pdbentry;
+ SequenceI[]seq;
+ String[]chains;
+ AlignmentPanel ap;
+ String protocol;
+ String tmpPDBFile;
+
+ public PDBViewer(PDBEntry pdbentry,
+ SequenceI[] seq,
+ String[] chains,
+ AlignmentPanel ap,
+ String protocol)
- public PDBViewer(PDBEntry entry,
- Sequence seq,
- SeqCanvas seqcanvas)
{
- /*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)
{
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();
- }
+ 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();
}
}
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");
}
});
viewMenu.setText("View");
+ background.setText("Background Colour...");
+ background.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ background_actionPerformed(e);
+ }
+ });
+ savePDB.setText("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();
while (userColours.hasMoreElements())
{
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+ 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)
+ 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);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(
+ radioItem.getText());
+ coloursMenu.remove(radioItem);
+ }
+ else
{
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ radioItem.addActionListener(new ActionListener()
{
- 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);
- if(option == JOptionPane.YES_OPTION)
+ 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)
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!
*/
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);
+ }
else
+ {
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();
{
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
{
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();
+ }
+ }
+
+ 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("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();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff