/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 jalview.appletgui;
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.api.SequenceStructureBinding;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.io.*;
-
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FileParse;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.TextArea;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
+
public class AppletJmol extends EmbmenuFrame implements
// StructureListener,
- KeyListener, ActionListener, ItemListener, SequenceStructureBinding
+ KeyListener, ActionListener, ItemListener
{
Menu fileMenu = new Menu(MessageManager.getString("action.file"));
Menu helpMenu = new Menu(MessageManager.getString("action.help"));
- MenuItem mappingMenuItem = new MenuItem(MessageManager.getString("label.view_mapping"));
+ MenuItem mappingMenuItem = new MenuItem(
+ MessageManager.getString("label.view_mapping"));
- CheckboxMenuItem seqColour = new CheckboxMenuItem(MessageManager.getString("action.by_sequence"), true);
+ CheckboxMenuItem seqColour = new CheckboxMenuItem(
+ MessageManager.getString("action.by_sequence"), true);
- CheckboxMenuItem jmolColour = new CheckboxMenuItem(MessageManager.getString("action.using_jmol"), false);
+ CheckboxMenuItem jmolColour = new CheckboxMenuItem(
+ MessageManager.getString("action.using_jmol"), false);
MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
- MenuItem charge = new MenuItem(MessageManager.getString("label.charge_cysteine"));
+ MenuItem charge = new MenuItem(
+ MessageManager.getString("label.charge_cysteine"));
MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
- MenuItem hydro = new MenuItem(MessageManager.getString("label.hydrophobicity"));
+ MenuItem hydro = new MenuItem(
+ MessageManager.getString("label.hydrophobicity"));
- MenuItem helix = new MenuItem(MessageManager.getString("label.helix_propensity"));
+ MenuItem helix = new MenuItem(
+ MessageManager.getString("label.helix_propensity"));
- MenuItem strand = new MenuItem(MessageManager.getString("label.strand_propensity"));
+ MenuItem strand = new MenuItem(
+ MessageManager.getString("label.strand_propensity"));
- MenuItem turn = new MenuItem(MessageManager.getString("label.turn_propensity"));
+ MenuItem turn = new MenuItem(
+ MessageManager.getString("label.turn_propensity"));
- MenuItem buried = new MenuItem(MessageManager.getString("label.buried_index"));
+ MenuItem buried = new MenuItem(
+ MessageManager.getString("label.buried_index"));
- MenuItem purinepyrimidine = new MenuItem(MessageManager.getString("label.purine_pyrimidine"));
+ MenuItem purinepyrimidine = new MenuItem(
+ MessageManager.getString("label.purine_pyrimidine"));
- MenuItem user = new MenuItem(MessageManager.getString("label.user_defined_colours"));
+ MenuItem user = new MenuItem(
+ MessageManager.getString("label.user_defined_colours"));
- MenuItem jmolHelp = new MenuItem(MessageManager.getString("label.jmol_help"));
+ MenuItem jmolHelp = new MenuItem(
+ MessageManager.getString("label.jmol_help"));
Panel scriptWindow;
String[][] boundchains, boolean align, AlignmentPanel ap,
String protocol)
{
- throw new Error("Not yet implemented.");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
}
if (freader == null)
{
- throw new Exception(
- "Invalid datasource. Could not obtain Reader.");
+ throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
}
jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
StringBuffer sb = new StringBuffer();
try
{
- for (int s = 0; s < jmb.pdbentry.length; s++)
+ for (int s = 0; s < jmb.getPdbCount(); s++)
{
- sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
+ sb.append(jmb.printMapping(jmb.getPdbEntry(s).getFile()));
sb.append("\n");
}
cap.setText(sb.toString());
.println("Out of memory when trying to create dialog box with sequence-structure mapping.");
return;
}
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"),
- 550, 600);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
}
else if (evt.getSource() == charge)
{
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
+ {
((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
+ }
}
centerViewer();
else if (evt.getSource() == seqColour)
{
setEnabled(seqColour);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
else if (!allChainsSelected)
+ {
centerViewer();
+ }
}
public void keyPressed(KeyEvent evt)
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
public void updateTitleAndMenus()
return;
}
setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
setTitle(jmb.getViewerTitle());
}
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
}
else
{
git://source.jalview.org / jalview.git / blobdiff