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package jalview.gui; |
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import java.awt.event.ActionEvent; |
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import java.awt.event.ActionListener; |
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import java.awt.event.ItemEvent; |
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import java.io.File; |
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import java.util.ArrayList; |
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import java.util.Collection; |
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import java.util.HashSet; |
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import java.util.LinkedHashMap; |
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import java.util.LinkedHashSet; |
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import java.util.List; |
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import java.util.Locale; |
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import java.util.Map; |
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import java.util.concurrent.Executors; |
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import javax.swing.JCheckBox; |
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import javax.swing.JComboBox; |
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import javax.swing.JLabel; |
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import javax.swing.JMenuItem; |
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import javax.swing.JPopupMenu; |
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import javax.swing.JProgressBar; |
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import javax.swing.JTable; |
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import javax.swing.SwingUtilities; |
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import javax.swing.table.AbstractTableModel; |
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import com.stevesoft.pat.Regex; |
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import jalview.analysis.AlignmentUtils; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.structures.JalviewStructureDisplayI; |
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import jalview.bin.Cache; |
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import jalview.bin.Console; |
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import jalview.bin.Jalview; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.ext.jmol.JmolParser; |
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import jalview.fts.api.FTSData; |
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import jalview.fts.api.FTSDataColumnI; |
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import jalview.fts.api.FTSRestClientI; |
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import jalview.fts.core.FTSDataColumnPreferences; |
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import jalview.fts.core.FTSRestRequest; |
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import jalview.fts.core.FTSRestResponse; |
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import jalview.fts.service.pdb.PDBFTSRestClient; |
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import jalview.fts.service.threedbeacons.TDB_FTSData; |
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import jalview.gui.StructureViewer.ViewerType; |
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import jalview.gui.structurechooser.PDBStructureChooserQuerySource; |
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import jalview.gui.structurechooser.StructureChooserQuerySource; |
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import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource; |
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import jalview.io.DataSourceType; |
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import jalview.io.JalviewFileChooser; |
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import jalview.io.JalviewFileView; |
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import jalview.jbgui.FilterOption; |
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import jalview.jbgui.GStructureChooser; |
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import jalview.structure.StructureImportSettings.TFType; |
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import jalview.structure.StructureMapping; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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import jalview.util.StringUtils; |
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import jalview.ws.DBRefFetcher; |
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import jalview.ws.DBRefFetcher.FetchFinishedListenerI; |
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import jalview.ws.datamodel.alphafold.PAEContactMatrix; |
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import jalview.ws.seqfetcher.DbSourceProxy; |
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import jalview.ws.sifts.SiftsSettings; |
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@author |
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@SuppressWarnings("serial") |
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| 39.8% |
Uncovered Elements: 523 (869) |
Complexity: 203 |
Complexity Density: 0.35 |
|
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public class StructureChooser extends GStructureChooser |
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implements IProgressIndicator |
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{ |
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private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; |
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private static final int THRESHOLD_WARN_UNIPROT_FETCH_NEEDED = 20; |
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private SequenceI selectedSequence; |
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private SequenceI[] selectedSequences; |
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private IProgressIndicator progressIndicator; |
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private Collection<FTSData> discoveredStructuresSet; |
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private StructureChooserQuerySource data; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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protected FTSDataColumnPreferences getFTSDocFieldPrefs() |
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{ |
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return data.getDocFieldPrefs(); |
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} |
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private String selectedPdbFileName; |
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private TFType localPdbTempfacType; |
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private String localPdbPaeMatrixFileName; |
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private boolean isValidPBDEntry; |
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private boolean cachedPDBExists; |
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private Collection<FTSData> lastDiscoveredStructuresSet; |
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private boolean canQueryTDB = false; |
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private boolean notQueriedTDBYet = true; |
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List<SequenceI> seqsWithoutSourceDBRef = null; |
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private boolean showChooserGUI = true; |
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private boolean dontQueryServices = false; |
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private static StructureViewer lastTargetedView = null; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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3 |
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,... |
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AlignmentPanel ap) |
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{ |
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this(selectedSeqs, selectedSeq, ap, true); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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3 |
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,... |
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AlignmentPanel ap, boolean showGUI) |
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{ |
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this(selectedSeqs, selectedSeq, ap, showGUI, false); |
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} |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 2 |
Complexity Density: 0.22 |
|
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public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,... |
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AlignmentPanel ap, boolean showGUI, boolean dontQueryServices) |
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{ |
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data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs); |
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initDialog(); |
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this.ap = ap; |
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this.selectedSequence = selectedSeq; |
