X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=32465c1e8cb6cf325d54e4dff54415699883ac3f;hb=a4780f236ded1ae07824254bca59b2aa0ea539ba;hp=d8b58fdd59a6e5fc0b40d2497ceaf8ef20b5c520;hpb=323a457c9d0643be2406b6661246e8e988c0d0f6;p=jalview.git
diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index d8b58fd..32465c1 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,82 +1,124 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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 org.jmol.api.*;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-
-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("File");
+ Menu fileMenu = new Menu(MessageManager.getString("action.file"));
+
+ Menu viewMenu = new Menu(MessageManager.getString("action.view"));
+
+ Menu coloursMenu = new Menu(MessageManager.getString("action.colour"));
- Menu viewMenu = new Menu("View");
+ Menu chainMenu = new Menu(MessageManager.getString("action.show_chain"));
- Menu coloursMenu = new Menu("Colours");
+ Menu helpMenu = new Menu(MessageManager.getString("action.help"));
- Menu chainMenu = new Menu("Show Chain");
+ MenuItem mappingMenuItem = new MenuItem(
+ MessageManager.getString("label.view_mapping"));
- Menu helpMenu = new Menu("Help");
+ CheckboxMenuItem seqColour = new CheckboxMenuItem(
+ MessageManager.getString("action.by_sequence"), true);
- MenuItem mappingMenuItem = new MenuItem("View Mapping");
+ CheckboxMenuItem jmolColour = new CheckboxMenuItem(
+ MessageManager.getString("action.using_jmol"), false);
- CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
+ MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
- CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false);
-
- MenuItem chain = new MenuItem("By Chain");
+ MenuItem charge = new MenuItem(
+ MessageManager.getString("label.charge_cysteine"));
- MenuItem charge = new MenuItem("Charge & Cysteine");
+ MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
- MenuItem zappo = new MenuItem("Zappo");
+ MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
- MenuItem taylor = new MenuItem("Taylor");
+ MenuItem hydro = new MenuItem(
+ MessageManager.getString("label.hydrophobicity"));
- MenuItem hydro = new MenuItem("Hydrophobicity");
+ MenuItem helix = new MenuItem(
+ MessageManager.getString("label.helix_propensity"));
- MenuItem helix = new MenuItem("Helix Propensity");
+ MenuItem strand = new MenuItem(
+ MessageManager.getString("label.strand_propensity"));
- MenuItem strand = new MenuItem("Strand Propensity");
+ MenuItem turn = new MenuItem(
+ MessageManager.getString("label.turn_propensity"));
- MenuItem turn = new MenuItem("Turn Propensity");
+ MenuItem buried = new MenuItem(
+ MessageManager.getString("label.buried_index"));
- MenuItem buried = new MenuItem("Buried Index");
-
- MenuItem purinepyrimidine = new MenuItem("Purine/Pyrimidine");
+ MenuItem purinepyrimidine = new MenuItem(
+ MessageManager.getString("label.purine_pyrimidine"));
- MenuItem user = new MenuItem("User Defined Colours");
+ MenuItem user = new MenuItem(
+ MessageManager.getString("label.user_defined_colours"));
- MenuItem jmolHelp = new MenuItem("Jmol Help");
+ MenuItem jmolHelp = new MenuItem(
+ MessageManager.getString("label.jmol_help"));
Panel scriptWindow;
@@ -87,6 +129,7 @@ public class AppletJmol extends EmbmenuFrame implements
RenderPanel renderPanel;
AlignmentPanel ap;
+
ArrayList _aps = new ArrayList();
String fileLoadingError;
@@ -127,17 +170,18 @@ public class AppletJmol extends EmbmenuFrame implements
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,
AlignmentPanel ap, String protocol)
{
this.ap = ap;
- jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains }, protocol);
+ jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
+ new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, new String[][]
+ { chains }, protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
@@ -159,13 +203,14 @@ public class AppletJmol extends EmbmenuFrame implements
}
String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager(ap.av.applet).alreadyMappedToFile(
- pdbentry.getId());
+ .getStructureSelectionManager(ap.av.applet)
+ .alreadyMappedToFile(pdbentry.getId());
MCview.PDBfile reader = null;
if (alreadyMapped != null)
{
- reader = StructureSelectionManager.getStructureSelectionManager(ap.av.applet)
- .setMapping(seq, chains, pdbentry.getFile(), protocol);
+ reader = StructureSelectionManager.getStructureSelectionManager(
+ ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
+ protocol);
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
}
@@ -191,7 +236,7 @@ public class AppletJmol extends EmbmenuFrame implements
buried.addActionListener(this);
purinepyrimidine.addActionListener(this);
user.addActionListener(this);
-
+
jmolHelp.addActionListener(this);
coloursMenu.add(seqColour);
@@ -301,8 +346,7 @@ public class AppletJmol extends EmbmenuFrame implements
}
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);
@@ -330,7 +374,7 @@ public class AppletJmol extends EmbmenuFrame implements
{
chainMenu.removeAll();
- MenuItem menuItem = new MenuItem("All");
+ MenuItem menuItem = new MenuItem(MessageManager.getString("label.all"));
menuItem.addActionListener(this);
chainMenu.add(menuItem);
@@ -385,10 +429,9 @@ public class AppletJmol extends EmbmenuFrame implements
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());
@@ -399,8 +442,9 @@ public class AppletJmol extends EmbmenuFrame implements
.println("Out of memory when trying to create dialog box with sequence-structure mapping.");
return;
}
- jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
- 550, 600);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
}
else if (evt.getSource() == charge)
{
@@ -448,9 +492,9 @@ public class AppletJmol extends EmbmenuFrame implements
setEnabled(buried);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
- else if(evt.getSource() == purinepyrimidine)
+ else if (evt.getSource() == purinepyrimidine)
{
- jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
}
else if (evt.getSource() == user)
{
@@ -475,7 +519,9 @@ public class AppletJmol extends EmbmenuFrame implements
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
+ {
((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
+ }
}
centerViewer();
@@ -484,8 +530,8 @@ public class AppletJmol extends EmbmenuFrame implements
}
/**
- * tick or untick the seqColour menu entry or jmoColour entry depending upon if it was selected
- * or not.
+ * tick or untick the seqColour menu entry or jmoColour entry depending upon
+ * if it was selected or not.
*
* @param itm
*/
@@ -502,14 +548,16 @@ public class AppletJmol extends EmbmenuFrame implements
{
setEnabled(jmolColour);
jmb.setColourBySequence(false);
- } else
- if (evt.getSource() == seqColour)
+ }
+ 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)
@@ -534,7 +582,7 @@ public class AppletJmol extends EmbmenuFrame implements
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
public void updateTitleAndMenus()
@@ -545,7 +593,7 @@ public class AppletJmol extends EmbmenuFrame implements
return;
}
setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
setTitle(jmb.getViewerTitle());
}
@@ -618,7 +666,8 @@ public class AppletJmol extends EmbmenuFrame implements
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
}
else
{
@@ -652,11 +701,11 @@ public class AppletJmol extends EmbmenuFrame implements
public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
{
- for (int i=0;i<_aps.size();i++)
+ for (int i = 0; i < _aps.size(); i++)
{
- if (((AlignmentPanel)_aps.get(i)).av.getAlignment()==alignment)
+ if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
{
- return ((AlignmentPanel)_aps.get(i));
+ return ((AlignmentPanel) _aps.get(i));
}
}
return ap;