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JAL-1793 spike branch updated to latest
[jalview.git]
/
src
/
jalview
/
gui
/
StructureChooser.java
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
da10e3f
..
20f4a49
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-157,8
+157,8
@@
public class StructureChooser extends GStructureChooser
Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
- discoveredStructuresSet = new LinkedHashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
+ discoveredStructuresSet = new LinkedHashSet<>();
+ HashSet<String> errors = new HashSet<>();
for (SequenceI seq : selectedSequences)
{
FTSRestRequest pdbRequest = new FTSRestRequest();
for (SequenceI seq : selectedSequences)
{
FTSRestRequest pdbRequest = new FTSRestRequest();
@@
-223,7
+223,7
@@
public class StructureChooser extends GStructureChooser
public void loadLocalCachedPDBEntries()
{
public void loadLocalCachedPDBEntries()
{
- ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
+ ArrayList<CachedPDB> entries = new ArrayList<>();
for (SequenceI seq : selectedSequences)
{
if (seq.getDatasetSequence() != null
for (SequenceI seq : selectedSequences)
{
if (seq.getDatasetSequence() != null
@@
-257,7
+257,7
@@
public class StructureChooser extends GStructureChooser
boolean isPDBRefsFound = false;
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
boolean isPDBRefsFound = false;
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
- Set<String> seqRefs = new LinkedHashSet<String>();
+ Set<String> seqRefs = new LinkedHashSet<>();
if (seq.getAllPDBEntries() != null
&& queryBuilder.length() < MAX_QLENGTH)
if (seq.getAllPDBEntries() != null
&& queryBuilder.length() < MAX_QLENGTH)
@@
-401,8
+401,8
@@
public class StructureChooser extends GStructureChooser
lbl_loading.setVisible(true);
Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
lbl_loading.setVisible(true);
Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
- Collection<FTSData> filteredResponse = new HashSet<FTSData>();
- HashSet<String> errors = new HashSet<String>();
+ Collection<FTSData> filteredResponse = new HashSet<>();
+ HashSet<String> errors = new HashSet<>();
for (SequenceI seq : selectedSequences)
{
for (SequenceI seq : selectedSequences)
{
@@
-453,7
+453,7
@@
public class StructureChooser extends GStructureChooser
if (!filteredResponse.isEmpty())
{
final int filterResponseCount = filteredResponse.size();
if (!filteredResponse.isEmpty())
{
final int filterResponseCount = filteredResponse.size();
- Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
+ Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
getResultTable().setModel(FTSRestResponse
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
getResultTable().setModel(FTSRestResponse
@@
-725,11
+725,10
@@
public class StructureChooser extends GStructureChooser
@Override
public void ok_ActionPerformed()
{
@Override
public void ok_ActionPerformed()
{
- final long progressSessionId = System.currentTimeMillis();
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+
final int preferredHeight = pnl_filter.getHeight();
final int preferredHeight = pnl_filter.getHeight();
- ssm.setProgressIndicator(this);
- ssm.setProgressSessionId(progressSessionId);
+
new Thread(new Runnable()
{
@Override
new Thread(new Runnable()
{
@Override
@@
-747,7
+746,7
@@
public class StructureChooser extends GStructureChooser
int[] selectedRows = getResultTable().getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
int[] selectedRows = getResultTable().getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
- List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
String pdbIdStr = getResultTable()
for (int row : selectedRows)
{
String pdbIdStr = getResultTable()
@@
-761,6
+760,7
@@
public class StructureChooser extends GStructureChooser
pdbEntry = getFindEntry(pdbIdStr,
selectedSeq.getAllPDBEntries());
}
pdbEntry = getFindEntry(pdbIdStr,
selectedSeq.getAllPDBEntries());
}
+
if (pdbEntry == null)
{
pdbEntry = new PDBEntry();
if (pdbEntry == null)
{
pdbEntry = new PDBEntry();
@@
-783,7
+783,7
@@
public class StructureChooser extends GStructureChooser
.getModelIndex();
int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
.getModelIndex();
.getModelIndex();
int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
.getModelIndex();