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this.selectedSequences = selectedSeqs; |
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this.progressIndicator = (ap == null) ? null : ap.alignFrame; |
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this.showChooserGUI = showGUI; |
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this.dontQueryServices = dontQueryServices; |
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init(); |
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} |
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| 85.2% |
Uncovered Elements: 4 (27) |
Complexity: 8 |
Complexity Density: 0.53 |
|
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3 |
private void populateSeqsWithoutSourceDBRef()... |
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{ |
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seqsWithoutSourceDBRef = new ArrayList<SequenceI>(); |
189 |
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boolean needCanonical = false; |
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3 |
for (SequenceI seq : selectedSequences) |
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{ |
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3 |
if (seq.isProtein()) |
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{ |
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3 |
int dbRef = ThreeDBStructureChooserQuerySource |
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.checkUniprotRefs(seq.getDBRefs()); |
196 |
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if (dbRef < 0) |
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{ |
198 |
2 |
if (dbRef == -1) |
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{ |
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1 |
needCanonical = true; |
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1 |
seqsWithoutSourceDBRef.add(seq); |
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} |
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else |
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{ |
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1 |
if (seq.getAllPDBEntries() == null |
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|| seq.getAllPDBEntries().size() == 0) |
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{ |
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seqsWithoutSourceDBRef.add(seq); |
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} |
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} |
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} |
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} |
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} |
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if (!seqsWithoutSourceDBRef.isEmpty()) |
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{ |
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canQueryTDB = true; |
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if (needCanonical) |
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{ |
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notQueriedTDBYet = true; |
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} |
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} |
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}; |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
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55 |
protected void init()... |
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{ |
233 |
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if (!Jalview.isHeadlessMode()) |
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{ |
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progressBar = new ProgressBar(this.statusPanel, this.statusBar); |
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} |
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chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true)); |
239 |
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btn_queryTDB.addActionListener(new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
242 |
0 |
@Override... |
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public void actionPerformed(ActionEvent e) |
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{ |
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promptForTDBFetch(false); |
246 |
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} |
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}); |
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249 |
55 |
if (!dontQueryServices) |
250 |
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{ |
251 |
3 |
Executors.defaultThreadFactory().newThread(new Runnable() |
252 |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
253 |
3 |
@Override... |
254 |
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public void run() |
255 |
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{ |
256 |
3 |
populateSeqsWithoutSourceDBRef(); |
257 |
3 |
initialStructureDiscovery(); |
258 |
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} |
259 |
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260 |
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}).start(); |
261 |
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} |
262 |
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else |
263 |
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{ |
264 |
52 |
Console.debug( |
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"Structure chooser not querying services to discover metadata."); |
266 |
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} |
267 |
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} |
268 |
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269 |
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| 100% |
Uncovered Elements: 0 (13) |
Complexity: 1 |
Complexity Density: 0.08 |
|
270 |
3 |
private void initialStructureDiscovery()... |
271 |
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{ |
272 |
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|
273 |
3 |
data = StructureChooserQuerySource.getQuerySourceFor(selectedSequences); |
274 |
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275 |
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276 |
3 |
populateFilterComboBox(true, cachedPDBExists); |
277 |
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278 |
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279 |
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280 |
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281 |
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282 |
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283 |
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284 |
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285 |
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286 |
3 |
long startTime = System.currentTimeMillis(); |
287 |
3 |
updateProgressIndicator( |
288 |
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MessageManager.getString("status.loading_cached_pdb_entries"), |
289 |
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startTime); |
290 |
3 |
loadLocalCachedPDBEntries(); |
291 |
3 |
updateProgressIndicator(null, startTime); |
292 |
3 |
updateProgressIndicator( |
293 |
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MessageManager.getString("status.searching_for_pdb_structures"), |
294 |
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startTime); |
295 |
3 |
fetchStructuresMetaData(); |
296 |
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|
297 |
3 |
populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); |
298 |
3 |
discoverStructureViews(); |
299 |
2 |
updateProgressIndicator(null, startTime); |
300 |
2 |
mainFrame.setVisible(showChooserGUI); |
301 |
2 |
updateCurrentView(); |
302 |
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} |
303 |
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304 |
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305 |
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306 |
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307 |
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@param |
308 |
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309 |
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| 0% |
Uncovered Elements: 29 (29) |
Complexity: 5 |
Complexity Density: 0.22 |
|
310 |
0 |
public void promptForTDBFetch(boolean ignoreGui)... |
311 |
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{ |
312 |
0 |
final long progressId = System.currentTimeMillis(); |
313 |
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|
314 |
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|
315 |
0 |
final Runnable strucDiscovery = new Runnable() |
316 |
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{ |
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| 0% |
Uncovered Elements: 23 (23) |
Complexity: 2 |
Complexity Density: 0.1 |
|
317 |
0 |
@Override... |
318 |
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public void run() |
319 |
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{ |
320 |
0 |
mainFrame.setEnabled(false); |
321 |
0 |
cmb_filterOption.setEnabled(false); |
322 |
0 |
progressBar.setProgressBar( |
323 |
|
MessageManager.getString("status.searching_3d_beacons"), |
324 |
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progressId); |
325 |
0 |
btn_queryTDB.setEnabled(false); |
326 |
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|
327 |
0 |
populateSeqsWithoutSourceDBRef(); |
