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Prov not used in this version
[jalview.git]
/
src
/
MCview
/
PDBViewer.java
diff --git
a/src/MCview/PDBViewer.java
b/src/MCview/PDBViewer.java
index
95d4b35
..
082ce6e
100755
(executable)
--- a/
src/MCview/PDBViewer.java
+++ b/
src/MCview/PDBViewer.java
@@
-19,9
+19,13
@@
public class PDBViewer extends JInternalFrame implements Runnable
Sequence seq,
\r
SeqCanvas seqcanvas)
\r
{
\r
Sequence seq,
\r
SeqCanvas seqcanvas)
\r
{
\r
+
\r
pdb = entry;
\r
sequence = seq;
\r
\r
pdb = entry;
\r
sequence = seq;
\r
\r
+ Thread worker = new Thread(this);
\r
+ worker.start();
\r
+
\r
try
\r
{
\r
jbInit();
\r
try
\r
{
\r
jbInit();
\r
@@
-42,10
+46,8
@@
public class PDBViewer extends JInternalFrame implements Runnable
title.append( " Chain:" );
\r
title.append( pdb.getProperty().get("chains"));
\r
}
\r
title.append( " Chain:" );
\r
title.append( pdb.getProperty().get("chains"));
\r
}
\r
- Desktop.addInternalFrame(this,title.toString(),400, 400);
\r
\r
\r
- Thread worker = new Thread(this);
\r
- worker.start();
\r
+ Desktop.addInternalFrame(this,title.toString(),400, 400);
\r
}
\r
\r
public void run()
\r
}
\r
\r
public void run()
\r
@@
-53,8
+55,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
try
\r
{
\r
EBIFetchClient ebi = new EBIFetchClient();
\r
try
\r
{
\r
EBIFetchClient ebi = new EBIFetchClient();
\r
- String[] result = ebi.fetchData("pdb:" + pdb.getId(), null,
\r
- null);
\r
+ String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");
\r
\r
PDBfile pdbfile = new PDBfile(result);
\r
\r
\r
PDBfile pdbfile = new PDBfile(result);
\r
\r
@@
-174,6
+175,15
@@
public class PDBViewer extends JInternalFrame implements Runnable
molecule_actionPerformed(e);
\r
}
\r
});
\r
molecule_actionPerformed(e);
\r
}
\r
});
\r
+ allchains.setSelected(true);
\r
+ allchains.setText("Show All Chains");
\r
+ allchains.addItemListener(new ItemListener()
\r
+ {
\r
+ public void itemStateChanged(ItemEvent e)
\r
+ {
\r
+ allchains_itemStateChanged(e);
\r
+ }
\r
+ });
\r
jMenuBar1.add(fileMenu);
\r
jMenuBar1.add(coloursMenu);
\r
fileMenu.add(saveMenu);
\r
jMenuBar1.add(fileMenu);
\r
jMenuBar1.add(coloursMenu);
\r
fileMenu.add(saveMenu);
\r
@@
-189,6
+199,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
coloursMenu.add(depth);
\r
coloursMenu.add(zbuffer);
\r
coloursMenu.add(molecule);
\r
coloursMenu.add(depth);
\r
coloursMenu.add(zbuffer);
\r
coloursMenu.add(molecule);
\r
+ coloursMenu.add(allchains);
\r
ButtonGroup bg = new ButtonGroup();
\r
bg.add(seqButton);
\r
bg.add(chain);
\r
ButtonGroup bg = new ButtonGroup();
\r
bg.add(seqButton);
\r
bg.add(chain);
\r
@@
-211,6
+222,7
@@
public class PDBViewer extends JInternalFrame implements Runnable
JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
\r
JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
\r
JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();
\r
JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
\r
JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
\r
JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();
\r
+ JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
\r
\r
/**
\r
* DOCUMENT ME!
\r
\r
/**
\r
* DOCUMENT ME!
\r
@@
-326,7
+338,12
@@
public class PDBViewer extends JInternalFrame implements Runnable
public void mapping_actionPerformed(ActionEvent e)
\r
{
\r
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
\r
public void mapping_actionPerformed(ActionEvent e)
\r
{
\r
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
\r
- Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 500, 600);
\r
+ Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
\r
cap.setText(pdbcanvas.mappingDetails.toString());
\r
}
\r
cap.setText(pdbcanvas.mappingDetails.toString());
\r
}
\r
+
\r
+ public void allchains_itemStateChanged(ItemEvent e)
\r
+ {
\r
+ pdbcanvas.setAllchainsVisible(allchains.getState());
\r
+ }
\r
}
\r
}
\r