- List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ List<SequenceI> selectedSeqsToView = new ArrayList<>();
for (int row : selectedRows)
{
PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
for (int row : selectedRows)
{
PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
@@
-805,7
+805,6
@@
public class StructureChooser extends GStructureChooser
{
selectedSequence = userSelectedSeq;
}
{
selectedSequence = userSelectedSeq;
}
-
String pdbIdStr = txt_search.getText();
PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
String pdbIdStr = txt_search.getText();
PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
@@
-847,6
+846,7
@@
public class StructureChooser extends GStructureChooser
{ selectedSequence });
}
closeAction(preferredHeight);
{ selectedSequence });
}
closeAction(preferredHeight);
+ mainFrame.dispose();
}
}).start();
}
}
}).start();
}
@@
-870,13
+870,15
@@
public class StructureChooser extends GStructureChooser
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
- ssm.setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"));
+ long progressId = sequences.hashCode();
+ setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"), progressId);
final StructureViewer sViewer = new StructureViewer(ssm);
final StructureViewer sViewer = new StructureViewer(ssm);
+ setProgressBar(null, progressId);
if (SiftsSettings.isMapWithSifts())
{
if (SiftsSettings.isMapWithSifts())
{
- List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
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
@@
-907,41
+909,43
@@
public class StructureChooser extends GStructureChooser
if (!seqsWithoutSourceDBRef.isEmpty())
{
int y = seqsWithoutSourceDBRef.size();
if (!seqsWithoutSourceDBRef.isEmpty())
{
int y = seqsWithoutSourceDBRef.size();
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_dbrefs_for_sequences_without_valid_refs",
"status.fetching_dbrefs_for_sequences_without_valid_refs",
- y));
+ y), progressId);
SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
int x = 0;
for (SequenceI fSeq : seqsWithoutSourceDBRef)
{
seqWithoutSrcDBRef[x++] = fSeq;
}
SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
int x = 0;
for (SequenceI fSeq : seqsWithoutSourceDBRef)
{
seqWithoutSrcDBRef[x++] = fSeq;
}
+
DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
dbRefFetcher.fetchDBRefs(true);
DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
dbRefFetcher.fetchDBRefs(true);
+
+ setProgressBar("Fetch complete.", progressId); // todo i18n
}
}
if (pdbEntriesToView.length > 1)
{
}
}
if (pdbEntriesToView.length > 1)
{
- ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+ ArrayList<SequenceI[]> seqsMap = new ArrayList<>();
for (SequenceI seq : sequences)
{
seqsMap.add(new SequenceI[] { seq });
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
for (SequenceI seq : sequences)
{
seqsMap.add(new SequenceI[] { seq });
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.getString(
- "status.fetching_3d_structures_for_selected_entries"));
+
+ setProgressBar(MessageManager
+ .getString("status.fetching_3d_structures_for_selected_entries"), progressId);
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
}
else
{
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
}
else
{
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_3d_structures_for",
"status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()));
+ pdbEntriesToView[0].getId()),progressId);
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
+ setProgressBar(null, progressId);
}
/**
}
/**
@@
-1000,7
+1004,7
@@
public class StructureChooser extends GStructureChooser
String searchTerm = txt_search.getText().toLowerCase();
searchTerm = searchTerm.split(":")[0];
// System.out.println(">>>>> search term : " + searchTerm);
String searchTerm = txt_search.getText().toLowerCase();
searchTerm = searchTerm.split(":")[0];
// System.out.println(">>>>> search term : " + searchTerm);
- List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ List<FTSDataColumnI> wantedFields = new ArrayList<>();
FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
@@
-1062,7
+1066,7
@@
public class StructureChooser extends GStructureChooser
public PDBEntryTableModel(List<CachedPDB> pdbEntries)
{
public PDBEntryTableModel(List<CachedPDB> pdbEntries)
{
- this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
+ this.pdbEntries = new ArrayList<>(pdbEntries);
}
@Override
}
@Override