X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBViewer.java;h=e16241bdc222c1d389a08a9336b37b480fdecc42;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=e586707c7a5581e214282a6673a7bf4d5a8b3bb9;hpb=0eda2ac2f334f55f6e5f137789453a9f4dfe4d73;p=jalview.git
diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index e586707..e16241b 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,38 +1,70 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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;
-
-public class PDBViewer
- extends JInternalFrame implements Runnable
+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
{
/**
@@ -41,18 +73,19 @@ public class PDBViewer
PDBCanvas pdbcanvas;
PDBEntry pdbentry;
- SequenceI[]seq;
- String[]chains;
+
+ SequenceI[] seq;
+
+ String[] chains;
+
AlignmentPanel ap;
+
String protocol;
- String tmpPDBFile;
- public PDBViewer(PDBEntry pdbentry,
- SequenceI[] seq,
- String[] chains,
- AlignmentPanel ap,
- String protocol)
+ String tmpPDBFile;
+ public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ AlignmentPanel ap, String protocol)
{
this.pdbentry = pdbentry;
this.seq = seq;
@@ -63,16 +96,13 @@ public class PDBViewer
try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
-
- StringBuffer title = new StringBuffer(seq[0].getName()
- + ":"
- + pdbentry.getFile());
+ StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+ + pdbentry.getFile());
pdbcanvas = new PDBCanvas();
@@ -83,13 +113,12 @@ public class PDBViewer
try
{
tmpPDBFile = pdbentry.getFile();
- PDBfile pdbfile = new PDBfile(tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
+ PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
+ jalview.io.AppletFormatAdapter.FILE);
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
- }
- catch (java.io.IOException ex)
+ } catch (java.io.IOException ex)
{
ex.printStackTrace();
}
@@ -100,8 +129,6 @@ public class PDBViewer
worker.start();
}
-
-
if (pdbentry.getProperty() != null)
{
if (pdbentry.getProperty().get("method") != null)
@@ -125,20 +152,20 @@ public class PDBViewer
EBIFetchClient ebi = new EBIFetchClient();
String query = "pdb:" + pdbentry.getId();
pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
- .getAbsolutePath());
+ .getAbsolutePath());
- if(pdbentry.getFile()!=null)
+ if (pdbentry.getFile() != null)
+ {
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
- }
- catch (Exception ex)
+ }
+ } catch (Exception ex)
{
- pdbcanvas.errorMessage = "Error retrieving file: "+pdbentry.getId();
+ pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
ex.printStackTrace();
}
}
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
this.addKeyListener(new KeyAdapter()
{
@@ -149,10 +176,10 @@ public class PDBViewer
});
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()
{
@@ -169,7 +196,7 @@ public class PDBViewer
eps_actionPerformed(e);
}
});
- mapping.setText("View Mapping");
+ mapping.setText(MessageManager.getString("label.view_mapping"));
mapping.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -177,7 +204,7 @@ public class PDBViewer
mapping_actionPerformed(e);
}
});
- wire.setText("Wireframe");
+ wire.setText(MessageManager.getString("label.wireframe"));
wire.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -186,7 +213,7 @@ public class PDBViewer
}
});
depth.setSelected(true);
- depth.setText("Depthcue");
+ depth.setText(MessageManager.getString("label.depthcue"));
depth.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -195,7 +222,7 @@ public class PDBViewer
}
});
zbuffer.setSelected(true);
- zbuffer.setText("Z Buffering");
+ zbuffer.setText(MessageManager.getString("label.z_buffering"));
zbuffer.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -203,7 +230,7 @@ public class PDBViewer
zbuffer_actionPerformed(e);
}
});
- charge.setText("Charge & Cysteine");
+ charge.setText(MessageManager.getString("label.charge_cysteine"));
charge.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -211,7 +238,7 @@ public class PDBViewer
charge_actionPerformed(e);
}
});
- chain.setText("By Chain");
+ chain.setText(MessageManager.getString("action.by_chain"));
chain.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -220,7 +247,7 @@ public class PDBViewer
}
});
seqButton.setSelected(true);
- seqButton.setText("By Sequence");
+ seqButton.setText(MessageManager.getString("action.by_sequence"));
seqButton.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -229,7 +256,7 @@ public class PDBViewer
}
});
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)
@@ -237,7 +264,7 @@ public class PDBViewer
allchains_itemStateChanged(e);
}
});
- zappo.setText("Zappo");
+ zappo.setText(MessageManager.getString("label.zappo"));
zappo.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -245,7 +272,7 @@ public class PDBViewer
zappo_actionPerformed(e);
}
});
- taylor.setText("Taylor");
+ taylor.setText(MessageManager.getString("label.taylor"));
taylor.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -253,7 +280,7 @@ public class PDBViewer
taylor_actionPerformed(e);
}
});
- hydro.setText("Hydro");
+ hydro.setText(MessageManager.getString("label.hydrophobicity"));
hydro.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -261,7 +288,7 @@ public class PDBViewer