328 |
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|
329 |
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|
330 |
0 |
previousWantedFields = null; |
331 |
0 |
lastSelected = (FilterOption) cmb_filterOption.getSelectedItem(); |
332 |
0 |
cmb_filterOption.setSelectedItem(null); |
333 |
0 |
cachedPDBExists = false; |
334 |
0 |
initialStructureDiscovery(); |
335 |
0 |
if (!isStructuresDiscovered()) |
336 |
|
{ |
337 |
0 |
progressBar.setProgressBar(MessageManager.getString( |
338 |
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"status.no_structures_discovered_from_3d_beacons"), |
339 |
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progressId); |
340 |
0 |
btn_queryTDB.setToolTipText(MessageManager.getString( |
341 |
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"status.no_structures_discovered_from_3d_beacons")); |
342 |
0 |
btn_queryTDB.setEnabled(false); |
343 |
0 |
pnl_queryTDB.setVisible(false); |
344 |
|
} |
345 |
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else |
346 |
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{ |
347 |
0 |
cmb_filterOption.setSelectedIndex(0); |
348 |
0 |
btn_queryTDB.setVisible(false); |
349 |
0 |
pnl_queryTDB.setVisible(false); |
350 |
0 |
progressBar.setProgressBar(null, progressId); |
351 |
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} |
352 |
0 |
mainFrame.setEnabled(true); |
353 |
0 |
cmb_filterOption.setEnabled(true); |
354 |
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} |
355 |
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}; |
356 |
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|
357 |
0 |
final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI() |
358 |
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{ |
359 |
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|
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
360 |
0 |
@Override... |
361 |
|
public void finished() |
362 |
|
{ |
363 |
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|
364 |
0 |
notQueriedTDBYet = false; |
365 |
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|
366 |
0 |
Executors.defaultThreadFactory().newThread(strucDiscovery).start(); |
367 |
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|
368 |
|
} |
369 |
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}; |
370 |
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|
371 |
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|
372 |
0 |
final Runnable discoverCanonicalDBrefs = () -> { |
373 |
0 |
btn_queryTDB.setEnabled(false); |
374 |
0 |
populateSeqsWithoutSourceDBRef(); |
375 |
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|
376 |
0 |
final int y = seqsWithoutSourceDBRef.size(); |
377 |
0 |
if (y > 0) |
378 |
|
{ |
379 |
0 |
final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef |
380 |
|
.toArray(new SequenceI[y]); |
381 |
0 |
DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef, |
382 |
|
progressBar, new DbSourceProxy[] |
383 |
|
{ new jalview.ws.dbsources.Uniprot() }, null, false); |
384 |
0 |
dbRefFetcher.addListener(afterDbRefFetch); |
385 |
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|
386 |
|
|
387 |
0 |
dbRefFetcher.fetchDBRefs(true); |
388 |
|
} |
389 |
|
else |
390 |
|
{ |
391 |
|
|
392 |
0 |
afterDbRefFetch.finished(); |
393 |
|
} |
394 |
|
}; |
395 |
0 |
final Runnable revertview = () -> { |
396 |
0 |
if (lastSelected != null) |
397 |
|
{ |
398 |
0 |
cmb_filterOption.setSelectedItem(lastSelected); |
399 |
|
} |
400 |
|
}; |
401 |
0 |
int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD", |
402 |
|
THRESHOLD_WARN_UNIPROT_FETCH_NEEDED); |
403 |
0 |
Console.debug("Using Uniprot fetch threshold of " + threshold); |
404 |
0 |
if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold) |
405 |
|
{ |
406 |
0 |
Executors.newSingleThreadExecutor().submit(discoverCanonicalDBrefs); |
407 |
0 |
return; |
408 |
|
} |
409 |
|
|
410 |
|
|
411 |
|
|
412 |
0 |
StructureChooser thisSC = this; |
413 |
0 |
JvOptionPane.newOptionDialog(thisSC.getFrame()) |
414 |
|
.setResponseHandler(JvOptionPane.OK_OPTION, |
415 |
|
discoverCanonicalDBrefs) |
416 |
|
.setResponseHandler(JvOptionPane.CANCEL_OPTION, revertview) |
417 |
|
.setResponseHandler(JvOptionPane.NO_OPTION, revertview) |
418 |
|
.showDialog( |
419 |
|
MessageManager.formatMessage( |
420 |
|
"label.fetch_references_for_3dbeacons", |
421 |
|
seqsWithoutSourceDBRef.size()), |
422 |
|
MessageManager.getString("label.3dbeacons"), |
423 |
|
JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE, |
424 |
|
null, new Object[] |
425 |
|
{ MessageManager.getString("action.ok"), |
426 |
|
MessageManager.getString("action.cancel") }, |
427 |
|
MessageManager.getString("action.ok"), false); |
428 |
|
} |
429 |
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|
430 |
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|
431 |
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|
432 |
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|
433 |
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|
434 |
|
|
|
|
| 48.3% |
Uncovered Elements: 15 (29) |
Complexity: 9 |
Complexity Density: 0.53 |
|
435 |
3 |
private void discoverStructureViews()... |
436 |
|
{ |
437 |
3 |
if (Desktop.instance != null) |
438 |
|
{ |
439 |
3 |
targetView.removeAllItems(); |
440 |
3 |
if (lastTargetedView != null && !lastTargetedView.isVisible()) |
441 |
|
{ |
442 |
0 |
lastTargetedView = null; |
443 |
|
} |
444 |
3 |
int linkedViewsAt = 0; |
445 |
3 |
for (StructureViewerBase view : Desktop.instance |
446 |
|
.getStructureViewers(null, null)) |
447 |
|
{ |
448 |
1 |
StructureViewer viewHandler = (lastTargetedView != null |
449 |
|
&& lastTargetedView.sview == view) ? lastTargetedView |
450 |
|
: StructureViewer.reconfigure(view); |
451 |
|
|
452 |
0 |
if (view.isLinkedWith(ap)) |
453 |
|
{ |
454 |
0 |
targetView.insertItemAt(viewHandler, linkedViewsAt++); |
455 |
|
} |
456 |
|
else |
457 |
|
{ |
458 |
0 |
targetView.addItem(viewHandler); |
459 |
|
} |
460 |
|
} |
461 |
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|
462 |
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|
463 |
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|
464 |
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|
465 |
2 |
targetView.setVisible(false); |
466 |
2 |
if (targetView.getItemCount() > 0) |
467 |
|
{ |
468 |
0 |
targetView.setVisible(true); |
469 |
0 |
if (lastTargetedView != null) |
470 |
|
{ |
471 |
0 |
targetView.setSelectedItem(lastTargetedView); |
472 |
|
} |
473 |
|
else |
474 |
|
{ |
475 |
0 |
targetView.setSelectedIndex(0); |
476 |
|
} |
477 |
|
} |
478 |
2 |
btn_add.setVisible(targetView.isVisible()); |
479 |
|
} |
480 |
|
} |
481 |
|
|
482 |
|
|
483 |
|
|
484 |
|
|
485 |
|
@param |
486 |
|
|
487 |
|
@param |
488 |
|
|
489 |
|
|
|
|
| 50% |
Uncovered Elements: 2 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
490 |
11 |
protected void updateProgressIndicator(String message, long id)... |
491 |
|
{ |
492 |
11 |
if (progressIndicator != null) |
493 |
|
{ |
494 |
0 |
progressIndicator.setProgressBar(message, id); |
495 |
|
} |
496 |
|
} |
497 |
|
|
498 |
|
|
499 |
|
|
500 |
|
|
501 |
|
|
|
|
| 83.3% |
Uncovered Elements: 7 (42) |
Complexity: 9 |
Complexity Density: 0.28 |
|
502 |
4 |
void fetchStructuresMetaData()... |
503 |
|
{ |
504 |
4 |
long startTime = System.currentTimeMillis(); |
505 |
4 |
Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs() |
506 |
|
.getStructureSummaryFields(); |
507 |
|
|
508 |
4 |
discoveredStructuresSet = new LinkedHashSet<>(); |
509 |
4 |
HashSet<String> errors = new HashSet<>(); |
510 |
|
|
511 |
4 |
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
512 |
|
.getSelectedItem()); |
513 |
|
|
514 |
4 |
for (SequenceI seq : selectedSequences) |
515 |
|
{ |
516 |
|
|
517 |
4 |
FTSRestResponse resultList; |
518 |
4 |
try |
519 |
|
{ |
520 |
4 |
resultList = data.fetchStructuresMetaData(seq, wantedFields, |
521 |
|
selectedFilterOpt, !chk_invertFilter.isSelected()); |
522 |
|
|
523 |
|
|
524 |
|
|
525 |
2 |
if (resultList == null) |
526 |
|
{ |
527 |
0 |
continue; |
528 |
|
} |
529 |
|
} catch (Exception e) |
530 |
|
{ |
531 |
2 |
Console.printStackTrace(e); |
532 |
2 |
errors.add(e.getMessage()); |
533 |
2 |
continue; |
534 |
|
} |
535 |
2 |
if (resultList.getSearchSummary() != null |
536 |
|
&& !resultList.getSearchSummary().isEmpty()) |
537 |
|
{ |
538 |
2 |
discoveredStructuresSet.addAll(resultList.getSearchSummary()); |
539 |
|
} |
540 |
|
} |
541 |
|
|
542 |
4 |
int noOfStructuresFound = 0; |
543 |
4 |
String totalTime = (System.currentTimeMillis() - startTime) |
544 |
|
+ " milli secs"; |
545 |
4 |
if (discoveredStructuresSet != null |
546 |
|
&& !discoveredStructuresSet.isEmpty()) |
547 |
|
{ |
548 |
2 |
getResultTable() |
549 |
|
.setModel(data.getTableModel(discoveredStructuresSet)); |
550 |
|
|
551 |
2 |
noOfStructuresFound = discoveredStructuresSet.size(); |
552 |
2 |
lastDiscoveredStructuresSet = discoveredStructuresSet; |
553 |
2 |
mainFrame.setTitle(MessageManager.formatMessage( |
554 |
|
"label.structure_chooser_no_of_structures", |
555 |
|
noOfStructuresFound, totalTime)); |
556 |
|
} |
557 |
|
else |
558 |
|
{ |
559 |
2 |
mainFrame.setTitle(MessageManager |
560 |
|
.getString("label.structure_chooser_manual_association")); |
561 |
2 |
if (errors.size() > 0) |
562 |
|
{ |
563 |
2 |
StringBuilder errorMsg = new StringBuilder(); |
564 |
2 |
for (String error : errors) |
565 |
|
{ |
566 |
2 |
errorMsg.append(error).append("\n"); |
567 |
|
} |
