/*
- * 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.bin.Cache;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.gui.OOMWarning;
+import jalview.gui.UserDefinedColours;
+import jalview.io.AppletFormatAdapter;
+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.ImageMaker;
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 java.util.Enumeration;
+
+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;
+import javax.swing.SwingUtilities;
+
public class PDBViewer extends JInternalFrame implements Runnable
{
try
{
tmpPDBFile = pdbentry.getFile();
- PDBfile pdbfile = new PDBfile(tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
+ PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
+ AppletFormatAdapter.FILE);
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
.getAbsolutePath());
if (pdbentry.getFile() != null)
+ {
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+ }
} catch (Exception ex)
{
pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
bg.add(buried);
bg.add(user);
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ if (UserDefinedColours.getUserColourSchemes() != null)
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ Enumeration userColours = UserDefinedColours
.getUserColourSchemes().keys();
while (userColours.hasMoreElements())
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
int option = JOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop,
+ Desktop.desktop,
MessageManager
.getString("label.remove_from_default_list"),
MessageManager
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
- jalview.gui.UserDefinedColours
+ UserDefinedColours
.removeColourFromDefaults(radioItem.getText());
coloursMenu.remove(radioItem);
}
*/
public void eps_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ makePDBImage(ImageMaker.TYPE.EPS);
}
/**
*/
public void png_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.PNG);
+ makePDBImage(ImageMaker.TYPE.PNG);
}
- void makePDBImage(int type)
+ void makePDBImage(ImageMaker.TYPE type)
{
int width = pdbcanvas.getWidth();
int height = pdbcanvas.getHeight();
- jalview.util.ImageMaker im;
+ ImageMaker im;
- if (type == jalview.util.ImageMaker.PNG)
+ if (type == ImageMaker.TYPE.PNG)
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+ im = new ImageMaker(this, ImageMaker.TYPE.PNG,
"Make PNG image from view", width, height, null, null);
}
- else
+ else if (type == ImageMaker.TYPE.EPS)
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+ im = new ImageMaker(this, ImageMaker.TYPE.EPS,
"Make EPS file from view", width, height, null,
this.getTitle());
}
+ else
+ {
+
+ im = new ImageMaker(this, ImageMaker.TYPE.SVG,
+ "Make SVG file from PCA",
+ width, height, null, this.getTitle());
+ }
if (im.getGraphics() != null)
{
public void mapping_actionPerformed(ActionEvent e)
{
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
cap.setText(pdbcanvas.mappingDetails.toString());
public void savePDB_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));