&& !resultList.getSearchSummary().isEmpty())
{
discoveredStructuresSet.addAll(resultList.getSearchSummary());
- updateSequenceDbRef(seq, resultList.getSearchSummary());
+ updateSequencePDBEntries(seq, resultList.getSearchSummary());
}
}
{
for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
{
+
String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
.getChainCode();
String[] pdbEntryRowData = new String[]
chain,
pdbEntry.getType(),
pdbEntry.getFile() };
- tableModel.addRow(pdbEntryRowData);
- cachedEntryMap.put(seq.getDisplayId(false) + pdbEntry.getId(),
+ if (pdbEntry.getFile() != null)
+ {
+ tableModel.addRow(pdbEntryRowData);
+ }
+ cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
pdbEntry);
}
}
}
/**
- * Update the DBRef entry for a given sequence with values retrieved from
+ * Update the PDBEntry for a given sequence with values retrieved from
* PDBResponseSummary
*
* @param seq
* @param responseSummaries
* a collection of PDBResponseSummary
*/
- public void updateSequenceDbRef(SequenceI seq,
+ public void updateSequencePDBEntries(SequenceI seq,
Collection<PDBResponseSummary> responseSummaries)
{
for (PDBResponseSummary response : responseSummaries)
{
- PDBEntry newEntry = new PDBEntry();
- newEntry.setId(response.getPdbId());
- newEntry.setType(PDBEntry.Type.PDB);
- seq.getDatasetSequence().addPDBId(newEntry);
+ String pdbIdStr = response.getPdbId();
+ PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ }
+ seq.getDatasetSequence().addPDBId(pdbEntry);
}
}
{
String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
.toString();
- PDBEntry pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
+
+ PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ }
pdbEntriesToView[count++] = pdbEntry;
}
-
launchStructureViewer(ap.getStructureSelectionManager(),
pdbEntriesToView, ap, selectedSequences);
}
int count = 0;
for (int row : selectedRows)
{
- String entryKey = tbl_local_pdb.getValueAt(row, 0).toString() + tbl_local_pdb.getValueAt(row, 1).toString();
+ String entryKey = tbl_local_pdb.getValueAt(row, 1).toString()
+ .toLowerCase();
pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
}
launchStructureViewer(ap.getStructureSelectionManager(),
{
selectedSequence = userSelectedSeq;
}
- PDBEntry pdbEntry = new PDBEntry();
- pdbEntry.setId(txt_search.getText());
- pdbEntry.setType(PDBEntry.Type.PDB);
+
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(txt_search.getText());
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ }
+
selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
PDBEntry[] pdbEntriesToView = new PDBEntry[]
{ pdbEntry };
}
}
+
}