/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* 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.
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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
{
public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap, String protocol)
-
{
this.pdbentry = pdbentry;
this.seq = seq;
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();
}
});
viewMenu.setText(MessageManager.getString("action.view"));
- background.setText(MessageManager.getString("label.background_colour") + "...");
+ background.setText(MessageManager.getString("label.background_colour")
+ + "...");
background.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
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,
- MessageManager.getString("label.remove_from_default_list"),
- MessageManager.getString("label.remove_user_defined_colour"),
+ 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
+ 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());
- 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)
{
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("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