*/
package jalview.appletgui;
+import jalview.bin.JalviewLite;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
}
public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, String protocol)
+ AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
- new String[][] { chains }, protocol);
+ protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
- if (protocol.equals(AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
pdbentry.setId("PASTED PDB"
+ (chains == null ? "_" : chains.toString()));
}
}
- if (jalview.bin.JalviewLite.debug)
+ if (JalviewLite.debug)
{
System.err
.println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
closeViewer();
}
});
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable());
- pdbentry.getProperty().put("protocol", protocol);
- }
+ pdbentry.setProperty("protocol", protocol);
if (pdbentry.getFile() != null)
+
{
// import structure data from pdbentry.getFile based on given protocol
- if (protocol.equals(AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
// TODO: JAL-623 : correctly record file contents for matching up later
// pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
loadInline(pdbentry.getFile());
}
- else if (protocol.equals(AppletFormatAdapter.FILE)
- || protocol.equals(AppletFormatAdapter.URL))
+ else if (protocol == DataSourceType.FILE
+ || protocol == DataSourceType.URL)
{
jmb.viewer.openFile(pdbentry.getFile());
}
jmb.loadInline(string);
}
- void setChainMenuItems(Vector<String> chains)
+ void setChainMenuItems(List<String> chains)
{
chainMenu.removeAll();
repaint();
return;
}
- setChainMenuItems(jmb.chainNames);
+ setChainMenuItems(jmb.getChainNames());
jmb.colourBySequence(ap);
setTitle(jmb.getViewerTitle());