X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=09b0fdd6c24669f26f7ac74222f927b216e418ed;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=a5006143922ff27bac244569bc4181f113252f61;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index a500614..09b0fdd 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,43 +1,85 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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 .
+ * 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.gui;
-import java.util.*;
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import java.awt.event.*;
-import java.io.*;
-
-import jalview.jbgui.GStructureViewer;
-import jalview.api.SequenceStructureBinding;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
-import jalview.io.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+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.ZappoColourScheme;
+import jalview.util.MessageManager;
import jalview.util.Platform;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
public class AppJmol extends GStructureViewer implements Runnable,
- SequenceStructureBinding, ViewSetProvider
+ ViewSetProvider, JalviewStructureDisplayI
{
AppJmolBinding jmb;
@@ -64,6 +106,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
* @param bounds
* @deprecated defaults to AppJmol(String[] files, ... , viewid);
*/
+ @Deprecated
public AppJmol(String file, String id, SequenceI[] seq,
AlignmentPanel ap, String loadStatus, Rectangle bounds)
{
@@ -73,6 +116,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
/**
* @deprecated
*/
+ @Deprecated
public AppJmol(String file, String id, SequenceI[] seq,
AlignmentPanel ap, String loadStatus, Rectangle bounds,
String viewid)
@@ -132,14 +176,14 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
jmb.setColourBySequence(false);
seqColour.setSelected(false);
- jmolColour.setSelected(true);
+ viewerColour.setSelected(true);
}
if (usetoColour)
{
useAlignmentPanelForColourbyseq(ap);
jmb.setColourBySequence(true);
seqColour.setSelected(true);
- jmolColour.setSelected(false);
+ viewerColour.setSelected(false);
}
this.setBounds(bounds);
initMenus();
@@ -161,7 +205,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
private void initMenus()
{
seqColour.setSelected(jmb.isColourBySequence());
- jmolColour.setSelected(!jmb.isColourBySequence());
+ viewerColour.setSelected(!jmb.isColourBySequence());
if (_colourwith == null)
{
_colourwith = new Vector();
@@ -171,7 +215,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
_alignwith = new Vector();
}
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+ seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
{
@@ -191,7 +235,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
});
viewMenu.add(seqColourBy);
final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
_alignwith, handler = new ItemListener()
{
@@ -199,13 +243,16 @@ public class AppJmol extends GStructureViewer implements Runnable,
public void itemStateChanged(ItemEvent e)
{
alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText("Align structures using "
- + _alignwith.size() + " linked alignment views");
+ alignStructs.setToolTipText(MessageManager
+ .formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ new String[]
+ { new Integer(_alignwith.size()).toString() }));
}
});
handler.itemStateChanged(null);
- jmolActionMenu.add(alpanels);
- jmolActionMenu.addMenuListener(new MenuListener()
+ viewerActionMenu.add(alpanels);
+ viewerActionMenu.addMenuListener(new MenuListener()
{
@Override
@@ -252,19 +299,25 @@ public class AppJmol extends GStructureViewer implements Runnable,
if (alreadyMapped != null)
{
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- pdbentry.getId() + " is already displayed."
- + "\nDo you want to re-use this viewer ?",
- "Map Sequences to Visible Window: " + pdbentry.getId(),
- JOptionPane.YES_NO_OPTION);
-
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed", new String[]
+ { pdbentry.getId() }), MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new String[]
+ { pdbentry.getId() }),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ return;
+ }
if (option == JOptionPane.YES_OPTION)
{
// TODO : Fix multiple seq to one chain issue here.
ap.getStructureSelectionManager().setMapping(seq, chains,
alreadyMapped, AppletFormatAdapter.FILE);
- if (ap.seqPanel.seqCanvas.fr != null)
+ if (ap.getSeqPanel().seqCanvas.fr != null)
{
- ap.seqPanel.seqCanvas.fr.featuresAdded();
+ ap.getSeqPanel().seqCanvas.fr.featuresAdded();
ap.paintAlignment(true);
}
@@ -310,11 +363,19 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
AppJmol topJmol = (AppJmol) jm.nextElement();
// TODO: highlight topJmol in view somehow
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "Do you want to add " + pdbentry.getId()
- + " to the view called\n'" + topJmol.getTitle()
- + "'\n", "Align to existing structure view",
- JOptionPane.YES_NO_OPTION);
+ int option = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.add_pdbentry_to_view", new String[]
+ { pdbentry.getId(), topJmol.getTitle() }),
+ MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ return;
+ }
if (option == JOptionPane.YES_OPTION)
{
topJmol.useAlignmentPanelForSuperposition(ap);
@@ -481,7 +542,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
useAlignmentPanelForColourbyseq(nap);
jmb.setColourBySequence(enableColourBySeq);
seqColour.setSelected(enableColourBySeq);
- jmolColour.setSelected(!enableColourBySeq);
+ viewerColour.setSelected(!enableColourBySeq);
}
public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
@@ -562,25 +623,22 @@ public class AppJmol extends GStructureViewer implements Runnable,
return;
}
- private Vector getJmolsFor(AlignmentPanel ap2)
+ private Vector getJmolsFor(AlignmentPanel apanel)
{
- Vector otherJmols = new Vector();
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
+ Vector result = new Vector();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
- for (int i = 0; i < frames.length; i++)
+ for (JInternalFrame frame : frames)
{
- if (frames[i] instanceof AppJmol)
+ if (frame instanceof AppJmol)
{
- AppJmol topJmol = ((AppJmol) frames[i]);
- if (topJmol.isLinkedWith(ap2))
+ if (((AppJmol) frame).isLinkedWith(apanel))
{
- otherJmols.addElement(topJmol);
+ result.addElement(frame);
}
}
}
- return otherJmols;
+ return result;
}
void initJmol(String command)
@@ -619,7 +677,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
return;
}
- JMenuItem menuItem = new JMenuItem("All");
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
@@ -628,7 +687,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
}
centerViewer();
allChainsSelected = false;
@@ -645,7 +706,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
+ {
centerViewer();
+ }
}
});
@@ -676,7 +739,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
jmb.centerViewer(toshow);
}
- void closeViewer()
+ public void closeViewer()
{
jmb.closeViewer();
ap = null;
@@ -716,7 +779,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
- progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
+ progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
}
try
{
@@ -732,7 +795,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
if (progressBar != null)
{
- progressBar.setProgressBar("Finished.", hdl);
+ progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
}
if (pdbseq != null)
{
@@ -781,11 +844,12 @@ public class AppJmol extends GStructureViewer implements Runnable,
if (errormsgs.length() > 0)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "The following pdb entries could not be retrieved from the PDB:\n"
- + errormsgs.toString()
- + "\nPlease try downloading them manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+ new String[]
+ { errormsgs.toString() }), MessageManager
+ .getString("label.couldnt_load_file"),
+ JOptionPane.ERROR_MESSAGE);
}
long lastnotify = jmb.getLoadNotifiesHandled();
@@ -833,7 +897,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
// need to wait around until script has finished
while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : (jmb.isFinishedInit() && jmb.getPdbFile().length != jmb.pdbentry.length))
+ : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+ .getPdbFile().length != jmb.pdbentry.length))
{
try
{
@@ -868,14 +933,15 @@ public class AppJmol extends GStructureViewer implements Runnable,
worker = null;
}
+ @Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@ -905,6 +971,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
}
+ @Override
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
@@ -923,50 +990,50 @@ public class AppJmol extends GStructureViewer implements Runnable,
cap.dispose();
return;
}
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
- 550, 600);
+ jalview.gui.Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
+ @Override
public void eps_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
+ @Override
public void png_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.PNG);
+ makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
}
- void makePDBImage(int type)
+ void makePDBImage(jalview.util.ImageMaker.TYPE type)
{
int width = getWidth();
int height = getHeight();
jalview.util.ImageMaker im;
- if (type == jalview.util.ImageMaker.PNG)
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.PNG,
"Make PNG image from view", width, height, null, null);
}
- else
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.EPS,
"Make EPS file from view", width, height, null,
this.getTitle());
}
+ else
+ {
+
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+ width, height, null, this.getTitle());
+ }
if (im.getGraphics() != null)
{
@@ -976,15 +1043,17 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
}
- public void jmolColour_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void viewerColour_actionPerformed(ActionEvent actionEvent)
{
- if (jmolColour.isSelected())
+ if (viewerColour.isSelected())
{
// disable automatic sequence colouring.
jmb.setColourBySequence(false);
}
}
+ @Override
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
jmb.setColourBySequence(seqColour.isSelected());
@@ -1005,87 +1074,100 @@ public class AppJmol extends GStructureViewer implements Runnable,
// Set the colour using the current view for the associated alignframe
for (AlignmentPanel ap : _colourwith)
{
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
}
}
+ @Override
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
chainColour.setSelected(true);
jmb.colourByChain();
}
+ @Override
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
chargeColour.setSelected(true);
jmb.colourByCharge();
}
+ @Override
public void zappoColour_actionPerformed(ActionEvent actionEvent)
{
zappoColour.setSelected(true);
jmb.setJalviewColourScheme(new ZappoColourScheme());
}
+ @Override
public void taylorColour_actionPerformed(ActionEvent actionEvent)
{
taylorColour.setSelected(true);
jmb.setJalviewColourScheme(new TaylorColourScheme());
}
+ @Override
public void hydroColour_actionPerformed(ActionEvent actionEvent)
{
hydroColour.setSelected(true);
jmb.setJalviewColourScheme(new HydrophobicColourScheme());
}
+ @Override
public void helixColour_actionPerformed(ActionEvent actionEvent)
{
helixColour.setSelected(true);
jmb.setJalviewColourScheme(new HelixColourScheme());
}
+ @Override
public void strandColour_actionPerformed(ActionEvent actionEvent)
{
strandColour.setSelected(true);
jmb.setJalviewColourScheme(new StrandColourScheme());
}
+ @Override
public void turnColour_actionPerformed(ActionEvent actionEvent)
{
turnColour.setSelected(true);
jmb.setJalviewColourScheme(new TurnColourScheme());
}
+ @Override
public void buriedColour_actionPerformed(ActionEvent actionEvent)
{
buriedColour.setSelected(true);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
+ @Override
public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
{
setJalviewColourScheme(new PurinePyrimidineColourScheme());
}
+ @Override
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);
new UserDefinedColours(this, null);
}
+ @Override
public void backGround_actionPerformed(ActionEvent actionEvent)
{
java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
+ MessageManager.getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
}
}
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
@@ -1146,7 +1228,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading file...", 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_file")
+ + "...", 20, currentSize.height / 2);
StringBuffer sb = new StringBuffer();
int lines = 0;
for (int e = 0; e < jmb.pdbentry.length; e++)
@@ -1171,7 +1254,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
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
{
@@ -1203,7 +1287,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
this.setTitle(jmb.getViewerTitle());
if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
{
- jmolActionMenu.setVisible(true);
+ viewerActionMenu.setVisible(true);
}
if (!jmb.isLoadingFromArchive())
{
@@ -1222,11 +1306,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
_alignwith.add(ap);
}
;
- for (Component c : jmolActionMenu.getMenuComponents())
+ for (Component c : viewerActionMenu.getMenuComponents())
{
if (c != alignStructs)
{
- jmolActionMenu.remove((JMenuItem) c);
+ viewerActionMenu.remove((JMenuItem) c);
}
}
final ItemListener handler;
@@ -1339,4 +1423,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
return !jmb.isColourBySequence();
}
+ public JalviewJmolBinding getBinding()
+ {
+ return jmb;
+ }
+
}