{
final long progressSessionId = System.currentTimeMillis();
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
{
final long progressSessionId = System.currentTimeMillis();
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
ssm.setProgressIndicator(this);
ssm.setProgressSessionId(progressSessionId);
new Thread(new Runnable()
ssm.setProgressIndicator(this);
ssm.setProgressSessionId(progressSessionId);
new Thread(new Runnable()
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- String currentView = selectedFilterOpt.getView();
- if (currentView == VIEWS_FILTER)
- {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
int pdbIdColIndex = getResultTable().getColumn("PDB Id")
.getModelIndex();
int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
int pdbIdColIndex = getResultTable().getColumn("PDB Id")
.getModelIndex();
int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
+ {
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
pdbEntry = getFindEntry(pdbIdStr,
selectedSeq.getAllPDBEntries());
}
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
pdbEntry = getFindEntry(pdbIdStr,
selectedSeq.getAllPDBEntries());
}
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
- }
- pdbEntriesToView[count++] = pdbEntry;
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ }
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
- }
- else if (currentView == VIEWS_LOCAL_PDB)
- {
- int[] selectedRows = tbl_local_pdb.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
+ }
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ int[] selectedRows = tbl_local_pdb.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
- int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
- .getModelIndex();
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
- pdbEntriesToView[count++] = pdbEntry;
- SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
+ int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+ .getModelIndex();
+ ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
+ {
+ PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+ pdbIdColIndex);
+ pdbEntriesToView[count++] = pdbEntry;
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
+ row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
- }
- else if (currentView == VIEWS_ENTER_ID)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
- String pdbIdStr = txt_search.getText();
- PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[] { selectedSequence });
launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[] { selectedSequence });
- }
- else if (currentView == VIEWS_FROM_FILE)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- jalview.io.AppletFormatAdapter.FILE,
- selectedSequence, true, Desktop.instance);
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq(selectedPdbFileName,
+ jalview.io.AppletFormatAdapter.FILE,
+ selectedSequence, true, Desktop.instance);
launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
new SequenceI[] { selectedSequence });
launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
new SequenceI[] { selectedSequence });
int p = 0;
// TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
// real PDB ID. For moment, we can also safely do this if there is already
int p = 0;
// TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
// real PDB ID. For moment, we can also safely do this if there is already