import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.io.DataSourceType;
import jalview.jbgui.GStructureChooser;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Objects;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBox;
boolean isPDBRefsFound = false;
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
- HashSet<String> seqRefs = new LinkedHashSet<String>();
+ Set<String> seqRefs = new LinkedHashSet<String>();
if (seq.getAllPDBEntries() != null)
{
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append("pdb_id")
- .append(":")
-.append(entry.getId().toLowerCase())
+ queryBuilder.append("pdb_id:")
+ .append(entry.getId().toLowerCase())
.append(" OR ");
isPDBRefsFound = true;
// seqRefs.add(entry.getId());
{
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
- queryBuilder
-.append("uniprot_accession").append(":")
+ queryBuilder.append("uniprot_accession:")
.append(getDBRefId(dbRef))
.append(" OR ");
- queryBuilder
-.append("uniprot_id")
- .append(":")
- .append(getDBRefId(dbRef)).append(" OR ");
+ queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
+ .append(" OR ");
isUniProtRefsFound = true;
}
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- queryBuilder.append("pdb_id")
- .append(":").append(getDBRefId(dbRef).toLowerCase())
+ queryBuilder.append("pdb_id:")
+ .append(getDBRefId(dbRef).toLowerCase())
.append(" OR ");
isPDBRefsFound = true;
}
lastPdbRequest, reorderedStructuresSet));
FTSRestResponse.configureTableColumn(getResultTable(),
- wantedFields);
+ wantedFields, tempUserPrefs);
getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
getResultTable().getColumn("Ref Sequence").setMinWidth(100);
getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
{
cmb_filterOption.addItem(new FilterOption("Best Quality",
"overall_quality", VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage",
- "uniprot_coverage", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Best Resolution",
"resolution", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
pdbEntry = new PDBEntry();
if (pdbIdStr.split(":").length > 1)
{
- pdbEntry.setChainCode(pdbIdStr.split(":")[1]);
+ pdbEntry.setId(pdbIdStr.split(":")[0]);
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
+ }
+ else
+ {
+ pdbEntry.setId(pdbIdStr);
}
- pdbEntry.setId(pdbIdStr);
pdbEntry.setType(PDBEntry.Type.PDB);
selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
}
}
PDBEntry fileEntry = new AssociatePdbFileWithSeq()
.associatePdbWithSeq(selectedPdbFileName,
- jalview.io.AppletFormatAdapter.FILE,
+ DataSourceType.FILE,
selectedSequence, true, Desktop.instance);
launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
new SequenceI[] { selectedSequence });
}
- mainFrame.dispose();
+ closeAction();
}
}).start();
}
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
- ssm.setProgressBar("Launching PDB structure viewer..");
+ ssm.setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"));
final StructureViewer sViewer = new StructureViewer(ssm);
if (SiftsSettings.isMapWithSifts())
{
int y = seqsWithoutSourceDBRef.size();
ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching db refs for " + y
- + " sequence" + (y > 1 ? "s" : "")
- + " without valid db ref required for SIFTS mapping");
+ ssm.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_dbrefs_for_sequences_without_valid_refs",
+ y));
SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
int x = 0;
for (SequenceI fSeq : seqsWithoutSourceDBRef)
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching PDB Structures for selected entries..");
+ ssm.setProgressBar(MessageManager
+ .getString("status.fetching_3d_structures_for_selected_entries"));
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
}
else
{
ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching PDB Structure for "
- + pdbEntriesToView[0].getId());
+ ssm.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()));
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
}