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JAL-1807 add j2s nature to project
[jalview.git]
/
src
/
MCview
/
PDBViewer.java
diff --git
a/src/MCview/PDBViewer.java
b/src/MCview/PDBViewer.java
index
bf285b9
..
a0fcacf
100755
(executable)
--- a/
src/MCview/PDBViewer.java
+++ b/
src/MCview/PDBViewer.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,12
+20,15
@@
*/
package MCview;
*/
package MCview;
+import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignmentPanel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignmentPanel;
+import jalview.gui.CutAndPasteTransfer;
import jalview.gui.Desktop;
import jalview.gui.OOMWarning;
import jalview.gui.UserDefinedColours;
import jalview.gui.Desktop;
import jalview.gui.OOMWarning;
import jalview.gui.UserDefinedColours;
+import jalview.io.AppletFormatAdapter;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.schemes.BuriedColourScheme;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.schemes.BuriedColourScheme;
@@
-36,6
+39,7
@@
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
+import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
@@
-52,6
+56,7
@@
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.PrintWriter;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.PrintWriter;
+import java.util.Enumeration;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
@@
-114,7
+119,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
{
tmpPDBFile = pdbentry.getFile();
PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
{
tmpPDBFile = pdbentry.getFile();
PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
+ AppletFormatAdapter.FILE);
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
@@
-379,9
+384,9
@@
public class PDBViewer extends JInternalFrame implements Runnable
bg.add(buried);
bg.add(user);
bg.add(buried);
bg.add(user);
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ if (UserDefinedColours.getUserColourSchemes() != null)
{
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ Enumeration userColours = UserDefinedColours
.getUserColourSchemes().keys();
while (userColours.hasMoreElements())
.getUserColourSchemes().keys();
while (userColours.hasMoreElements())
@@
-399,7
+404,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
int option = JOptionPane.showInternalConfirmDialog(
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
int option = JOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop,
+ Desktop.desktop,
MessageManager
.getString("label.remove_from_default_list"),
MessageManager
MessageManager
.getString("label.remove_from_default_list"),
MessageManager
@@
-407,7
+412,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
- jalview.gui.UserDefinedColours
+ UserDefinedColours
.removeColourFromDefaults(radioItem.getText());
coloursMenu.remove(radioItem);
}
.removeColourFromDefaults(radioItem.getText());
coloursMenu.remove(radioItem);
}
@@
-500,7
+505,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
*/
public void eps_actionPerformed(ActionEvent e)
{
*/
public void eps_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
+ makePDBImage(ImageMaker.TYPE.EPS);
}
/**
}
/**
@@
-511,34
+516,32
@@
public class PDBViewer extends JInternalFrame implements Runnable
*/
public void png_actionPerformed(ActionEvent e)
{
*/
public void png_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
+ makePDBImage(ImageMaker.TYPE.PNG);
}
}
- void makePDBImage(jalview.util.ImageMaker.TYPE type)
+ void makePDBImage(ImageMaker.TYPE type)
{
int width = pdbcanvas.getWidth();
int height = pdbcanvas.getHeight();
{
int width = pdbcanvas.getWidth();
int height = pdbcanvas.getHeight();
- jalview.util.ImageMaker im;
+ ImageMaker im;
- if (type == jalview.util.ImageMaker.TYPE.PNG)
+ if (type == ImageMaker.TYPE.PNG)
{
{
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG,
+ im = new ImageMaker(this, ImageMaker.TYPE.PNG,
"Make PNG image from view", width, height, null, null);
}
"Make PNG image from view", width, height, null, null);
}
- else if (type == jalview.util.ImageMaker.TYPE.EPS)
+ else if (type == ImageMaker.TYPE.EPS)
{
{
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS,
+ im = new ImageMaker(this, ImageMaker.TYPE.EPS,
"Make EPS file from view", width, height, null,
this.getTitle());
}
else
{
"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",
+ im = new ImageMaker(this, ImageMaker.TYPE.SVG,
+ "Make SVG file from PCA",
width, height, null, this.getTitle());
}
width, height, null, this.getTitle());
}
@@
-609,7
+612,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
public void mapping_actionPerformed(ActionEvent e)
{
public void mapping_actionPerformed(ActionEvent e)
{
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
{
cap.setText(pdbcanvas.mappingDetails.toString());
try
{
cap.setText(pdbcanvas.mappingDetails.toString());
@@
-711,7
+714,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
public void savePDB_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
public void savePDB_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));