import jalview.api.AlignmentViewPanel;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Console;
-import jalview.datamodel.AlignmentI;
+import jalview.bin.Jalview;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.ws.dbsources.EBIAlfaFold;
-import jalview.ws.dbsources.Pdb;
-import jalview.ws.utils.UrlDownloadClient;
import javajs.util.BS;
public class AppJmolBinding extends JalviewJmolBinding
{
jmolViewer.setJmolCallbackListener(this);
// BH comment: can't do this yet [for JS only, or generally?]
- return Platform.isJS() ? null
+ return Platform.isJS() || Jalview.isHeadlessMode() ? null
: new AppConsole(jmolViewer, consolePanel, buttonsToShow);
}
{
// todo - record which pdbids were successfully imported.
StringBuilder errormsgs = new StringBuilder();
-
+
List<String> files = new ArrayList<>();
String pdbid = "";
try
String[] filesInViewer = getStructureFiles();
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
-
+
for (int pi = 0; pi < getPdbCount(); pi++)
{
PDBEntry strucEntry = getPdbEntry(pi);
if (file == null)
{
pdbid = strucEntry.getId();
- try{
+ try
+ {
file = structureViewer.fetchPdbFile(strucEntry);
} catch (OutOfMemoryError oomerror)
{
ex.printStackTrace();
errormsgs.append("'").append(pdbid).append("'");
}
- if (file!=null)
+ if (file != null)
{
// success
files.add(file);