import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
+import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
- new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains }, protocol);
+ new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
+ new String[][] { chains }, protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
String alreadyMapped = StructureSelectionManager
.getStructureSelectionManager(ap.av.applet)
.alreadyMappedToFile(pdbentry.getId());
- MCview.PDBfile reader = null;
+ StructureFile reader = null;
if (alreadyMapped != null)
{
reader = StructureSelectionManager.getStructureSelectionManager(
this.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent evt)
{
closeViewer();
}
if (freader == null)
{
- throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
+ throw new Exception(
+ MessageManager
+ .getString("exception.invalid_datasource_couldnt_obtain_reader"));
}
jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
this.setVisible(false);
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == mappingMenuItem)
jmb.setColourBySequence(itm == seqColour);
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == jmolColour)
}
}
+ @Override
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
}
+ @Override
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
{
Dimension currentSize = new Dimension();
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
currentSize = this.getSize();