import jalview.datamodel.StructureViewerModel.StructureData;
import jalview.ext.varna.RnaModel;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.schemabinding.version2.Annotation;
if (entry.getProperty() != null && !entry.getProperty().isEmpty())
{
PdbentryItem item = new PdbentryItem();
- Hashtable properties = entry.getProperty();
- Enumeration en2 = properties.keys();
+ Hashtable<String, String> properties = entry.getProperty();
+ Enumeration<String> en2 = properties.keys();
while (en2.hasMoreElements())
{
Property prop = new Property();
- String key = en2.nextElement().toString();
+ String key = en2.nextElement();
prop.setName(key);
- prop.setValue(properties.get(key).toString());
+ prop.setValue(properties.get(key));
item.addProperty(prop);
}
pdb.addPdbentryItem(item);
StructureData filedat = oldFiles.get(id);
String pdbFile = filedat.getFilePath();
SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
- binding.getSsm().setMapping(seq, null, pdbFile,
- jalview.io.AppletFormatAdapter.FILE);
+ binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
binding.addSequenceForStructFile(pdbFile, seq);
}
// and add the AlignmentPanel's reference to the view panel
af = new AlignFrame(al, view.getWidth(), view.getHeight(),
uniqueSeqSetId, viewId);
- af.setFileName(file, "Jalview");
+ af.setFileName(file, FileFormat.Jalview);
for (int i = 0; i < JSEQ.length; i++)
{