568 |
2 |
if (!Jalview.isHeadlessMode()) |
569 |
|
{ |
570 |
2 |
JvOptionPane.showMessageDialog(this, errorMsg.toString(), |
571 |
|
MessageManager.getString("label.pdb_web-service_error"), |
572 |
|
JvOptionPane.ERROR_MESSAGE); |
573 |
|
} |
574 |
|
else |
575 |
|
{ |
576 |
0 |
Console.error( |
577 |
|
MessageManager.getString("label.pdb_web-service_error")); |
578 |
0 |
Console.debug(errorMsg.toString()); |
579 |
|
} |
580 |
|
} |
581 |
|
} |
582 |
|
} |
583 |
|
|
|
|
| 61.5% |
Uncovered Elements: 5 (13) |
Complexity: 4 |
Complexity Density: 0.44 |
|
584 |
3 |
protected void loadLocalCachedPDBEntries()... |
585 |
|
{ |
586 |
3 |
ArrayList<CachedPDB> entries = new ArrayList<>(); |
587 |
3 |
for (SequenceI seq : selectedSequences) |
588 |
|
{ |
589 |
3 |
if (seq.getDatasetSequence() != null |
590 |
|
&& seq.getDatasetSequence().getAllPDBEntries() != null) |
591 |
|
{ |
592 |
3 |
for (PDBEntry pdbEntry : seq.getDatasetSequence() |
593 |
|
.getAllPDBEntries()) |
594 |
|
{ |
595 |
0 |
if (pdbEntry.getFile() != null) |
596 |
|
{ |
597 |
0 |
entries.add(new CachedPDB(seq, pdbEntry)); |
598 |
|
} |
599 |
|
} |
600 |
|
} |
601 |
|
} |
602 |
3 |
cachedPDBExists = !entries.isEmpty(); |
603 |
3 |
PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); |
604 |
3 |
tbl_local_pdb.setModel(tableModelx); |
605 |
|
} |
606 |
|
|
607 |
|
|
608 |
|
|
609 |
|
|
610 |
|
@param |
611 |
|
|
612 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
613 |
1 |
void filterResultSet(final String fieldToFilterBy)... |
614 |
|
{ |
615 |
1 |
Thread filterThread = new Thread(new Runnable() |
616 |
|
{ |
617 |
|
|
|
|
| 68.3% |
Uncovered Elements: 13 (41) |
Complexity: 6 |
Complexity Density: 0.17 |
|
618 |
1 |
@Override... |
619 |
|
public void run() |
620 |
|
{ |
621 |
1 |
long startTime = System.currentTimeMillis(); |
622 |
1 |
lbl_loading.setVisible(true); |
623 |
1 |
Collection<FTSDataColumnI> wantedFields = data.getDocFieldPrefs() |
624 |
|
.getStructureSummaryFields(); |
625 |
1 |
Collection<FTSData> filteredResponse = new HashSet<>(); |
626 |
1 |
HashSet<String> errors = new HashSet<>(); |
627 |
|
|
628 |
1 |
for (SequenceI seq : selectedSequences) |
629 |
|
{ |
630 |
|
|
631 |
1 |
FTSRestResponse resultList; |
632 |
1 |
try |
633 |
|
{ |
634 |
1 |
resultList = data.selectFirstRankedQuery(seq, |
635 |
|
discoveredStructuresSet, wantedFields, fieldToFilterBy, |
636 |
|
!chk_invertFilter.isSelected()); |
637 |
|
|
638 |
|
} catch (Exception e) |
639 |
|
{ |
640 |
0 |
Console.debugPrintStackTrace(e); |
641 |
0 |
errors.add(e.getMessage()); |
642 |
0 |
continue; |
643 |
|
} |
644 |
1 |
if (resultList.getSearchSummary() != null |
645 |
|
&& !resultList.getSearchSummary().isEmpty()) |
646 |
|
{ |
647 |
1 |
filteredResponse.addAll(resultList.getSearchSummary()); |
648 |
|
} |
649 |
|
} |
650 |
|
|
651 |
1 |
String totalTime = (System.currentTimeMillis() - startTime) |
652 |
|
+ " milli secs"; |
653 |
1 |
if (!filteredResponse.isEmpty()) |
654 |
|
{ |
655 |
1 |
final int filterResponseCount = filteredResponse.size(); |
656 |
1 |
Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>(); |
657 |
1 |
reorderedStructuresSet.addAll(filteredResponse); |
658 |
1 |
reorderedStructuresSet.addAll(discoveredStructuresSet); |
659 |
1 |
getResultTable() |
660 |
|
.setModel(data.getTableModel(reorderedStructuresSet)); |
661 |
|
|
662 |
1 |
FTSRestResponse.configureTableColumn(getResultTable(), |
663 |
|
wantedFields, tempUserPrefs); |
664 |
1 |
getResultTable().getColumn("Ref Sequence").setPreferredWidth(120); |
665 |
1 |
getResultTable().getColumn("Ref Sequence").setMinWidth(100); |
666 |
1 |
getResultTable().getColumn("Ref Sequence").setMaxWidth(200); |
667 |
|
|
668 |
1 |
getResultTable().addRowSelectionInterval(0, |
669 |
|
filterResponseCount - 1); |
670 |
1 |
mainFrame.setTitle(MessageManager.formatMessage( |
671 |
|
"label.structure_chooser_filter_time", totalTime)); |
672 |
|
} |
673 |
|
else |
674 |
|
{ |
675 |
0 |
mainFrame.setTitle(MessageManager.formatMessage( |
676 |
|
"label.structure_chooser_filter_time", totalTime)); |
677 |
0 |
if (errors.size() > 0) |
678 |
|
{ |
679 |
0 |
StringBuilder errorMsg = new StringBuilder(); |
680 |
0 |
for (String error : errors) |
681 |
|
{ |
682 |
0 |
errorMsg.append(error).append("\n"); |
683 |
|
} |
684 |
0 |
JvOptionPane.showMessageDialog(null, errorMsg.toString(), |
685 |
|
MessageManager.getString("label.pdb_web-service_error"), |
686 |
|
JvOptionPane.ERROR_MESSAGE); |
687 |
|
} |
688 |
|
} |
689 |
|
|
690 |
1 |
lbl_loading.setVisible(false); |
691 |
|
|
692 |
1 |
validateSelections(); |
693 |
|
} |
694 |
|
}); |
695 |
1 |
filterThread.start(); |
696 |
|
} |
697 |
|
|
698 |
|
|
699 |
|
|
700 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 5 |
Complexity Density: 0.33 |
|
701 |
0 |
@Override... |
702 |
|
protected void pdbFromFile_actionPerformed() |
703 |
|
{ |
704 |
|
|
705 |
|
|
706 |
|
|
707 |
0 |
JalviewFileChooser chooser = new JalviewFileChooser( |
708 |
|
Cache.getProperty("LAST_DIRECTORY")); |
709 |
0 |
chooser.setFileView(new JalviewFileView()); |
710 |
0 |
chooser.setDialogTitle( |
711 |
|
MessageManager.formatMessage("label.select_pdb_file_for", |
712 |
|
selectedSequence.getDisplayId(false))); |
713 |
0 |
chooser.setToolTipText(MessageManager.formatMessage( |
714 |
|
"label.load_pdb_file_associate_with_sequence", |
715 |
|
selectedSequence.getDisplayId(false))); |
716 |
|
|
717 |
0 |
int value = chooser.showOpenDialog(null); |
718 |
0 |
if (value == JalviewFileChooser.APPROVE_OPTION) |
719 |
|
{ |
720 |
0 |
selectedPdbFileName = chooser.getSelectedFile().getPath(); |
721 |
0 |
Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName); |
722 |
0 |
boolean guessTFType = localPdbPaeMatrixFileName == null; |
723 |
0 |
localPdbPaeMatrixFileName = guessPAEFilename(); |
724 |
0 |
guessTFType |= localPdbPaeMatrixFileName != null; |
725 |
0 |
Regex alphaFold = JmolParser.getNewAlphafoldValidator(); |
726 |
0 |
if (guessTFType |
727 |
|
&& alphaFold.search(new File(selectedPdbFileName).getName()) |
728 |
|
&& !tempFacAsChanged) |
729 |
|
{ |
730 |
|
|
731 |
|
|
732 |
0 |
combo_tempFacAs.setSelectedItem(TFType.PLDDT); |
733 |
|
} |
734 |
0 |
validateSelections(); |
735 |
|
} |
736 |
|
} |
737 |
|
|
738 |
|
|
739 |
|
|
740 |
|
|
|
|
| 0% |
Uncovered Elements: 36 (36) |
Complexity: 7 |
Complexity Density: 0.27 |
|
741 |
0 |
@Override... |
742 |
|
protected void paeMatrixFile_actionPerformed() |
743 |
|
{ |
744 |
0 |
File pdbFile = new File(selectedPdbFileName); |
745 |
0 |
String setFile = Cache.getProperty("LAST_DIRECTORY"); |
746 |
0 |
if (localPdbPaeMatrixFileName != null) |
747 |
|
{ |
748 |
0 |
File paeFile = new File(localPdbPaeMatrixFileName); |
749 |
0 |
if (paeFile.exists()) |
750 |
0 |
setFile = paeFile.getAbsolutePath(); |
751 |
0 |
else if (paeFile.getParentFile().exists()) |
752 |
0 |
setFile = paeFile.getParentFile().getAbsolutePath(); |
753 |
|
} |
754 |
|
else |
755 |
|
{ |
756 |
0 |
String guess = guessPAEFilename(); |
757 |
0 |
if (guess != null) |
758 |
0 |
setFile = guess; |
759 |
|
} |
760 |
0 |
JalviewFileChooser chooser = new JalviewFileChooser(setFile); |
761 |
0 |
chooser.setFileView(new JalviewFileView()); |
762 |
0 |
chooser.setDialogTitle(MessageManager.formatMessage( |
763 |
|
"label.select_pae_matrix_file_for", pdbFile.getName())); |
764 |
0 |
chooser.setToolTipText(MessageManager.formatMessage( |
765 |
|
"label.load_pae_matrix_file_associate_with_structure", |
766 |
|
pdbFile.getName())); |
767 |
|
|
768 |
|
|
769 |
0 |
int value = chooser.showOpenDialog(null); |
770 |
0 |
if (value == JalviewFileChooser.APPROVE_OPTION) |
771 |
|
{ |
772 |
0 |
String fileName = chooser.getSelectedFile().getPath(); |
773 |
0 |
try |
774 |
|
{ |
775 |
0 |
PAEContactMatrix.validateContactMatrixFile(fileName); |
776 |
|
} catch (Exception thr) |
777 |
|
{ |
778 |
0 |
JvOptionPane.showInternalMessageDialog(this, MessageManager |
779 |
|
.formatMessage("label.couldnt_load_file", new Object[] |
780 |
|
{ fileName }) + "<br>" + thr.getLocalizedMessage(), |
781 |
|
MessageManager.getString("label.error_loading_file"), |
782 |
|
JvOptionPane.WARNING_MESSAGE); |
783 |
0 |
Console.error("Couldn't import " + fileName + " as a PAE matrix", |
784 |
|
thr); |
785 |
0 |
return; |
786 |
|
} |
787 |
0 |
localPdbPaeMatrixFileName = fileName; |
788 |
0 |
Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName); |
789 |
|
} |
790 |
0 |
validateAssociationFromFile(); |
791 |
|
} |
792 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 6 |
Complexity Density: 0.55 |
|
793 |
0 |
private String guessPAEFilename()... |
794 |
|
{ |
795 |
0 |
if (selectedPdbFileName.toLowerCase(Locale.ROOT).endsWith(".pdb") |
796 |
|
|| selectedPdbFileName.toLowerCase(Locale.ROOT) |
797 |
|
.endsWith(".cif")) |
798 |
|
{ |
799 |
0 |
String jsonExt = selectedPdbFileName.substring(0, |
800 |
|
selectedPdbFileName.length() - 4) + ".json"; |
801 |
|
|
802 |
0 |
String guessFile1 = StringUtils.replaceLast(jsonExt, "model", |
803 |
|
"predicted_aligned_error"); |
804 |
|
|
805 |
0 |
String guessFile2 = StringUtils.replaceLast(jsonExt, ".json", |
806 |
|
"_scores.json"); |
807 |
0 |
if (new File(guessFile1).exists()) |
808 |
|
{ |
809 |
0 |
return guessFile1; |
810 |
|
} |
811 |
0 |
else if (new File(jsonExt).exists()) |
812 |
|
{ |
813 |
0 |
return jsonExt; |
814 |
|
} |
815 |
0 |
else if (new File(guessFile2).exists()) |
816 |
|
{ |
817 |
0 |
return guessFile2; |
818 |
|
} |
819 |
|
} |
820 |
0 |
return null; |
821 |
|
} |
822 |
|
|
823 |
|
|
824 |
|
|
825 |
|
|
826 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
827 |
9 |
protected void populateFilterComboBox(boolean haveData,... |
828 |
|
boolean cachedPDBExist) |
829 |
|
{ |
830 |
9 |
populateFilterComboBox(haveData, cachedPDBExist, null); |
831 |
|
} |
832 |
|
|
833 |
|
|
834 |
|
|
835 |
|
|
836 |
|
|
|
|
| 86.5% |
Uncovered Elements: 5 (37) |
Complexity: 9 |
Complexity Density: 0.36 |
|
837 |
9 |
protected void populateFilterComboBox(boolean haveData,... |
838 |
|
boolean cachedPDBExist, FilterOption lastSel) |
839 |
|
{ |
840 |
|
|
841 |
|
|
842 |
|
|
843 |
|
|
844 |
9 |
cmb_filterOption.removeItemListener(this); |
845 |
9 |
int selSet = -1; |
846 |
9 |
cmb_filterOption.removeAllItems(); |
847 |
9 |
if (haveData) |
848 |
|
{ |
849 |
6 |
List<FilterOption> filters = data |
850 |
|
.getAvailableFilterOptions(VIEWS_FILTER); |
851 |
6 |
data.updateAvailableFilterOptions(VIEWS_FILTER, filters, |
852 |
|
lastDiscoveredStructuresSet); |
853 |
6 |
int p = 0; |
854 |
6 |
for (FilterOption filter : filters) |
855 |
|
{ |
856 |
39 |
if (lastSel != null && filter.equals(lastSel)) |
857 |
|
{ |
858 |
0 |
selSet = p; |
859 |
|
} |
860 |
39 |
p++; |
861 |
39 |
cmb_filterOption.addItem(filter); |
862 |
|
} |
863 |
|
} |
864 |
|
|
865 |
9 |
cmb_filterOption.addItem( |
866 |
|
new FilterOption(MessageManager.getString("label.enter_pdb_id"), |
867 |
|
"-", VIEWS_ENTER_ID, false, null)); |
868 |
9 |
cmb_filterOption.addItem( |
869 |
|
new FilterOption(MessageManager.getString("label.from_file"), |
870 |
|
"-", VIEWS_FROM_FILE, false, null)); |
871 |
9 |
if (canQueryTDB && notQueriedTDBYet) |
872 |
|
{ |
873 |
2 |
btn_queryTDB.setVisible(true); |
874 |
2 |
pnl_queryTDB.setVisible(true); |
875 |
|
} |
876 |
|
|
877 |
9 |
if (cachedPDBExist) |
878 |
|
{ |
879 |
1 |
FilterOption cachedOption = new FilterOption( |
880 |
|
MessageManager.getString("label.cached_structures"), "-", |
881 |
|
VIEWS_LOCAL_PDB, false, null); |
882 |
1 |
cmb_filterOption.addItem(cachedOption); |
883 |
1 |
if (selSet == -1) |
884 |
|
{ |
885 |
1 |
cmb_filterOption.setSelectedItem(cachedOption); |
886 |
|
} |
887 |
|
} |
888 |
9 |
if (selSet > -1) |
889 |
|
{ |
890 |
0 |
cmb_filterOption.setSelectedIndex(selSet); |
891 |
|
} |
892 |
9 |
cmb_filterOption.addItemListener(this); |
893 |
|
} |
894 |
|
|
895 |
|
|
896 |
|
|
897 |
|
|
|
|
| 75.9% |
Uncovered Elements: 7 (29) |
Complexity: 7 |
Complexity Density: 0.33 |
|
898 |
2 |
protected void updateCurrentView()... |
899 |
|
{ |
900 |
2 |
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
901 |
|
.getSelectedItem()); |
902 |
|
|
903 |
2 |
if (lastSelected == selectedFilterOpt) |
904 |
|
{ |
905 |
|
|
906 |
0 |
return; |
907 |
|
} |
908 |
|
|
909 |
|
|
910 |
2 |
lastSelected = selectedFilterOpt; |
911 |
|
|
912 |
2 |
layout_switchableViews.show(pnl_switchableViews, |
913 |
|
selectedFilterOpt.getView()); |
914 |
2 |
String filterTitle = mainFrame.getTitle(); |
915 |
2 |
mainFrame.setTitle(frameTitle); |
916 |
2 |
chk_invertFilter.setVisible(false); |
917 |
|
|
918 |
2 |
if (selectedFilterOpt.getView() == VIEWS_FILTER) |
919 |
|
{ |
920 |
1 |
mainFrame.setTitle(filterTitle); |
921 |
|
|
922 |
1 |
chk_invertFilter.setVisible(selectedFilterOpt |
923 |
|
.getQuerySource() instanceof PDBStructureChooserQuerySource); |
924 |
|
|
925 |
1 |
if (data != selectedFilterOpt.getQuerySource() |
926 |
|
|| data.needsRefetch(selectedFilterOpt)) |
927 |
|
{ |
928 |
0 |
data = selectedFilterOpt.getQuerySource(); |
929 |
|
|
930 |
0 |
tabRefresh(); |
931 |
0 |
return; |
932 |
|
} |
933 |
|
else |
934 |
|
{ |
935 |
1 |
filterResultSet(selectedFilterOpt.getValue()); |
936 |
|
} |
937 |
|
} |
938 |
1 |
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID |
939 |
|
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE) |
940 |
|
{ |
941 |
1 |
mainFrame.setTitle(MessageManager |
942 |
|
.getString("label.structure_chooser_manual_association")); |
943 |
1 |
idInputAssSeqPanel.loadCmbAssSeq(); |
944 |
1 |
fileChooserAssSeqPanel.loadCmbAssSeq(); |
945 |
|
} |
946 |
2 |
validateSelections(); |
947 |
|
} |
948 |
|
|
949 |
|
|
950 |
|
|
951 |
|
|
952 |
|
|
953 |
|
|
954 |
|
|
955 |
|
|
956 |
|
|
957 |
|
|
958 |
|
|
|
|
| 63.3% |
Uncovered Elements: 11 (30) |
Complexity: 7 |
Complexity Density: 0.39 |
|
959 |
5 |
@Override... |
960 |
|
protected void validateSelections() |
961 |
|
{ |
962 |
5 |
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
963 |
|
.getSelectedItem()); |
964 |
5 |
btn_add.setEnabled(false); |
965 |
5 |
String currentView = selectedFilterOpt.getView(); |
966 |
5 |
int selectedCount = 0; |
967 |
5 |
if (currentView == VIEWS_FILTER) |
968 |
|
{ |
969 |
2 |
selectedCount = getResultTable().getSelectedRows().length; |
970 |
2 |
if (selectedCount > 0) |
971 |
|
{ |
972 |
1 |
btn_add.setEnabled(true); |
973 |
|
} |
974 |
|
} |
975 |
3 |
else if (currentView == VIEWS_LOCAL_PDB) |
976 |
|
{ |
977 |
0 |
selectedCount = tbl_local_pdb.getSelectedRows().length; |
978 |
0 |
if (selectedCount > 0) |
979 |
|
{ |
980 |
0 |
btn_add.setEnabled(true); |
981 |
|
} |
982 |
|
} |
983 |
3 |
else if (currentView == VIEWS_ENTER_ID) |
984 |
|
{ |
985 |
3 |
validateAssociationEnterPdb(); |
986 |
|
} |
987 |
0 |
else if (currentView == VIEWS_FROM_FILE) |
988 |
|
{ |
989 |
0 |
validateAssociationFromFile(); |
990 |
|
} |
991 |
|
|
992 |
5 |
btn_newView.setEnabled(btn_add.isEnabled()); |
993 |
|
|
994 |
|
|
995 |
|
|
996 |
|
|
997 |
|
|
998 |
5 |
chk_superpose |
999 |
|
.setEnabled(selectedCount > 1 || targetView.getItemCount() > 0); |
1000 |
|
} |
1001 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 5 |
Complexity Density: 0.33 |
|
1002 |
0 |
@Override... |
1003 |
|
protected boolean showPopupFor(int selectedRow, int x, int y) |
1004 |
|
{ |
1005 |
0 |
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
1006 |
|
.getSelectedItem()); |
1007 |
0 |
String currentView = selectedFilterOpt.getView(); |
1008 |
|
|
1009 |
0 |
if (currentView == VIEWS_FILTER |
1010 |
|
&& data instanceof ThreeDBStructureChooserQuerySource) |
1011 |
|
{ |
1012 |
|
|
1013 |
0 |
TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data) |
1014 |
|
.getFTSDataFor(getResultTable(), selectedRow, |
1015 |
|
discoveredStructuresSet); |
1016 |
0 |
String pageUrl = row.getModelViewUrl(); |
1017 |
|
|
1018 |
0 |
JPopupMenu popup = new JPopupMenu("3D Beacons"); |
1019 |
0 |
JMenuItem viewUrl = new JMenuItem("View model web page"); |
1020 |
0 |
if (pageUrl == null || "".equals(pageUrl.trim())) |
1021 |
|
{ |
1022 |
0 |
viewUrl.setEnabled(false); |
1023 |
0 |
viewUrl.setText("No model page available."); |
1024 |
|
} |
1025 |
0 |
viewUrl.addActionListener(new ActionListener() |
1026 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1027 |
0 |
@Override... |
1028 |
|
public void actionPerformed(ActionEvent e) |
1029 |
|
{ |
1030 |
0 |
Desktop.showUrl(pageUrl); |
1031 |
|
} |
1032 |
|
}); |
1033 |
0 |
popup.add(viewUrl); |
1034 |
0 |
SwingUtilities.invokeLater(new Runnable() |
1035 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1036 |
0 |
@Override... |
1037 |
|
public void run() |
1038 |
|
{ |
1039 |
0 |
popup.show(getResultTable(), x, y); |
1040 |
|
} |
1041 |
|
}); |
1042 |
0 |
return true; |
1043 |
|
} |
1044 |
|
|
1045 |
0 |
return false; |
1046 |
|
} |
1047 |
|
|
1048 |
|
|
1049 |
|
|
1050 |
|
|
|
|
| 50% |
Uncovered Elements: 12 (24) |
Complexity: 6 |
Complexity Density: 0.38 |
|
1051 |
3 |
protected void validateAssociationEnterPdb()... |
1052 |
|
{ |
1053 |
3 |
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel |
1054 |
|
.getCmb_assSeq().getSelectedItem(); |
1055 |
3 |
lbl_pdbManualFetchStatus.setIcon(errorImage); |
1056 |
3 |
lbl_pdbManualFetchStatus.setToolTipText(""); |
1057 |
3 |
if (txt_search.getText().length() > 0) |
1058 |
|
{ |
1059 |
0 |
lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true, |
1060 |
|
MessageManager.formatMessage("info.no_pdb_entry_found_for", |
1061 |
|
txt_search.getText()))); |
1062 |
|
} |
1063 |
|
|
1064 |
3 |
if (errorWarning.length() > 0) |
1065 |
|
{ |
1066 |
0 |
lbl_pdbManualFetchStatus.setIcon(warningImage); |
1067 |
0 |
lbl_pdbManualFetchStatus.setToolTipText( |
1068 |
|
JvSwingUtils.wrapTooltip(true, errorWarning.toString())); |
1069 |
|
} |
1070 |
|
|
1071 |
3 |
if (selectedSequences.length == 1 || !assSeqOpt.getName() |
1072 |
|
.equalsIgnoreCase("-Select Associated Seq-")) |
1073 |
|
{ |
1074 |
3 |
txt_search.setEnabled(true); |
1075 |
3 |
if (isValidPBDEntry) |
1076 |
|
{ |
1077 |
0 |
btn_add.setEnabled(true); |
1078 |
0 |
lbl_pdbManualFetchStatus.setToolTipText(""); |
1079 |
0 |
lbl_pdbManualFetchStatus.setIcon(goodImage); |
1080 |
|
} |
1081 |
|
} |
1082 |
|
else |
1083 |
|
{ |
1084 |
0 |
txt_search.setEnabled(false); |
1085 |
0 |
lbl_pdbManualFetchStatus.setIcon(errorImage); |
1086 |
|
} |
1087 |
|
} |
1088 |
|
|
1089 |
|
|
1090 |
|
|
1091 |
|
|
|
|
| 0% |
Uncovered Elements: 34 (34) |
Complexity: 8 |
Complexity Density: 0.29 |
|
1092 |
0 |
protected void validateAssociationFromFile()... |
1093 |
|
{ |
1094 |
0 |
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel |
1095 |
|
.getCmb_assSeq().getSelectedItem(); |
1096 |
|
|
1097 |
0 |
String pdbFileString = ""; |
1098 |
0 |
String pdbFileTooltip = ""; |
1099 |
0 |
if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt |
1100 |
|
.getName().equalsIgnoreCase("-Select Associated Seq-"))) |
1101 |
|
{ |
1102 |
0 |
btn_pdbFromFile.setEnabled(true); |
1103 |
0 |
if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) |
1104 |
|
{ |
1105 |
0 |
btn_add.setEnabled(true); |
1106 |
|
|
1107 |
0 |
pdbFileString = new File(selectedPdbFileName).getName(); |
1108 |
0 |
pdbFileTooltip = new File(selectedPdbFileName).getAbsolutePath(); |
1109 |
0 |
setPdbOptionsEnabled(true); |
1110 |
|
} |
1111 |
|
else |
1112 |
|
{ |
1113 |
0 |
pdbFileString = MessageManager.getString("label.none"); |
1114 |
0 |
pdbFileTooltip = MessageManager.getString("label.nothing_selected"); |
1115 |
0 |
setPdbOptionsEnabled(false); |
1116 |
|
} |
1117 |
|
} |
1118 |
|
else |
1119 |
|
{ |
1120 |
0 |
btn_pdbFromFile.setEnabled(false); |
1121 |
0 |
setPdbOptionsEnabled(false); |
1122 |
|
|
1123 |
0 |
pdbFileString = MessageManager.getString("label.none"); |
1124 |
0 |
pdbFileTooltip = MessageManager.getString("label.nothing_selected"); |
1125 |
|
} |
1126 |
0 |
lbl_pdbFile.setText(pdbFileString); |
1127 |
0 |
lbl_pdbFile.setToolTipText(pdbFileTooltip); |
1128 |
|
|
1129 |
|
|
1130 |
0 |
String paeFileString = ""; |
1131 |
0 |
String paeFileTooltip = ""; |
1132 |
0 |
if (localPdbPaeMatrixFileName != null |
1133 |
|
&& localPdbPaeMatrixFileName.length() > 0) |
1134 |
|
{ |
1135 |
0 |
paeFileString = new File(localPdbPaeMatrixFileName).getName(); |
1136 |
0 |
paeFileTooltip = new File(localPdbPaeMatrixFileName) |
1137 |
|
.getAbsolutePath(); |
1138 |
|
} |
1139 |
|
else |
1140 |
|
{ |
1141 |
0 |
paeFileString = MessageManager.getString("label.none"); |
1142 |
0 |
paeFileTooltip = MessageManager.getString("label.nothing_selected"); |
1143 |
|
} |
1144 |
0 |
lbl_paeFile.setText(paeFileString); |
1145 |
0 |
lbl_paeFile.setToolTipText(paeFileTooltip); |
1146 |
|
} |
1147 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1148 |
2 |
@Override... |
1149 |
|
protected void cmbAssSeqStateChanged() |
1150 |
|
{ |
1151 |
2 |
validateSelections(); |
1152 |
|
} |
1153 |
|
|
1154 |
|
private FilterOption lastSelected = null; |
1155 |
|
|
1156 |
|
|
1157 |
|
|
1158 |
|
|
1159 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
1160 |
0 |
@Override... |
1161 |
|
protected void stateChanged(ItemEvent e) |
1162 |
|
{ |
1163 |
0 |
if (e.getSource() instanceof JCheckBox) |
1164 |
|
{ |
1165 |
0 |
updateCurrentView(); |
1166 |
|
} |
1167 |
|
else |
1168 |
|
{ |
1169 |
0 |
if (e.getStateChange() == ItemEvent.SELECTED) |
1170 |
|
{ |
1171 |
0 |
updateCurrentView(); |
1172 |
|
} |
1173 |
|
} |
1174 |
|
|
1175 |
|
} |
1176 |
|
|
1177 |
|
|
1178 |
|
|
1179 |
|
|
1180 |
|
@param |
1181 |
|
@return |
1182 |
|
|
|
|
| 0% |
Uncovered Elements: 25 (25) |
Complexity: 7 |
Complexity Density: 0.54 |
|
1183 |
0 |
public boolean selectStructure(String... pdbids)... |
1184 |
|
{ |
1185 |
0 |
boolean found = false; |
1186 |
|
|
1187 |
0 |
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
1188 |
|
.getSelectedItem()); |
1189 |
0 |
String currentView = selectedFilterOpt.getView(); |
1190 |
0 |
JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() |
1191 |
0 |
: (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null; |
1192 |
|
|
1193 |
0 |
if (restable == null) |
1194 |
|
{ |
1195 |
|
|
1196 |
|
|
1197 |
0 |
return false; |
1198 |
|
} |
1199 |
|
|
1200 |
0 |
int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex(); |
1201 |
0 |
for (int r = 0; r < restable.getRowCount(); r++) |
1202 |
|
{ |
1203 |
0 |
for (int p = 0; p < pdbids.length; p++) |
1204 |
|
{ |
1205 |
0 |
if (String.valueOf(restable.getValueAt(r, pdbIdColIndex)) |
1206 |
|
.equalsIgnoreCase(pdbids[p])) |
1207 |
|
{ |
1208 |
0 |
restable.setRowSelectionInterval(r, r); |
1209 |
0 |
found = true; |
1210 |
|
} |
1211 |
|
} |
1212 |
|
} |
1213 |
0 |
return found; |
1214 |
|
} |
1215 |
|
|
1216 |
|
|
1217 |
|
|
1218 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1219 |
0 |
@Override... |
1220 |
|
protected void newView_ActionPerformed() |
1221 |
|
{ |
1222 |
0 |
targetView.setSelectedItem(null); |
1223 |
0 |
showStructures(false); |
1224 |
|
} |
1225 |
|
|
1226 |
|
|
1227 |
|
|
1228 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1229 |
0 |
@Override... |
1230 |
|
protected void add_ActionPerformed() |
1231 |
|
{ |
1232 |
0 |
showStructures(false); |
1233 |
|
} |
1234 |
|
|
1235 |
|
|
1236 |
|
|
1237 |
|
|
1238 |
|
private StructureViewer sViewer = null; |
1239 |
|
|
|
|
| 0% |
Uncovered Elements: 23 (23) |
Complexity: 6 |
Complexity Density: 0.4 |
|
1240 |
0 |
public void showStructures(boolean waitUntilFinished)... |
1241 |
|
{ |
1242 |
|
|
1243 |
0 |
final StructureSelectionManager ssm = ap.getStructureSelectionManager(); |
1244 |
|
|
1245 |
0 |
final int preferredHeight = pnl_filter.getHeight(); |
1246 |
0 |
btn_add.setEnabled(false); |
1247 |
0 |
btn_newView.setEnabled(false); |
1248 |
0 |
btn_cancel.setEnabled(false); |
1249 |
0 |
actionsPanel.setEnabled(false); |
1250 |
|
|
1251 |
0 |
final String progress = MessageManager |
1252 |
|
.getString("label.working_ellipsis"); |
1253 |
0 |
setProgressBar(progress, progress.hashCode()); |
1254 |
0 |
Runnable viewStruc = new Runnable() |
1255 |
|
{ |
|
|
| 0% |
Uncovered Elements: 69 (69) |
Complexity: 10 |
Complexity Density: 0.2 |
|
1256 |
0 |
@Override... |
1257 |
|
public void run() |
1258 |
|
{ |
1259 |
0 |
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption |
1260 |
|
.getSelectedItem()); |
1261 |
0 |
String currentView = selectedFilterOpt.getView(); |
1262 |
0 |
JTable restable = (currentView == VIEWS_FILTER) ? getResultTable() |
1263 |
|
: tbl_local_pdb; |
1264 |
|
|
1265 |
0 |
if (currentView == VIEWS_FILTER) |
1266 |
|
{ |
1267 |
0 |
int[] selectedRows = restable.getSelectedRows(); |
1268 |
0 |
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; |
1269 |
0 |
List<SequenceI> selectedSeqsToView = new ArrayList<>(); |
1270 |
0 |
pdbEntriesToView = data.collectSelectedRows(restable, |
1271 |
|
selectedRows, selectedSeqsToView); |
1272 |
|
|
1273 |
0 |
SequenceI[] selectedSeqs = selectedSeqsToView |
1274 |
|
.toArray(new SequenceI[selectedSeqsToView.size()]); |
1275 |
0 |
sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, |
1276 |
|
selectedSeqs); |
1277 |
|
} |
1278 |
0 |
else if (currentView == VIEWS_LOCAL_PDB) |
1279 |
|
{ |
1280 |
0 |
int[] selectedRows = tbl_local_pdb.getSelectedRows(); |
1281 |
0 |
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; |
1282 |
0 |
int count = 0; |
1283 |
0 |
int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id") |
1284 |
|
.getModelIndex(); |
1285 |
0 |
int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") |
1286 |
|
.getModelIndex(); |
1287 |
0 |
List<SequenceI> selectedSeqsToView = new ArrayList<>(); |
1288 |
0 |
for (int row : selectedRows) |
1289 |
|
{ |
1290 |
0 |
PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb |
1291 |
|
.getModel()).getPDBEntryAt(row).getPdbEntry(); |
1292 |
|
|
1293 |
0 |
pdbEntriesToView[count++] = pdbEntry; |
1294 |
0 |
SequenceI selectedSeq = (SequenceI) tbl_local_pdb |
1295 |
|
.getValueAt(row, refSeqColIndex); |
1296 |
0 |
selectedSeqsToView.add(selectedSeq); |
1297 |
|
} |
1298 |
0 |
SequenceI[] selectedSeqs = selectedSeqsToView |
1299 |
|
.toArray(new SequenceI[selectedSeqsToView.size()]); |
1300 |
0 |
sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, |
1301 |
|
selectedSeqs); |
1302 |
|
} |
1303 |
0 |
else if (currentView == VIEWS_ENTER_ID) |
1304 |
|
{ |
1305 |
0 |
SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel |
1306 |
|
.getCmb_assSeq().getSelectedItem()).getSequence(); |
1307 |
0 |
if (userSelectedSeq != null) |
1308 |
|
{ |
1309 |
0 |
selectedSequence = userSelectedSeq; |
1310 |
|
} |
1311 |
0 |
String pdbIdStr = txt_search.getText(); |
1312 |
0 |
PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr); |
1313 |
0 |
if (pdbEntry == null) |
1314 |
|
{ |
1315 |
0 |
pdbEntry = new PDBEntry(); |
1316 |
0 |
if (pdbIdStr.split(":").length > 1) |
1317 |
|
{ |
1318 |
0 |
pdbEntry.setId(pdbIdStr.split(":")[0]); |
1319 |
0 |
pdbEntry.setChainCode( |
1320 |
|
pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT)); |
1321 |
|
} |
1322 |
|
else |
1323 |
|
{ |
1324 |
0 |
pdbEntry.setId(pdbIdStr); |
1325 |
|
} |
1326 |
0 |
pdbEntry.setType(PDBEntry.Type.PDB); |
1327 |
0 |
selectedSequence.getDatasetSequence().addPDBId(pdbEntry); |
1328 |
|
} |
1329 |
|
|
1330 |
0 |
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; |
1331 |
0 |
sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap, |
1332 |
|
new SequenceI[] |
1333 |
|
{ selectedSequence }); |
1334 |
|
} |
1335 |
0 |
else if (currentView == VIEWS_FROM_FILE) |
1336 |
|
{ |
1337 |
0 |
StructureChooser sc = StructureChooser.this; |
1338 |
0 |
TFType tft = (TFType) sc.combo_tempFacAs.getSelectedItem(); |
1339 |
0 |
String paeFilename = sc.localPdbPaeMatrixFileName; |
1340 |
0 |
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel |
1341 |
|
.getCmb_assSeq().getSelectedItem(); |
1342 |
0 |
SequenceI userSelectedSeq = assSeqOpt.getSequence(); |
1343 |
0 |
if (userSelectedSeq != null) |
1344 |
|
{ |
1345 |
0 |
selectedSequence = userSelectedSeq; |
1346 |
|
} |
1347 |
0 |
String pdbFilename = selectedPdbFileName; |
1348 |
|
|
1349 |
0 |
StructureChooser.openStructureFileForSequence(ssm, sc, ap, |
1350 |
|
selectedSequence, true, pdbFilename, tft, paeFilename, |
1351 |
|
false, true, false, |
1352 |
|
getTargetedStructureViewer(ssm).getViewerType()); |
1353 |
|
} |
1354 |
0 |
SwingUtilities.invokeLater(new Runnable() |
1355 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1356 |
0 |
@Override... |
1357 |
|
public void run() |
1358 |
|
{ |
1359 |
0 |
setProgressBar("Complete.", progress.hashCode()); |
1360 |
0 |
closeAction(preferredHeight); |
1361 |
0 |
mainFrame.dispose(); |
1362 |
|
} |
1363 |
|
}); |
1364 |
|
} |
1365 |
|
}; |
1366 |
0 |
Thread runner = new Thread(viewStruc); |
1367 |
0 |
runner.start(); |
1368 |
0 |
if (waitUntilFinished) |
1369 |
|
{ |
1370 |
0 |
while (sViewer == null ? runner.isAlive() |
1371 |
0 |
: (sViewer.sview == null ? true |
1372 |
|
: !sViewer.sview.hasMapping())) |
1373 |
|
{ |
1374 |
0 |
try |
1375 |
|
{ |
1376 |
0 |
Thread.sleep(300); |
1377 |
|
} catch (InterruptedException ie) |
1378 |
|
{ |
1379 |
|
|
1380 |
|
} |
1381 |
|
} |
1382 |
|
} |
1383 |
|
} |
1384 |
|
|
1385 |
|
|
1386 |
|
|
1387 |
|
|
1388 |
|
|
1389 |
|
@param |
1390 |
|
@return |
1391 |
|
|
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1392 |
36 |
StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)... |
1393 |
|
{ |
1394 |
36 |
Object sv = targetView.getSelectedItem(); |
1395 |
|
|
1396 |
36 |
return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv; |
1397 |
|
} |
1398 |
|
|
1399 |
|
|
1400 |
|
|
1401 |
|
|
1402 |
|
@param |
1403 |
|
@param |
1404 |
|
@param |
1405 |
|
@param |
1406 |
|
@return |
1407 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1408 |
0 |
private StructureViewer launchStructureViewer(... |
1409 |
|
StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, |
1410 |
|
final AlignmentPanel alignPanel, SequenceI[] sequences) |
1411 |
|
{ |
1412 |
0 |
return launchStructureViewer(ssm, pdbEntriesToView, alignPanel, |
1413 |
|
sequences, null); |
1414 |
|
} |
1415 |
|
|
|
|
| 37% |
Uncovered Elements: 34 (54) |
Complexity: 11 |
Complexity Density: 0.29 |
|
1416 |
36 |
private StructureViewer launchStructureViewer(... |
1417 |
|
StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, |
1418 |
|
final AlignmentPanel alignPanel, SequenceI[] sequences, |
1419 |
|
ViewerType viewerType) |
1420 |
|
{ |
1421 |
36 |
long progressId = sequences.hashCode(); |
1422 |
36 |
setProgressBar(MessageManager |
1423 |
|
.getString("status.launching_3d_structure_viewer"), progressId); |
1424 |
36 |
final StructureViewer theViewer = getTargetedStructureViewer(ssm); |
1425 |
36 |
boolean superimpose = chk_superpose.isSelected(); |
1426 |
36 |
theViewer.setSuperpose(superimpose); |
1427 |
|
|
1428 |
|
|
1429 |
36 |
if (Jalview.isHeadlessMode()) |
1430 |
|
{ |
1431 |
19 |
theViewer.setAsync(false); |
1432 |
|
} |
1433 |
|
|
1434 |
|
|
1435 |
|
|
1436 |
|
|
1437 |
36 |
Cache.setProperty(AUTOSUPERIMPOSE, |
1438 |
|
Boolean.valueOf(superimpose).toString()); |
1439 |
|
|
1440 |
36 |
setProgressBar(null, progressId); |
1441 |
36 |
if (SiftsSettings.isMapWithSifts()) |
1442 |
|
{ |
1443 |
0 |
List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>(); |
1444 |
0 |
int p = 0; |
1445 |
|
|
1446 |
|
|
1447 |
|
|
1448 |
0 |
for (SequenceI seq : sequences) |
1449 |
|
{ |
1450 |
0 |
PDBEntry pdbe = pdbEntriesToView[p++]; |
1451 |
0 |
if (pdbe != null && pdbe.getFile() != null) |
1452 |
|
{ |
1453 |
0 |
StructureMapping[] smm = ssm.getMapping(pdbe.getFile()); |
1454 |
0 |
if (smm != null && smm.length > 0) |
1455 |
|
{ |
1456 |
0 |
for (StructureMapping sm : smm) |
1457 |
|
{ |
1458 |
0 |
if (sm.getSequence() == seq) |
1459 |
|
{ |
1460 |
0 |
continue; |
1461 |
|
} |
1462 |
|
} |
1463 |
|
} |
1464 |
|
} |
1465 |
0 |
if (seq.getPrimaryDBRefs().isEmpty()) |
1466 |
|
{ |
1467 |
0 |
seqsWithoutSourceDBRef.add(seq); |
1468 |
0 |
continue; |
1469 |
|
} |
1470 |
|
} |
1471 |
0 |
if (!seqsWithoutSourceDBRef.isEmpty()) |
1472 |
|
{ |
1473 |
0 |
int y = seqsWithoutSourceDBRef.size(); |
1474 |
0 |
setProgressBar(MessageManager.formatMessage( |
1475 |
|
"status.fetching_dbrefs_for_sequences_without_valid_refs", |
1476 |
|
y), progressId); |
1477 |
0 |
SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef |
1478 |
|
.toArray(new SequenceI[y]); |
1479 |
0 |
DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); |
1480 |
0 |
dbRefFetcher.fetchDBRefs(true); |
1481 |
|
|
1482 |
0 |
setProgressBar("Fetch complete.", progressId); |
1483 |
|
} |
1484 |
|
} |
1485 |
36 |
if (pdbEntriesToView.length > 1) |
1486 |
|
{ |
1487 |
0 |
setProgressBar( |
1488 |
|
MessageManager.getString( |
1489 |
|
"status.fetching_3d_structures_for_selected_entries"), |
1490 |
|
progressId); |
1491 |
0 |
theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel, |
1492 |
|
viewerType); |
1493 |
|
} |
1494 |
|
else |
1495 |
|
{ |
1496 |
36 |
setProgressBar(MessageManager.formatMessage( |
1497 |
|
"status.fetching_3d_structures_for", |
1498 |
|
pdbEntriesToView[0].getId()), progressId); |
1499 |
|
|
1500 |
36 |
theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel, |
1501 |
|
viewerType); |
1502 |
|
} |
1503 |
36 |
setProgressBar(null, progressId); |
1504 |
|
|
1505 |
36 |
lastTargetedView = theViewer; |
1506 |
36 |
return theViewer; |
1507 |
|
} |
1508 |
|
|
1509 |
|
|
1510 |
|
|
1511 |
|
|
1512 |
|
|
|
|
| 73.3% |
Uncovered Elements: 4 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
1513 |
2 |
@Override... |
1514 |
|
protected void populateCmbAssociateSeqOptions( |
1515 |
|
JComboBox<AssociateSeqOptions> cmb_assSeq, |
1516 |
|
JLabel lbl_associateSeq) |
1517 |
|
{ |
1518 |
2 |
cmb_assSeq.removeAllItems(); |
1519 |
2 |
cmb_assSeq.addItem( |
1520 |
|
new AssociateSeqOptions("-Select Associated Seq-", null)); |
1521 |
2 |
lbl_associateSeq.setVisible(false); |
1522 |
2 |
if (selectedSequences.length > 1) |
1523 |
|
{ |
1524 |
0 |
for (SequenceI seq : selectedSequences) |
1525 |
|
{ |
1526 |
0 |
cmb_assSeq.addItem(new AssociateSeqOptions(seq)); |
1527 |
|
} |
1528 |
|
} |
1529 |
|
else |
1530 |
|
{ |
1531 |
2 |
String seqName = selectedSequence.getDisplayId(false); |
1532 |
2 |
seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39); |
1533 |
2 |
lbl_associateSeq.setText(seqName); |
1534 |
2 |
lbl_associateSeq.setVisible(true); |
1535 |
2 |
cmb_assSeq.setVisible(false); |
1536 |
|
} |
1537 |
|
} |
1538 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1539 |
3 |
protected boolean isStructuresDiscovered()... |
1540 |
|
{ |
1541 |
3 |
return discoveredStructuresSet != null |
1542 |
|
&& !discoveredStructuresSet.isEmpty(); |
1543 |
|
} |
1544 |
|
|
1545 |
|
protected int PDB_ID_MIN = 3; |
1546 |
|
|
1547 |
|
|
1548 |
|
|
1549 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1550 |
0 |
@Override... |
1551 |
|
protected void txt_search_ActionPerformed() |
1552 |
|
{ |
1553 |
0 |
String text = txt_search.getText().trim(); |
1554 |
0 |
if (text.length() >= PDB_ID_MIN) |
1555 |
0 |
new Thread() |
1556 |
|
{ |
1557 |
|
|
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 5 |
Complexity Density: 0.21 |
|
1558 |
0 |
@Override... |
1559 |
|
public void run() |
1560 |
|
{ |
1561 |
0 |
errorWarning.setLength(0); |
1562 |
0 |
isValidPBDEntry = false; |
1563 |
0 |
if (text.length() > 0) |
1564 |
|
{ |
1565 |
|
|
1566 |
|
|
1567 |
|
|
1568 |
0 |
String searchTerm = text.toLowerCase(Locale.ROOT); |
1569 |
0 |
searchTerm = searchTerm.split(":")[0]; |
1570 |
|
|
1571 |
|
|
1572 |
0 |
List<FTSDataColumnI> wantedFields = new ArrayList<>(); |
1573 |
0 |
FTSRestRequest pdbRequest = new FTSRestRequest(); |
1574 |
0 |
pdbRequest.setAllowEmptySeq(false); |
1575 |
0 |
pdbRequest.setResponseSize(1); |
1576 |
0 |
pdbRequest.setFieldToSearchBy("(pdb_id:"); |
1577 |
0 |
pdbRequest.setWantedFields(wantedFields); |
1578 |
0 |
pdbRequest.setSearchTerm(searchTerm + ")"); |
1579 |
0 |
pdbRequest.setAssociatedSequence(selectedSequence); |
1580 |
0 |
FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance(); |
1581 |
0 |
wantedFields.add(pdbRestClient.getPrimaryKeyColumn()); |
1582 |
0 |
FTSRestResponse resultList; |
1583 |
0 |
try |
1584 |
|
{ |
1585 |
0 |
resultList = pdbRestClient.executeRequest(pdbRequest); |
1586 |
|
} catch (Exception e) |
1587 |
|
{ |
1588 |
0 |
errorWarning.append(e.getMessage()); |
1589 |
0 |
return; |
1590 |
|
} finally |
1591 |
|
{ |
1592 |
0 |
validateSelections(); |
1593 |
|
} |
1594 |
0 |
if (resultList.getSearchSummary() != null |
1595 |
|
&& resultList.getSearchSummary().size() > 0) |
1596 |
|
{ |
1597 |
0 |
isValidPBDEntry = true; |
1598 |
|
} |
1599 |
|
} |
1600 |
0 |
validateSelections(); |
1601 |
|
} |
1602 |
|
}.start(); |
1603 |
|
} |
1604 |
|
|
|
|
| 33.3% |
Uncovered Elements: 4 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1605 |
55 |
@Override... |
1606 |
|
protected void tabRefresh() |
1607 |
|
{ |
1608 |
55 |
if (selectedSequences != null) |
1609 |
|
{ |
1610 |
0 |
lbl_loading.setVisible(true); |
1611 |
0 |
Thread refreshThread = new Thread(new Runnable() |
1612 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1613 |
0 |
@Override... |
1614 |
|
public void run() |
1615 |
|
{ |
1616 |
0 |
fetchStructuresMetaData(); |
1617 |
|
|
1618 |
|
|
1619 |
0 |
filterResultSet( |
1620 |
|
((FilterOption) cmb_filterOption.getSelectedItem()) |
1621 |
|
.getValue()); |
1622 |
0 |
lbl_loading.setVisible(false); |
1623 |
|
} |
1624 |
|
}); |
1625 |
0 |
refreshThread.start(); |
1626 |
|
} |
1627 |
|
} |
1628 |
|
|
|
|
| 21.1% |
Uncovered Elements: 30 (38) |
Complexity: 15 |
Complexity Density: 0.58 |
|
1629 |
|
public class PDBEntryTableModel extends AbstractTableModel |
1630 |
|
{ |
1631 |
|
String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", |
1632 |
|
"File" }; |
1633 |
|
|
1634 |
|
private List<CachedPDB> pdbEntries; |
1635 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1636 |
3 |
public PDBEntryTableModel(List<CachedPDB> pdbEntries)... |
1637 |
|
{ |
1638 |
3 |
this.pdbEntries = new ArrayList<>(pdbEntries); |
1639 |
|
} |
1640 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1641 |