hydro_actionPerformed(e);
}
});
- helix.setText("Helix");
+ helix.setText(MessageManager.getString("label.helix_propensity"));
helix.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -269,7 +296,7 @@ public class PDBViewer
helix_actionPerformed(e);
}
});
- strand.setText("Strand");
+ strand.setText(MessageManager.getString("label.strand_propensity"));
strand.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -277,7 +304,7 @@ public class PDBViewer
strand_actionPerformed(e);
}
});
- turn.setText("Turn");
+ turn.setText(MessageManager.getString("label.turn_propensity"));
turn.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -285,7 +312,7 @@ public class PDBViewer
turn_actionPerformed(e);
}
});
- buried.setText("Buried");
+ buried.setText(MessageManager.getString("label.buried_index"));
buried.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -293,7 +320,7 @@ public class PDBViewer
buried_actionPerformed(e);
}
});
- user.setText("User Defined...");
+ user.setText(MessageManager.getString("action.user_defined"));
user.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -301,8 +328,9 @@ public class PDBViewer
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)
@@ -310,7 +338,7 @@ public class PDBViewer
background_actionPerformed(e);
}
});
- savePDB.setText("PDB File");
+ savePDB.setText(MessageManager.getString("label.pdb_file"));
savePDB.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -353,32 +381,34 @@ public class PDBViewer
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
- getUserColourSchemes().keys();
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
while (userColours.hasMoreElements())
{
final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.
- nextElement().toString());
+ userColours.nextElement().toString());
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
public void mousePressed(MouseEvent evt)
{
- if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ if (evt.isControlDown()
+ || SwingUtilities.isRightMouseButton(evt))
{
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
- Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
- JOptionPane.YES_NO_OPTION);
+ int option = JOptionPane.showInternalConfirmDialog(
+ jalview.gui.Desktop.desktop,
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
+ JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
- jalview.gui.UserDefinedColours.removeColourFromDefaults(
- radioItem.getText());
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
coloursMenu.remove(radioItem);
}
else
@@ -413,74 +443,103 @@ public class PDBViewer
}
JMenuBar jMenuBar1 = new JMenuBar();
+
JMenu fileMenu = new JMenu();
+
JMenu coloursMenu = new JMenu();
+
JMenu saveMenu = new JMenu();
+
JMenuItem png = new JMenuItem();
+
JMenuItem eps = new JMenuItem();
+
JMenuItem mapping = new JMenuItem();
+
JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
+
JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
+
JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
+
JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem user = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
+
JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
+
JMenu viewMenu = new JMenu();
+
JMenuItem background = new JMenuItem();
+
JMenuItem savePDB = new JMenuItem();
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void eps_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
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.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.PNG,
- "Make PNG image from view",
- width, height,
- null, null);
+ 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());
+ jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+ width, height, null, this.getTitle());
}
if (im.getGraphics() != null)
@@ -551,8 +610,17 @@ public class PDBViewer
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)
@@ -560,7 +628,6 @@ public class PDBViewer
pdbcanvas.setAllchainsVisible(allchains.getState());
}
-
public void zappo_actionPerformed(ActionEvent e)
{
pdbcanvas.bysequence = false;
@@ -611,14 +678,15 @@ public class PDBViewer
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);
+ // new UserDefinedColours(pdbcanvas, null);
}
else
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.
- getUserColourSchemes().get(e.getActionCommand());
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ .getUserColourSchemes().get(e.getActionCommand());
pdbcanvas.pdb.setColours(udc);
pdbcanvas.redrawneeded = true;
@@ -629,8 +697,8 @@ public class PDBViewer
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)
{
@@ -643,12 +711,11 @@ public class PDBViewer
public void savePDB_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"));
+ 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);
@@ -661,18 +728,16 @@ public class PDBViewer
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
String data;
- while ( (data = in.readLine()) != null)
+ while ((data = in.readLine()) != null)
{
- if (
- ! (data.indexOf("") > -1 || data.indexOf("") > -1)
- )
+ if (!(data.indexOf("") > -1 || data.indexOf("") > -1))
{
out.println(data);
}
}
out.close();
- }
- catch (Exception ex)
+ in.close();
+ } catch (Exception ex)
{
ex.printStackTrace();
}