/*
- * 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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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.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.List;
+import java.util.Vector;
+
public class AppletJmol extends EmbmenuFrame implements
// StructureListener,
KeyListener, ActionListener, ItemListener
AlignmentPanel ap;
- ArrayList _aps = new ArrayList();
+ List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
+ // added to
String fileLoadingError;
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,
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
- new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains }, protocol);
+ new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
+ new String[][] { chains }, protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
dispose();
return;
}
- jmb.newJmolPopup(true, "Jmol", true);
+ // jmb.newJmolPopup(true, "Jmol", true);
this.addWindowListener(new WindowAdapter()
{
if (freader == null)
{
throw new Exception(
- "Invalid datasource. Could not obtain Reader.");
+ MessageManager
+ .getString("exception.invalid_datasource_couldnt_obtain_reader"));
}
jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
jmb.loadInline(string);
}
- void setChainMenuItems(Vector chains)
+ void setChainMenuItems(Vector<String> chains)
{
chainMenu.removeAll();
chainMenu.add(menuItem);
CheckboxMenuItem menuItemCB;
- for (int c = 0; c < chains.size(); c++)
+ for (String ch : chains)
{
- menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
- true);
+ menuItemCB = new CheckboxMenuItem(ch, true);
menuItemCB.addItemListener(this);
chainMenu.add(menuItemCB);
}
void centerViewer()
{
- Vector toshow = new Vector();
- String lbl;
- int mlength, p, mnum;
+ Vector<String> toshow = new Vector<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
StringBuffer sb = new StringBuffer();
try
{
- for (int s = 0; s < jmb.pdbentry.length; s++)
- {
- sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
- sb.append("\n");
- }
- cap.setText(sb.toString());
+ cap.setText(jmb.printMappings());
} catch (OutOfMemoryError ex)
{
frame.dispose();
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);
}
else if (!allChainsSelected)
+ {
centerViewer();
+ }
}
public void keyPressed(KeyEvent evt)
if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
{
jmb.eval(inputLine.getText());
- history.append("\n$ " + inputLine.getText());
+ addToHistory("$ " + inputLine.getText());
inputLine.setText("");
}
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source;
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ AlignmentPanel panel = (AlignmentPanel) source;
+ jmb.colourBySequence(panel);
}
public void updateTitleAndMenus()
return;
}
setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ jmb.colourBySequence(ap);
setTitle(jmb.getViewerTitle());
}
{
Dimension currentSize = new Dimension();
- Rectangle rectClip = new Rectangle();
-
public void update(Graphics g)
{
paint(g);
public void paint(Graphics g)
{
currentSize = this.getSize();
- rectClip = g.getClipBounds();
if (jmb.viewer == null)
{
}
else
{
- jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+ jmb.viewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
}
}
}
{
for (int i = 0; i < _aps.size(); i++)
{
- if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
+ if (_aps.get(i).av.getAlignment() == alignment)
{
- return ((AlignmentPanel) _aps.get(i));
+ return (_aps.get(i));
}
}
return ap;
}
+
+ /**
+ * Append the given text to the history object
+ *
+ * @param text
+ */
+ public void addToHistory(String text)
+ {
+ // actually currently never initialised
+ if (history != null)
+ {
+ history.append("\n" + text);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff