X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2FMCview%2FPDBViewer.java;h=f9c7602cef45fdffb92cb832323cdd9a22125e3d;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=50a501d0ab213a132e37bd4141dbe39cc79a91c6;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 50a501d..f9c7602 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,34 +1,68 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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 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.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.OOMWarning;
+import jalview.gui.UserDefinedColours;
+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.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
-import java.awt.BorderLayout;
+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 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
{
@@ -52,7 +86,6 @@ 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;
@@ -80,7 +113,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
try
{
tmpPDBFile = pdbentry.getFile();
- PDBfile pdbfile = new PDBfile(tmpPDBFile,
+ PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
jalview.io.AppletFormatAdapter.FILE);
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
@@ -122,7 +155,9 @@ public class PDBViewer extends JInternalFrame implements Runnable
.getAbsolutePath());
if (pdbentry.getFile() != null)
+ {
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+ }
} catch (Exception ex)
{
pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
@@ -141,10 +176,10 @@ public class PDBViewer extends JInternalFrame implements Runnable
});
this.setJMenuBar(jMenuBar1);
- fileMenu.setText("File");
- coloursMenu.setText("Colours");
- saveMenu.setActionCommand("Save Image");
- saveMenu.setText("Save As");
+ fileMenu.setText(MessageManager.getString("action.file"));
+ coloursMenu.setText(MessageManager.getString("label.colours"));
+ saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
+ saveMenu.setText(MessageManager.getString("action.save_as"));
png.setText("PNG");
png.addActionListener(new ActionListener()
{
@@ -161,7 +196,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
eps_actionPerformed(e);
}
});
- mapping.setText("View Mapping");
+ mapping.setText(MessageManager.getString("label.view_mapping"));
mapping.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -169,7 +204,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
mapping_actionPerformed(e);
}
});
- wire.setText("Wireframe");
+ wire.setText(MessageManager.getString("label.wireframe"));
wire.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -178,7 +213,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
}
});
depth.setSelected(true);
- depth.setText("Depthcue");
+ depth.setText(MessageManager.getString("label.depthcue"));
depth.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -187,7 +222,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
}
});
zbuffer.setSelected(true);
- zbuffer.setText("Z Buffering");
+ zbuffer.setText(MessageManager.getString("label.z_buffering"));
zbuffer.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -195,7 +230,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
zbuffer_actionPerformed(e);
}
});
- charge.setText("Charge & Cysteine");
+ charge.setText(MessageManager.getString("label.charge_cysteine"));
charge.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -203,7 +238,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
charge_actionPerformed(e);
}
});
- chain.setText("By Chain");
+ chain.setText(MessageManager.getString("action.by_chain"));
chain.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -212,7 +247,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
}
});
seqButton.setSelected(true);
- seqButton.setText("By Sequence");
+ seqButton.setText(MessageManager.getString("action.by_sequence"));
seqButton.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -221,7 +256,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
}
});
allchains.setSelected(true);
- allchains.setText("Show All Chains");
+ allchains.setText(MessageManager.getString("label.show_all_chains"));
allchains.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
@@ -229,7 +264,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
allchains_itemStateChanged(e);
}
});
- zappo.setText("Zappo");
+ zappo.setText(MessageManager.getString("label.zappo"));
zappo.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -237,7 +272,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
zappo_actionPerformed(e);
}
});
- taylor.setText("Taylor");
+ taylor.setText(MessageManager.getString("label.taylor"));
taylor.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -245,7 +280,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
taylor_actionPerformed(e);
}
});
- hydro.setText("Hydro");
+ hydro.setText(MessageManager.getString("label.hydrophobicity"));
hydro.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -253,7 +288,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
hydro_actionPerformed(e);
}
});
- helix.setText("Helix");
+ helix.setText(MessageManager.getString("label.helix_propensity"));
helix.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -261,7 +296,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
helix_actionPerformed(e);
}
});
- strand.setText("Strand");
+ strand.setText(MessageManager.getString("label.strand_propensity"));
strand.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -269,7 +304,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
strand_actionPerformed(e);
}
});
- turn.setText("Turn");
+ turn.setText(MessageManager.getString("label.turn_propensity"));
turn.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -277,7 +312,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
turn_actionPerformed(e);
}
});
- buried.setText("Buried");
+ buried.setText(MessageManager.getString("label.buried_index"));
buried.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -285,7 +320,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
buried_actionPerformed(e);
}
});
- user.setText("User Defined...");
+ user.setText(MessageManager.getString("action.user_defined"));
user.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -293,8 +328,9 @@ public class PDBViewer extends JInternalFrame implements Runnable
user_actionPerformed(e);
}
});
- viewMenu.setText("View");
- background.setText("Background Colour...");
+ viewMenu.setText(MessageManager.getString("action.view"));
+ background.setText(MessageManager.getString("label.background_colour")
+ + "...");
background.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -302,7 +338,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
background_actionPerformed(e);
}
});
- savePDB.setText("PDB File");
+ savePDB.setText(MessageManager.getString("label.pdb_file"));
savePDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -360,13 +396,14 @@ public class PDBViewer extends JInternalFrame implements Runnable
if (evt.isControlDown()
|| SwingUtilities.isRightMouseButton(evt))
{
- radioItem
- .removeActionListener(radioItem.getActionListeners()[0]);
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
@@ -463,7 +500,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
*/
public void eps_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
/**
@@ -474,26 +511,35 @@ public class PDBViewer extends JInternalFrame implements Runnable
*/
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 = pdbcanvas.getWidth();
int height = pdbcanvas.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 if (type == jalview.util.ImageMaker.TYPE.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.EPS,
- "Make EPS file from view", width, height, null, this
- .getTitle());
+
+ 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)
@@ -564,8 +610,17 @@ public class PDBViewer extends JInternalFrame implements Runnable
public void mapping_actionPerformed(ActionEvent e)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
- cap.setText(pdbcanvas.mappingDetails.toString());
+ try
+ {
+ cap.setText(pdbcanvas.mappingDetails.toString());
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Opening sequence to structure mapping report", oom);
+ cap.dispose();
+ }
}
public void allchains_itemStateChanged(ItemEvent e)
@@ -623,7 +678,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
public void user_actionPerformed(ActionEvent e)
{
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getActionCommand().equals(
+ MessageManager.getString("action.user_defined")))
{
// new UserDefinedColours(pdbcanvas, null);
}
@@ -641,7 +697,8 @@ public class PDBViewer extends JInternalFrame implements Runnable
public void background_actionPerformed(ActionEvent e)
{
java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", pdbcanvas.backgroundColour);
+ MessageManager.getString("label.select_backgroud_colour"),
+ pdbcanvas.backgroundColour);
if (col != null)
{
@@ -653,12 +710,12 @@ public class PDBViewer extends JInternalFrame implements Runnable
public void savePDB_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
+ 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);
@@ -679,6 +736,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
}
}
out.close();
+ in.close();
} catch (Exception ex)
{
ex.printStackTrace();