import jalview.datamodel.SequenceI;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
import jalview.gui.UserDefinedColours;
+import jalview.io.DataSourceType;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.schemes.BuriedColourScheme;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
+import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.PrintWriter;
+import java.util.Map;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
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
AlignmentPanel ap;
- String protocol;
+ DataSourceType protocol;
String tmpPDBFile;
public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, String protocol)
+ AlignmentPanel ap, DataSourceType protocol)
{
this.pdbentry = pdbentry;
this.seq = seq;
{
tmpPDBFile = pdbentry.getFile();
PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
+ DataSourceType.FILE);
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
{
EBIFetchClient ebi = new EBIFetchClient();
String query = "pdb:" + pdbentry.getId();
- pdbentry.setFile(ebi.fetchDataAsFile(query, "default", ".xml")
+ pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "xml")
.getAbsolutePath());
if (pdbentry.getFile() != null)
bg.add(buried);
bg.add(user);
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
+ .getUserColourSchemes();
+ if (userColourSchemes != null)
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
+ for (String userColour : userColourSchemes.keySet())
{
final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
+ userColour);
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
{
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
- int option = JOptionPane.showInternalConfirmDialog(
+ int option = JvOptionPane.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)
+ JvOptionPane.YES_NO_OPTION);
+ if (option == JvOptionPane.YES_OPTION)
{
jalview.gui.UserDefinedColours
.removeColourFromDefaults(radioItem.getText());
}
else
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ UserColourScheme udc = UserDefinedColours
.getUserColourSchemes().get(e.getActionCommand());
pdbcanvas.pdb.setColours(udc);
public void background_actionPerformed(ActionEvent e)
{
- java.awt.Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_backgroud_colour"),
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_background_colour"),
pdbcanvas.backgroundColour);
if (col != null)