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JAL-2110 throw implementation error if not given a dataset for CDS alignment synthesis
[jalview.git]
/
src
/
MCview
/
PDBViewer.java
diff --git
a/src/MCview/PDBViewer.java
b/src/MCview/PDBViewer.java
index
12367b2
..
d5f0d0b
100755
(executable)
--- a/
src/MCview/PDBViewer.java
+++ b/
src/MCview/PDBViewer.java
@@
-62,7
+62,6
@@
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JRadioButtonMenuItem;
-import javax.swing.SwingUtilities;
public class PDBViewer extends JInternalFrame implements Runnable
{
public class PDBViewer extends JInternalFrame implements Runnable
{
@@
-145,13
+144,14
@@
public class PDBViewer extends JInternalFrame implements Runnable
Desktop.addInternalFrame(this, title.toString(), 400, 400);
}
Desktop.addInternalFrame(this, title.toString(), 400, 400);
}
+ @Override
public void run()
{
try
{
EBIFetchClient ebi = new EBIFetchClient();
String query = "pdb:" + pdbentry.getId();
public void run()
{
try
{
EBIFetchClient ebi = new EBIFetchClient();
String query = "pdb:" + pdbentry.getId();
- pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+ pdbentry.setFile(ebi.fetchDataAsFile(query, "default", ".xml")
.getAbsolutePath());
if (pdbentry.getFile() != null)
.getAbsolutePath());
if (pdbentry.getFile() != null)
@@
-169,6
+169,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
{
this.addKeyListener(new KeyAdapter()
{
{
this.addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
pdbcanvas.keyPressed(evt);
public void keyPressed(KeyEvent evt)
{
pdbcanvas.keyPressed(evt);
@@
-183,6
+184,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
png.setText("PNG");
png.addActionListener(new ActionListener()
{
png.setText("PNG");
png.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
png_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
png_actionPerformed(e);
@@
-191,6
+193,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
eps.setText("EPS");
eps.addActionListener(new ActionListener()
{
eps.setText("EPS");
eps.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
eps_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
eps_actionPerformed(e);
@@
-199,6
+202,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
mapping.setText(MessageManager.getString("label.view_mapping"));
mapping.addActionListener(new ActionListener()
{
mapping.setText(MessageManager.getString("label.view_mapping"));
mapping.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
mapping_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
mapping_actionPerformed(e);
@@
-207,6
+211,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
wire.setText(MessageManager.getString("label.wireframe"));
wire.addActionListener(new ActionListener()
{
wire.setText(MessageManager.getString("label.wireframe"));
wire.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
wire_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
wire_actionPerformed(e);
@@
-216,6
+221,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
depth.setText(MessageManager.getString("label.depthcue"));
depth.addActionListener(new ActionListener()
{
depth.setText(MessageManager.getString("label.depthcue"));
depth.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
depth_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
depth_actionPerformed(e);
@@
-225,6
+231,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
zbuffer.setText(MessageManager.getString("label.z_buffering"));
zbuffer.addActionListener(new ActionListener()
{
zbuffer.setText(MessageManager.getString("label.z_buffering"));
zbuffer.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zbuffer_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
zbuffer_actionPerformed(e);
@@
-233,6
+240,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
charge.setText(MessageManager.getString("label.charge_cysteine"));
charge.addActionListener(new ActionListener()
{
charge.setText(MessageManager.getString("label.charge_cysteine"));
charge.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
charge_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
charge_actionPerformed(e);
@@
-241,6
+249,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
chain.setText(MessageManager.getString("action.by_chain"));
chain.addActionListener(new ActionListener()
{
chain.setText(MessageManager.getString("action.by_chain"));
chain.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
chain_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
chain_actionPerformed(e);
@@
-250,6
+259,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
seqButton.setText(MessageManager.getString("action.by_sequence"));
seqButton.addActionListener(new ActionListener()
{
seqButton.setText(MessageManager.getString("action.by_sequence"));
seqButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
seqButton_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
seqButton_actionPerformed(e);
@@
-259,6
+269,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
allchains.setText(MessageManager.getString("label.show_all_chains"));
allchains.addItemListener(new ItemListener()
{
allchains.setText(MessageManager.getString("label.show_all_chains"));
allchains.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
allchains_itemStateChanged(e);
public void itemStateChanged(ItemEvent e)
{
allchains_itemStateChanged(e);
@@
-267,6
+278,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
zappo.setText(MessageManager.getString("label.zappo"));
zappo.addActionListener(new ActionListener()
{
zappo.setText(MessageManager.getString("label.zappo"));
