/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package MCview;
-import java.io.*;
-
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.*;
-import jalview.schemes.*;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.OOMWarning;
+import jalview.gui.UserDefinedColours;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.PrintWriter;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+
public class PDBViewer extends JInternalFrame implements Runnable
{
try
{
tmpPDBFile = pdbentry.getFile();
- PDBfile pdbfile = new PDBfile(tmpPDBFile,
+ PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
jalview.io.AppletFormatAdapter.FILE);
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
worker.start();
}
- if (pdbentry.getProperty() != null)
+ String method = (String) pdbentry.getProperty("method");
+ if (method != null)
{
- if (pdbentry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
- }
- if (pdbentry.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
- }
+ title.append(" Method: ");
+ title.append(method);
+ }
+ String ch = (String) pdbentry.getProperty("chains");
+ if (ch != null)
+ {
+ title.append(" Chain:");
+ title.append(ch);
}
Desktop.addInternalFrame(this, title.toString(), 400, 400);
}
+ @Override
public void run()
{
try
{
EBIFetchClient ebi = new EBIFetchClient();
String query = "pdb:" + pdbentry.getId();
- pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+ pdbentry.setFile(ebi.fetchDataAsFile(query, "default", ".xml")
.getAbsolutePath());
if (pdbentry.getFile() != null)
+ {
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+ }
} catch (Exception ex)
{
pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
{
this.addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
pdbcanvas.keyPressed(evt);
png.setText("PNG");
png.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
png_actionPerformed(e);
eps.setText("EPS");
eps.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
eps_actionPerformed(e);
mapping.setText(MessageManager.getString("label.view_mapping"));
mapping.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
mapping_actionPerformed(e);
wire.setText(MessageManager.getString("label.wireframe"));
wire.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
wire_actionPerformed(e);
depth.setText(MessageManager.getString("label.depthcue"));
depth.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
depth_actionPerformed(e);
zbuffer.setText(MessageManager.getString("label.z_buffering"));
zbuffer.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zbuffer_actionPerformed(e);
charge.setText(MessageManager.getString("label.charge_cysteine"));
charge.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
charge_actionPerformed(e);
chain.setText(MessageManager.getString("action.by_chain"));
chain.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
chain_actionPerformed(e);
seqButton.setText(MessageManager.getString("action.by_sequence"));
seqButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
seqButton_actionPerformed(e);
allchains.setText(MessageManager.getString("label.show_all_chains"));
allchains.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
allchains_itemStateChanged(e);
zappo.setText(MessageManager.getString("label.zappo"));
zappo.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zappo_actionPerformed(e);
taylor.setText(MessageManager.getString("label.taylor"));
taylor.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
taylor_actionPerformed(e);
hydro.setText(MessageManager.getString("label.hydrophobicity"));
hydro.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hydro_actionPerformed(e);
helix.setText(MessageManager.getString("label.helix_propensity"));
helix.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
helix_actionPerformed(e);
strand.setText(MessageManager.getString("label.strand_propensity"));
strand.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
strand_actionPerformed(e);
turn.setText(MessageManager.getString("label.turn_propensity"));
turn.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
turn_actionPerformed(e);
buried.setText(MessageManager.getString("label.buried_index"));
buried.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
buried_actionPerformed(e);
user.setText(MessageManager.getString("action.user_defined"));
user.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
user_actionPerformed(e);
}
});
viewMenu.setText(MessageManager.getString("action.view"));
- background.setText(MessageManager.getString("label.background_colour") + "...");
+ background
+ .setText(MessageManager.getString("action.background_colour"));
background.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
background_actionPerformed(e);
savePDB.setText(MessageManager.getString("label.pdb_file"));
savePDB.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
savePDB_actionPerformed(e);
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
- if (evt.isControlDown()
- || SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger()) // Mac
{
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- 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());
- coloursMenu.remove(radioItem);
- }
- else
+ offerRemoval(radioItem);
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
+ {
+ offerRemoval(radioItem);
+ }
+ }
+
+ /**
+ * @param radioItem
+ */
+ void offerRemoval(final JRadioButtonMenuItem radioItem)
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ 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());
+ coloursMenu.remove(radioItem);
+ }
+ else
+ {
+ radioItem.addActionListener(new ActionListener()
{
- radioItem.addActionListener(new ActionListener()
+ @Override
+ public void actionPerformed(ActionEvent evt)
{
- public void actionPerformed(ActionEvent evt)
- {
- user_actionPerformed(evt);
- }
- });
- }
+ user_actionPerformed(evt);
+ }
+ });
}
}
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
user_actionPerformed(evt);
*/
public void eps_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
/**
*/
public void png_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.PNG);
+ makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
}
- void makePDBImage(int type)
+ void makePDBImage(jalview.util.ImageMaker.TYPE type)
{
int width = pdbcanvas.getWidth();
int height = pdbcanvas.getHeight();
jalview.util.ImageMaker im;
- if (type == jalview.util.ImageMaker.PNG)
+ if (type == jalview.util.ImageMaker.TYPE.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.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null, null, 0, false);
+ }
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle(), null, 0, false);
}
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.TYPE.SVG, "Make SVG file from PCA",
+ width, height, null, this.getTitle(), null, 0, false);
}
if (im.getGraphics() != null)
try
{
cap.setText(pdbcanvas.mappingDetails.toString());
- Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"), 550, 600);
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
} catch (OutOfMemoryError oom)
{
new OOMWarning("Opening sequence to structure mapping report", oom);
public void user_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))
+ if (e.getActionCommand().equals(
+ MessageManager.getString("action.user_defined")))
{
// new UserDefinedColours(pdbcanvas, null);
}
public void background_actionPerformed(ActionEvent e)
{
java.awt.Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_backgroud_colour"), pdbcanvas.backgroundColour);
+ MessageManager.getString("label.select_backgroud_colour"),
+ pdbcanvas.backgroundColour);
if (col != null)
{
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
git://source.jalview.org / jalview.git / blobdiff