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JAL-2326 updated references of JOptionPane to JvOptionPane
[jalview.git]
/
src
/
jalview
/
gui
/
StructureChooser.java
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
af8b2f3
..
0c3aa2a
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-81,6
+81,10
@@
public class StructureChooser extends GStructureChooser implements
private boolean isValidPBDEntry;
private boolean isValidPBDEntry;
+ private boolean cachedPDBExists;
+
+ private static int MAX_QLENGHT = 7820;
+
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
@@
-102,7
+106,7
@@
public class StructureChooser extends GStructureChooser implements
}
// ensure a filter option is in force for search
}
// ensure a filter option is in force for search
- populateFilterComboBox(true);
+ populateFilterComboBox(true, cachedPDBExists);
Thread discoverPDBStructuresThread = new Thread(new Runnable()
{
@Override
Thread discoverPDBStructuresThread = new Thread(new Runnable()
{
@Override
@@
-118,7
+122,7
@@
public class StructureChooser extends GStructureChooser implements
startTime);
fetchStructuresMetaData();
// revise filter options if no results were found
startTime);
fetchStructuresMetaData();
// revise filter options if no results were found
- populateFilterComboBox(isStructuresDiscovered());
+ populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
updateProgressIndicator(null, startTime);
mainFrame.setVisible(true);
updateCurrentView();
updateProgressIndicator(null, startTime);
mainFrame.setVisible(true);
updateCurrentView();
@@
-195,7
+199,7
@@
public class StructureChooser extends GStructureChooser implements
{
getResultTable().setModel(
FTSRestResponse.getTableModel(lastPdbRequest,
{
getResultTable().setModel(
FTSRestResponse.getTableModel(lastPdbRequest,
- discoveredStructuresSet));
+ discoveredStructuresSet));
noOfStructuresFound = discoveredStructuresSet.size();
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
noOfStructuresFound = discoveredStructuresSet.size();
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
@@
-212,9
+216,9
@@
public class StructureChooser extends GStructureChooser implements
{
errorMsg.append(error).append("\n");
}
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(this, errorMsg.toString(),
+ JvOptionPane.showMessageDialog(this, errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
}
}
}
@@
-237,7
+241,7
@@
public class StructureChooser extends GStructureChooser implements
}
}
}
}
}
}
-
+ cachedPDBExists = !entries.isEmpty();
PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
tbl_local_pdb.setModel(tableModelx);
}
PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
tbl_local_pdb.setModel(tableModelx);
}
@@
-257,17
+261,16
@@
public class StructureChooser extends GStructureChooser implements
StringBuilder queryBuilder = new StringBuilder();
Set<String> seqRefs = new LinkedHashSet<String>();
StringBuilder queryBuilder = new StringBuilder();
Set<String> seqRefs = new LinkedHashSet<String>();
- if (seq.getAllPDBEntries() != null)
+ if (seq.getAllPDBEntries() != null
+ && queryBuilder.length() < MAX_QLENGHT)
{
for (PDBEntry entry : seq.getAllPDBEntries())
{
if (isValidSeqName(entry.getId()))
{
queryBuilder.append("pdb_id:")
{
for (PDBEntry entry : seq.getAllPDBEntries())
{
if (isValidSeqName(entry.getId()))
{
queryBuilder.append("pdb_id:")
- .append(entry.getId().toLowerCase())
- .append(" OR ");
+ .append(entry.getId().toLowerCase()).append(" OR ");
isPDBRefsFound = true;
isPDBRefsFound = true;
- // seqRefs.add(entry.getId());
}
}
}
}
}
}
@@
-276,13
+279,13
@@
public class StructureChooser extends GStructureChooser implements
{
for (DBRefEntry dbRef : seq.getDBRefs())
{
{
for (DBRefEntry dbRef : seq.getDBRefs())
{
- if (isValidSeqName(getDBRefId(dbRef)))
+ if (isValidSeqName(getDBRefId(dbRef))
+ && queryBuilder.length() < MAX_QLENGHT)
{
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
queryBuilder.append("uniprot_accession:")
{
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
queryBuilder.append("uniprot_accession:")
- .append(getDBRefId(dbRef))
- .append(" OR ");
+ .append(getDBRefId(dbRef)).append(" OR ");
queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
.append(" OR ");
isUniProtRefsFound = true;
queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
.append(" OR ");
isUniProtRefsFound = true;
@@
-291,8
+294,7
@@
public class StructureChooser extends GStructureChooser implements
{
queryBuilder.append("pdb_id:")
{
queryBuilder.append("pdb_id:")
- .append(getDBRefId(dbRef).toLowerCase())
- .append(" OR ");
+ .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
isPDBRefsFound = true;
}
else
isPDBRefsFound = true;
}
else
@@
-347,7
+349,6
@@
public class StructureChooser extends GStructureChooser implements
.replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
}
.replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
}
-
/**
* Ensures sequence ref names are not less than 3 characters and does not
* contain a database name
/**
* Ensures sequence ref names are not less than 3 characters and does not
* contain a database name
@@
-458,8
+459,8
@@
public class StructureChooser extends GStructureChooser implements
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
getResultTable().setModel(
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
getResultTable().setModel(
- FTSRestResponse.getTableModel(
- lastPdbRequest, reorderedStructuresSet));
+ FTSRestResponse.getTableModel(lastPdbRequest,
+ reorderedStructuresSet));
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
@@
-483,11
+484,11
@@
public class StructureChooser extends GStructureChooser implements
{
errorMsg.append(error).append("\n");
}
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(
+ JvOptionPane.showMessageDialog(
null,
errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
null,
errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
}
@@
-528,7
+529,8
@@
public class StructureChooser extends GStructureChooser implements
* Populates the filter combo-box options dynamically depending on discovered
* structures
*/
* Populates the filter combo-box options dynamically depending on discovered
* structures
*/
- protected void populateFilterComboBox(boolean haveData)
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExists)
{
/*
* temporarily suspend the change listener behaviour
{
/*
* temporarily suspend the change listener behaviour
@@
-553,8
+555,14
@@
public class StructureChooser extends GStructureChooser implements
VIEWS_ENTER_ID));
cmb_filterOption.addItem(new FilterOption("From File", "-",
VIEWS_FROM_FILE));
VIEWS_ENTER_ID));
cmb_filterOption.addItem(new FilterOption("From File", "-",
VIEWS_FROM_FILE));
- cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
- VIEWS_LOCAL_PDB));
+ FilterOption cachedOption = new FilterOption("Cached PDB Entries", "-",
+ VIEWS_LOCAL_PDB);
+ cmb_filterOption.addItem(cachedOption);
+
+ if (/*!haveData &&*/cachedPDBExists)
+ {
+ cmb_filterOption.setSelectedItem(cachedOption);
+ }
cmb_filterOption.addItemListener(this);
}
cmb_filterOption.addItemListener(this);
}
@@
-898,9
+906,9
@@
public class StructureChooser extends GStructureChooser implements
}
if (seq.getPrimaryDBRefs().size() == 0)
{
}
if (seq.getPrimaryDBRefs().size() == 0)
{
- seqsWithoutSourceDBRef.add(seq);
- continue;
- }
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
}
if (!seqsWithoutSourceDBRef.isEmpty())
{
}
if (!seqsWithoutSourceDBRef.isEmpty())
{
@@
-1003,8
+1011,7
@@
public class StructureChooser extends GStructureChooser implements
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setWantedFields(wantedFields);
- pdbRequest
-.setSearchTerm(searchTerm + ")");
+ pdbRequest.setSearchTerm(searchTerm + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
pdbRestCleint = PDBFTSRestClient.getInstance();
wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
pdbRequest.setAssociatedSequence(selectedSequence);
pdbRestCleint = PDBFTSRestClient.getInstance();
wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());