zappo.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zappo_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
zappo_actionPerformed(e);
@@
-275,6
+287,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
taylor.setText(MessageManager.getString("label.taylor"));
taylor.addActionListener(new ActionListener()
{
taylor.setText(MessageManager.getString("label.taylor"));
taylor.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
taylor_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
taylor_actionPerformed(e);
@@
-283,6
+296,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
hydro.setText(MessageManager.getString("label.hydrophobicity"));
hydro.addActionListener(new ActionListener()
{
hydro.setText(MessageManager.getString("label.hydrophobicity"));
hydro.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hydro_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
hydro_actionPerformed(e);
@@
-291,6
+305,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
helix.setText(MessageManager.getString("label.helix_propensity"));
helix.addActionListener(new ActionListener()
{
helix.setText(MessageManager.getString("label.helix_propensity"));
helix.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
helix_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
helix_actionPerformed(e);
@@
-299,6
+314,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
strand.setText(MessageManager.getString("label.strand_propensity"));
strand.addActionListener(new ActionListener()
{
strand.setText(MessageManager.getString("label.strand_propensity"));
strand.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
strand_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
strand_actionPerformed(e);
@@
-307,6
+323,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
turn.setText(MessageManager.getString("label.turn_propensity"));
turn.addActionListener(new ActionListener()
{
turn.setText(MessageManager.getString("label.turn_propensity"));
turn.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
turn_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
turn_actionPerformed(e);
@@
-315,6
+332,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
buried.setText(MessageManager.getString("label.buried_index"));
buried.addActionListener(new ActionListener()
{
buried.setText(MessageManager.getString("label.buried_index"));
buried.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
buried_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
buried_actionPerformed(e);
@@
-323,15
+341,18
@@
public class PDBViewer extends JInternalFrame implements Runnable
user.setText(MessageManager.getString("action.user_defined"));
user.addActionListener(new ActionListener()
{
user.setText(MessageManager.getString("action.user_defined"));
user.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
user_actionPerformed(e);
}
});
viewMenu.setText(MessageManager.getString("action.view"));
public void actionPerformed(ActionEvent e)
{
user_actionPerformed(e);
}
});
viewMenu.setText(MessageManager.getString("action.view"));
- background.setText(MessageManager.getString("action.background_colour"));
+ background
+ .setText(MessageManager.getString("action.background_colour"));
background.addActionListener(new ActionListener()
{
background.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
background_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
background_actionPerformed(e);
@@
-340,6
+361,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
savePDB.setText(MessageManager.getString("label.pdb_file"));
savePDB.addActionListener(new ActionListener()
{
savePDB.setText(MessageManager.getString("label.pdb_file"));
savePDB.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
savePDB_actionPerformed(e);
public void actionPerformed(ActionEvent e)
{
savePDB_actionPerformed(e);
@@
-390,10
+412,10
@@
public class PDBViewer extends JInternalFrame implements Runnable
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
public void mousePressed(MouseEvent evt)
{
- if (evt.isControlDown()
- || SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger())
{
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
{
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
@@
-414,6
+436,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
{
radioItem.addActionListener(new ActionListener()
{
{
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
user_actionPerformed(evt);
public void actionPerformed(ActionEvent evt)
{
user_actionPerformed(evt);
@@
-425,6
+448,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
});
radioItem.addActionListener(new ActionListener()
{
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
user_actionPerformed(evt);
public void actionPerformed(ActionEvent evt)
{
user_actionPerformed(evt);
@@
-523,22
+547,21
@@
public class PDBViewer extends JInternalFrame implements Runnable
if (type == jalview.util.ImageMaker.TYPE.PNG)
{
im = new jalview.util.ImageMaker(this,
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);
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null, null, 0, false);
}
else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
im = new jalview.util.ImageMaker(this,
}
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());
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle(), null, 0, false);
}
else
{
im = new jalview.util.ImageMaker(this,
jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
}
else
{
im = new jalview.util.ImageMaker(this,
jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle());
+ width, height, null, this.getTitle(), null, 0, false);
}
if (im.getGraphics() != null)
}
if (im.getGraphics() != null)