15 |
@Override... |
1642 |
|
public String getColumnName(int columnIndex) |
1643 |
|
{ |
1644 |
15 |
return columns[columnIndex]; |
1645 |
|
} |
1646 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1647 |
18 |
@Override... |
1648 |
|
public int getRowCount() |
1649 |
|
{ |
1650 |
18 |
return pdbEntries.size(); |
1651 |
|
} |
1652 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1653 |
18 |
@Override... |
1654 |
|
public int getColumnCount() |
1655 |
|
{ |
1656 |
18 |
return columns.length; |
1657 |
|
} |
1658 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1659 |
0 |
@Override... |
1660 |
|
public boolean isCellEditable(int row, int column) |
1661 |
|
{ |
1662 |
0 |
return false; |
1663 |
|
} |
1664 |
|
|
|
|
| 0% |
Uncovered Elements: 21 (21) |
Complexity: 7 |
Complexity Density: 0.37 |
|
1665 |
0 |
@Override... |
1666 |
|
public Object getValueAt(int rowIndex, int columnIndex) |
1667 |
|
{ |
1668 |
0 |
Object value = "??"; |
1669 |
0 |
CachedPDB entry = pdbEntries.get(rowIndex); |
1670 |
0 |
switch (columnIndex) |
1671 |
|
{ |
1672 |
0 |
case 0: |
1673 |
0 |
value = entry.getSequence(); |
1674 |
0 |
break; |
1675 |
0 |
case 1: |
1676 |
0 |
value = entry.getQualifiedId(); |
1677 |
0 |
break; |
1678 |
0 |
case 2: |
1679 |
0 |
value = entry.getPdbEntry().getChainCode() == null ? "_" |
1680 |
|
: entry.getPdbEntry().getChainCode(); |
1681 |
0 |
break; |
1682 |
0 |
case 3: |
1683 |
0 |
value = entry.getPdbEntry().getType(); |
1684 |
0 |
break; |
1685 |
0 |
case 4: |
1686 |
0 |
value = entry.getPdbEntry().getFile(); |
1687 |
0 |
break; |
1688 |
|
} |
1689 |
0 |
return value; |
1690 |
|
} |
1691 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
1692 |
0 |
@Override... |
1693 |
|
public Class<?> getColumnClass(int columnIndex) |
1694 |
|
{ |
1695 |
0 |
return columnIndex == 0 ? SequenceI.class : PDBEntry.class; |
1696 |
|
} |
1697 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1698 |
0 |
public CachedPDB getPDBEntryAt(int row)... |
1699 |
|
{ |
1700 |
0 |
return pdbEntries.get(row); |
1701 |
|
} |
1702 |
|
|
1703 |
|
} |
1704 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 5 |
Complexity Density: 0.71 |
|
1705 |
|
private class CachedPDB |
1706 |
|
{ |
1707 |
|
private SequenceI sequence; |
1708 |
|
|
1709 |
|
private PDBEntry pdbEntry; |
1710 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1711 |
0 |
public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)... |
1712 |
|
{ |
1713 |
0 |
this.sequence = sequence; |
1714 |
0 |
this.pdbEntry = pdbEntry; |
1715 |
|
} |
1716 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1717 |
0 |
public String getQualifiedId()... |
1718 |
|
{ |
1719 |
0 |
if (pdbEntry.hasProvider()) |
1720 |
|
{ |
1721 |
0 |
return pdbEntry.getProvider() + ":" + pdbEntry.getId(); |
1722 |
|
} |
1723 |
0 |
return pdbEntry.toString(); |
1724 |
|
} |
1725 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1726 |
0 |
public SequenceI getSequence()... |
1727 |
|
{ |
1728 |
0 |
return sequence; |
1729 |
|
} |
1730 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1731 |
0 |
public PDBEntry getPdbEntry()... |
1732 |
|
{ |
1733 |
0 |
return pdbEntry; |
1734 |
|
} |
1735 |
|
|
1736 |
|
} |
1737 |
|
|
1738 |
|
private IProgressIndicator progressBar; |
1739 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 3 |
Complexity Density: 1.5 |
|
1740 |
144 |
@Override... |
1741 |
|
public void setProgressBar(String message, long id) |
1742 |
|
{ |
1743 |
144 |
if (!Platform.isHeadless() && progressBar != null) |
1744 |
68 |
progressBar.setProgressBar(message, id); |
1745 |
|
} |
1746 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1747 |
0 |
@Override... |
1748 |
|
public void registerHandler(long id, IProgressIndicatorHandler handler) |
1749 |
|
{ |
1750 |
0 |
if (progressBar != null) |
1751 |
0 |
progressBar.registerHandler(id, handler); |
1752 |
|
} |
1753 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
1754 |
0 |
@Override... |
1755 |
|
public boolean operationInProgress() |
1756 |
|
{ |
1757 |
0 |
return progressBar == null ? false : progressBar.operationInProgress(); |
1758 |
|
} |
1759 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
1760 |
0 |
public JalviewStructureDisplayI getOpenedStructureViewer()... |
1761 |
|
{ |
1762 |
0 |
return sViewer == null ? null : sViewer.sview; |
1763 |
|
} |
1764 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1765 |
0 |
@Override... |
1766 |
|
protected void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs) |
1767 |
|
{ |
1768 |
0 |
data.setDocFieldPrefs(newPrefs); |
1769 |
|
|
1770 |
|
} |
1771 |
|
|
1772 |
|
|
1773 |
|
|
1774 |
|
@return |
1775 |
|
|
1776 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1777 |
12 |
public boolean isDialogVisible()... |
1778 |
|
{ |
1779 |
12 |
return mainFrame != null && data != null && cmb_filterOption != null |
1780 |
|
&& mainFrame.isVisible() |
1781 |
|
&& cmb_filterOption.getSelectedItem() != null; |
1782 |
|
} |
1783 |
|
|
1784 |
|
|
1785 |
|
|
1786 |
|
@return |
1787 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1788 |
1 |
public boolean isCanQueryTDB()... |
1789 |
|
{ |
1790 |
1 |
return canQueryTDB; |
1791 |
|
} |
1792 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1793 |
1 |
public boolean isNotQueriedTDBYet()... |
1794 |
|
{ |
1795 |
1 |
return notQueriedTDBYet; |
1796 |
|
} |
1797 |
|
|
1798 |
|
|
1799 |
|
|
1800 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1801 |
0 |
public static void openStructureFileForSequence(... |
1802 |
|
StructureSelectionManager ssm, StructureChooser sc, |
1803 |
|
AlignmentPanel ap, SequenceI seq, boolean prompt, |
1804 |
|
String sFilename, TFType tft, String paeFilename, |
1805 |
|
boolean doXferSettings) |
1806 |
|
{ |
1807 |
0 |
openStructureFileForSequence(ssm, sc, ap, seq, prompt, sFilename, tft, |
1808 |
|
paeFilename, false, true, doXferSettings, null); |
1809 |
|
} |
1810 |
|
|
1811 |
|
|
1812 |
|
|
1813 |
|
@param |
1814 |
|
@param |
1815 |
|
@param |
1816 |
|
@param |
1817 |
|
@param |
1818 |
|
@param |
1819 |
|
@param |
1820 |
|
@param |
1821 |
|
@param |
1822 |
|
@param |
1823 |
|
@param |
1824 |
|
@param |
1825 |
|
|
1826 |
|
|
1827 |
|
@return |
1828 |
|
|
|
|
| 91.7% |
Uncovered Elements: 2 (24) |
Complexity: 6 |
Complexity Density: 0.38 |
|
1829 |
52 |
public static StructureViewer openStructureFileForSequence(... |
1830 |
|
StructureSelectionManager ssm, StructureChooser sc, |
1831 |
|
AlignmentPanel ap, SequenceI seq, boolean prompt, |
1832 |
|
String sFilename, TFType tft, String paeFilename, |
1833 |
|
boolean forceHeadless, boolean showRefAnnotations, |
1834 |
|
boolean doXferSettings, ViewerType viewerType) |
1835 |
|
{ |
1836 |
52 |
StructureViewer sv = null; |
1837 |
52 |
boolean headless = forceHeadless; |
1838 |
52 |
if (sc == null) |
1839 |
|
{ |
1840 |
|
|
1841 |
52 |
prompt = false; |
1842 |
|
|
1843 |
52 |
sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false, |
1844 |
|
true); |
1845 |
|
} |
1846 |
52 |
if (ssm == null) |
1847 |
|
{ |
1848 |
52 |
ssm = ap.getStructureSelectionManager(); |
1849 |
52 |
StructureSelectionManager.doConfigureStructurePrefs(ssm); |
1850 |
|
} |
1851 |
|
|
1852 |
52 |
PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq( |
1853 |
|
sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance, |
1854 |
|
tft, paeFilename, doXferSettings); |
1855 |
|
|
1856 |
|
|
1857 |
|
|
1858 |
52 |
if (!headless && !(viewerType == null)) |
1859 |
|
{ |
1860 |
36 |
sv = sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, |
1861 |
|
new SequenceI[] |
1862 |
|
{ seq }, viewerType); |
1863 |
|
|
1864 |
36 |
sv.getJalviewStructureDisplay().raiseViewer(); |
1865 |
|
} |
1866 |
|
|
1867 |
52 |
sc.mainFrame.dispose(); |
1868 |
|
|
1869 |
|
|
1870 |
|
|
1871 |
52 |
if (showRefAnnotations) |
1872 |
|
{ |
1873 |
37 |
showReferenceAnnotationsForSequence(ap.alignFrame, seq); |
1874 |
|
} |
1875 |
|
|
1876 |
52 |
return sv; |
1877 |
|
} |
1878 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
|
1879 |
37 |
public static void showReferenceAnnotationsForSequence(AlignFrame af,... |
1880 |
|
SequenceI sequence) |
1881 |
|
{ |
1882 |
37 |
AlignViewport av = af.getCurrentView(); |
1883 |
37 |
AlignmentI al = av.getAlignment(); |
1884 |
|
|
1885 |
37 |
List<SequenceI> forSequences = new ArrayList<>(); |
1886 |
37 |
forSequences.add(sequence); |
1887 |
37 |
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>(); |
1888 |
37 |
AlignmentUtils.findAddableReferenceAnnotations(forSequences, null, |
1889 |
|
candidates, al); |
1890 |
37 |
final SequenceGroup selectionGroup = av.getSelectionGroup(); |
1891 |
37 |
AlignmentUtils.addReferenceAnnotations(candidates, al, selectionGroup); |
1892 |
37 |
for (AlignmentViewPanel ap : af.getAlignPanels()) |
1893 |
|
{ |
1894 |
|
|
1895 |
|
|
1896 |
37 |
ap.adjustAnnotationHeight(); |
1897 |
|
} |
1898 |
|
|
1899 |
|
} |
1900 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1901 |
0 |
@Override... |
1902 |
|
public JProgressBar getProgressBar(long id) |
1903 |
|
{ |
1904 |
0 |
return progressBar.getProgressBar(id); |
1905 |
|
} |
1906 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1907 |
0 |
public String getMessage(long id)... |
1908 |
|
{ |
1909 |
0 |
return progressIndicator.getMessage(id); |
1910 |
|
} |
1911 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1912 |
0 |
public void setProgressBarMessage(long id, String message)... |
1913 |
|
{ |
1914 |
0 |
progressIndicator.setProgressBarMessage(id, message); |
1915 |
|
} |
1916 |
|
} |