/*
+
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Vector;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
-import javax.swing.ListSelectionModel;
+import javax.swing.JLabel;
/**
* Provides the behaviors for the Structure chooser Panel
private IProgressIndicator progressIndicator;
- private Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
+ private Collection<PDBResponseSummary> discoveredStructuresSet;
- private PDBRestRequest pdbRequest;
+ private PDBRestRequest lastPdbRequest;
private PDBRestClient pdbRestCleint;
Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
.getStructureSummaryFields();
- pdbRequest = new PDBRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(500);
- pdbRequest.setFieldToSearchBy("(text:");
- pdbRequest.setWantedFields(wantedFields);
+ discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
for (SequenceI seq : selectedSequences)
{
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq.getName());
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
+ tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
discoveredStructuresSet));
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
*/
public void filterResultSet(final String fieldToFilterBy)
{
+
+ // SwingWorker aWorker = new SwingWorker()
+ // {
+ // long startTime = System.currentTimeMillis();
+ //
+ // @Override
+ // protected Object doInBackground() throws Exception
+ // {
+ // lbl_loading.setVisible(true);
+ //
+ // Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ // .getStructureSummaryFields();
+ // Collection<PDBResponseSummary> filteredResponse = new
+ // HashSet<PDBResponseSummary>();
+ // for (SequenceI seq : selectedSequences)
+ // {
+ // PDBRestRequest pdbRequest = new PDBRestRequest();
+ // pdbRequest.setAllowEmptySeq(false);
+ // pdbRequest.setResponseSize(1);
+ // pdbRequest.setFieldToSearchBy("(text:");
+ // pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ // !chk_invertFilter.isSelected());
+ // pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ // pdbRequest.setWantedFields(wantedFields);
+ // pdbRequest.setAssociatedSequence(seq.getName());
+ // pdbRestCleint = new PDBRestClient();
+ // PDBRestResponse resultList = pdbRestCleint
+ // .executeRequest(pdbRequest);
+ // lastPdbRequest = pdbRequest;
+ // if (resultList.getSearchSummary() != null
+ // && !resultList.getSearchSummary().isEmpty())
+ // {
+ // filteredResponse.addAll(resultList.getSearchSummary());
+ // }
+ // }
+ //
+ // if (!filteredResponse.isEmpty())
+ // {
+ // final int filterResponseCount = filteredResponse.size();
+ // Collection<PDBResponseSummary> reorderedStructuresSet = new
+ // LinkedHashSet<PDBResponseSummary>();
+ // reorderedStructuresSet.addAll(filteredResponse);
+ // reorderedStructuresSet.addAll(discoveredStructuresSet);
+ // tbl_summary.setModel(PDBRestResponse.getTableModel(
+ // lastPdbRequest, reorderedStructuresSet));
+ //
+ // // Update the model here
+ // // ListSelectionModel model = tbl_summary.getSelectionModel();
+ // // model.clearSelection();
+ // // model.addSelectionInterval(0, filterResponseCount - 1);
+ // // EventQueue.invokeLater(new Runnable()
+ // // {
+ // // public void run()
+ // // {
+ // // tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+ //
+ // // }
+ // // });
+ // // Discard unwanted objects to make them eligible for garbage
+ // // collection
+ // reorderedStructuresSet = null;
+ // }
+ // return null;
+ // }
+ //
+ // public void done()
+ // {
+ // lbl_loading.setVisible(false);
+ // tbl_summary.addRowSelectionInterval(0, 2);
+ // String totalTime = (System.currentTimeMillis() - startTime)
+ // + " milli secs";
+ // mainFrame.setTitle("Structure Chooser - Filter time (" + totalTime
+ // + ")");
+ // validateSelections();
+ // }
+ // };
+ // aWorker.execute();
+
Thread filterThread = new Thread(new Runnable()
{
@Override
try
{
lbl_loading.setVisible(true);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(text:");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
for (SequenceI seq : selectedSequences)
{
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ !chk_invertFilter.isSelected());
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
pdbRequest.setAssociatedSequence(seq.getName());
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList = pdbRestCleint
.executeRequest(pdbRequest);
+ lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
}
}
- if (filteredResponse != null)
+ if (!filteredResponse.isEmpty())
{
- int filterResponseCount = filteredResponse.size();
- List<PDBResponseSummary> originalDiscoveredStructuresList = new ArrayList<PDBResponseSummary>(
- discoveredStructuresSet);
- originalDiscoveredStructuresList.removeAll(filteredResponse);
- Collection<PDBResponseSummary> reorderedStructuresSet = new ArrayList<PDBResponseSummary>();
+ final int filterResponseCount = filteredResponse.size();
+ Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
reorderedStructuresSet.addAll(filteredResponse);
- reorderedStructuresSet.addAll(originalDiscoveredStructuresList);
-
- tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
- reorderedStructuresSet));
-
- ListSelectionModel model = tbl_summary.getSelectionModel();
- model.clearSelection();
- for (int x = 0; x < filterResponseCount; x++)
- {
- model.addSelectionInterval(x, x);
- }
-
+ reorderedStructuresSet.addAll(discoveredStructuresSet);
+ tbl_summary.setModel(PDBRestResponse.getTableModel(
+ lastPdbRequest, reorderedStructuresSet));
+
+ // Update the model here
+ // ListSelectionModel model = tbl_summary.getSelectionModel();
+ // model.clearSelection();
+ // model.addSelectionInterval(0, filterResponseCount - 1);
+ // EventQueue.invokeLater(new Runnable()
+ // {
+ // public void run()
+ // {
+ tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+
+ // }
+ // });
// Discard unwanted objects to make them eligible for garbage
// collection
- originalDiscoveredStructuresList = null;
reorderedStructuresSet = null;
}
lbl_loading.setVisible(false);
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ mainFrame.setTitle("Structure Chooser - Filter time ("
+ + totalTime + ")");
+
+ validateSelections();
} catch (Exception e)
{
e.printStackTrace();
}
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- mainFrame.setTitle("Structure Chooser - Filter time (" + totalTime
- + ")");
-
- validateSelections();
}
});
filterThread.start();
}
-
/**
* Handles action event for btn_pdbFromFile
*/
{
validateAssociationFromFile();
}
-
}
/**
if (currentView == VIEWS_FILTER)
{
int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
- pdbRequest.getWantedFields(), true);
+ lastPdbRequest.getWantedFields(), true);
int[] selectedRows = tbl_summary.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
* a unique sequence when more than one sequence selection is made.
*/
public void populateCmbAssociateSeqOptions(
- JComboBox<AssociateSeqOptions> cmb_assSeq)
+ JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
{
cmb_assSeq.removeAllItems();
cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
null));
// cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null));
+ lbl_associateSeq.setVisible(false);
if (selectedSequences.length > 1)
{
for (SequenceI seq : selectedSequences)
}
else
{
+ String seqName = selectedSequence.getDisplayId(false);
+ seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
+ lbl_associateSeq.setText(seqName);
+ lbl_associateSeq.setVisible(true);
cmb_assSeq.setVisible(false);
}
}
{
List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
wantedFields.add(PDBDocField.PDB_ID);
- pdbRequest = new PDBRestRequest();
+ PDBRestRequest pdbRequest = new PDBRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(pdb_id:");
validateSelections();
}
+ @Override
+ public void tabRefresh()
+ {
+ if (selectedSequences != null)
+ {
+ Thread refreshThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ fetchStructuresMetaData();
+ filterResultSet(((FilterOption) cmb_filterOption
+ .getSelectedItem()).getValue());
+ }
+ });
+ refreshThread.start();
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff