*/
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.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import java.util.List;
import java.util.Vector;
-import org.jmol.util.Logger;
-
public class AppletJmol extends EmbmenuFrame implements
// StructureListener,
KeyListener, ActionListener, ItemListener
MenuItem charge = new MenuItem(
MessageManager.getString("label.charge_cysteine"));
- MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
+ MenuItem zappo = new MenuItem(
+ MessageManager.getString("label.colourScheme_zappo"));
- MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
+ MenuItem taylor = new MenuItem(
+ MessageManager.getString("label.colourScheme_taylor"));
MenuItem hydro = new MenuItem(
- MessageManager.getString("label.hydrophobicity"));
+ MessageManager.getString("label.colourScheme_hydrophobic"));
MenuItem helix = new MenuItem(
- MessageManager.getString("label.helix_propensity"));
+ MessageManager.getString("label.colourScheme_helix_propensity"));
MenuItem strand = new MenuItem(
- MessageManager.getString("label.strand_propensity"));
+ MessageManager.getString("label.colourScheme_strand_propensity"));
MenuItem turn = new MenuItem(
- MessageManager.getString("label.turn_propensity"));
+ MessageManager.getString("label.colourScheme_turn_propensity"));
MenuItem buried = new MenuItem(
- MessageManager.getString("label.buried_index"));
+ MessageManager.getString("label.colourScheme_buried_index"));
MenuItem purinepyrimidine = new MenuItem(
- MessageManager.getString("label.purine_pyrimidine"));
+ MessageManager.getString("label.colourScheme_purine/pyrimidine"));
MenuItem user = new MenuItem(
MessageManager.getString("label.user_defined_colours"));
}
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() + "'");
jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
+ "_jmol_", ap.av.applet.getDocumentBase(),
ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
- Logger.setLogLevel(Logger.LEVEL_WARN);
} catch (Exception e)
{
System.err
}
});
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();
public void updateTitleAndMenus()
{
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ if (jmb.hasFileLoadingError())
{
repaint();
return;
}
- setChainMenuItems(jmb.chainNames);
+ setChainMenuItems(jmb.getChainNames());
jmb.colourBySequence(ap);
setTitle(jmb.getViewerTitle());