import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
public JalviewJmolBinding(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
- String protocol)
+ DataSourceType protocol)
{
super(ssm, pdbentry, sequenceIs, protocol);
/*
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, AppletFormatAdapter.PASTE);
+ pdbfile, DataSourceType.PASTE, getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
// needs
// to be tested. See mantis bug
// https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- String protocol = AppletFormatAdapter.URL;
+ DataSourceType protocol = DataSourceType.URL;
try
{
if (fl.exists())
{
- protocol = AppletFormatAdapter.FILE;
+ protocol = DataSourceType.FILE;
}
} catch (Exception e)
{
}
// Explicitly map to the filename used by Jmol ;
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- fileName, protocol);
+ fileName, protocol, getIProgressIndicator());
// pdbentry[pe].getFile(), protocol);
}
return chainNames;
}
+ protected abstract IProgressIndicator getIProgressIndicator();
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);