package jalview.gui;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
import jalview.jbgui.GStructureChooser;
import jalview.jbgui.PDBDocFieldPreferences;
import jalview.structure.StructureSelectionManager;
public void run()
{
long startTime = System.currentTimeMillis();
- String msg = MessageManager.getString("status.fetching_db_refs");
- updateProgressIndicator(msg, startTime);
+ updateProgressIndicator(MessageManager
+ .getString("status.loading_cached_pdb_entries"), startTime);
loadLocalCachedPDBEntries();
+ updateProgressIndicator(null, startTime);
+ updateProgressIndicator(MessageManager
+ .getString("status.searching_for_pdb_structures"),
+ startTime);
fetchStructuresMetaData();
populateFilterComboBox();
updateProgressIndicator(null, startTime);
+ totalTime + ")");
if (errors.size() > 0)
{
- StringBuilder errorMsg = new StringBuilder(
- "Operation unsucessful due to the following: \n");
+ StringBuilder errorMsg = new StringBuilder();
for (String error : errors)
{
errorMsg.append(error).append("\n");
*/
public void pdbFromFile_actionPerformed()
{
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new jalview.io.JalviewFileView());
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.formatMessage(
"label.select_pdb_file_for", new String[]
{ selectedSequence.getDisplayId(false) }));
{ selectedSequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ if (value == JalviewFileChooser.APPROVE_OPTION)
{
selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
validateSelections();
}
}
}
PDBEntry fileEntry = new AssociatePdbFileWithSeq()
.associatePdbWithSeq(
- selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
+ selectedPdbFileName, AppletFormatAdapter.FILE,
selectedSequence, true, Desktop.instance);
launchStructureViewer(ap.getStructureSelectionManager(),
private void launchStructureViewer(StructureSelectionManager ssm,
PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
- SequenceI[] selectedSequences)
+ SequenceI[] sequences)
{
StructureViewer sViewer = new StructureViewer(ssm);
if (pdbEntriesToView.length > 1)
{
- sViewer.viewStructures(alignPanel, pdbEntriesToView,
- alignPanel.av.collateForPDB(pdbEntriesToView));
+ sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView),
+ alignPanel);
}
else
{
- sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
+ sViewer.viewStructures(pdbEntriesToView[0], sequences,
alignPanel);
}
}
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
- // JOptionPane.showMessageDialog(this, e.getMessage(),
- // "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
errorWarning.append(e.getMessage());
return;
} finally
{
- // System.out.println(">>>>> executing finally block");
validateSelections();
}
if (resultList.getSearchSummary() != null