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package jalview.gui.structurechooser; |
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import java.util.Locale; |
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import java.util.Collection; |
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import java.util.List; |
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import java.util.Objects; |
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import java.util.Vector; |
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import javax.swing.JTable; |
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import javax.swing.table.TableModel; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SequenceI; |
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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.jbgui.FilterOption; |
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@author |
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@param |
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| 44% |
Uncovered Elements: 42 (75) |
Complexity: 25 |
Complexity Density: 0.54 |
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public abstract class StructureChooserQuerySource |
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{ |
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protected FTSDataColumnPreferences docFieldPrefs; |
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protected static int MAX_QLENGTH = 7820; |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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public StructureChooserQuerySource()... |
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{ |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public static StructureChooserQuerySource getPDBfts()... |
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{ |
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return new PDBStructureChooserQuerySource(); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public static StructureChooserQuerySource getTDBfts()... |
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{ |
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return new ThreeDBStructureChooserQuerySource(); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public FTSDataColumnPreferences getDocFieldPrefs()... |
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{ |
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return docFieldPrefs; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public void setDocFieldPrefs(FTSDataColumnPreferences docFieldPrefs)... |
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{ |
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this.docFieldPrefs = docFieldPrefs; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public FTSDataColumnPreferences getInitialFieldPreferences()... |
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{ |
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return docFieldPrefs; |
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} |
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@param |
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@return |
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public abstract String buildQuery(SequenceI seq); |
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@param |
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@return |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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public static String sanitizeSeqName(String seqName)... |
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{ |
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Objects.requireNonNull(seqName); |
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return seqName.replaceAll("\\[\\d*\\]", "") |
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.replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+"); |
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} |
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@param |
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@return |
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| 0% |
Uncovered Elements: 16 (16) |
Complexity: 4 |
Complexity Density: 0.4 |
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static boolean isValidSeqName(String seqName)... |
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{ |
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String ignoreList = "pdb,uniprot,swiss-prot"; |
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if (seqName.length() < 3) |
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return false; |
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} |
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if (seqName.contains(":")) |
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return false; |
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} |
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seqName = seqName.toLowerCase(Locale.ROOT); |
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for (String ignoredEntry : ignoreList.split(",")) |
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{ |
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if (seqName.contains(ignoredEntry)) |
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return false; |
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} |
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} |
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return true; |
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} |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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static String getDBRefId(DBRefEntry dbRef)... |
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{ |
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String ref = dbRef.getAccessionId().replaceAll("GO:", ""); |
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return ref; |
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} |
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| 0% |
Uncovered Elements: 9 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
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static PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)... |
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{ |
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Objects.requireNonNull(id); |
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Objects.requireNonNull(pdbEntries); |
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PDBEntry foundEntry = null; |
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for (PDBEntry entry : pdbEntries) |
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if (entry.getId().equalsIgnoreCase(id)) |
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return entry; |
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} |
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} |
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return foundEntry; |
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} |
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@param |
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@param |
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@param |
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@param |
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@return |
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@throws |
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public abstract FTSRestResponse fetchStructuresMetaData(SequenceI seq, |
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Collection<FTSDataColumnI> wantedFields, |
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FilterOption selectedFilterOpt, boolean b) throws Exception; |
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@param |
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@param |
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@param |
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@return |
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@throws |
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public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq, |
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Collection<FTSData> discoveredStructuresSet, |
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Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy, |
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boolean b) throws Exception; |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public TableModel getTableModel(... |
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Collection<FTSData> discoveredStructuresSet) |
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{ |
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return FTSRestResponse.getTableModel(getLastFTSRequest(), |
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discoveredStructuresSet); |
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} |
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protected abstract FTSRestRequest getLastFTSRequest(); |
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public abstract PDBEntry[] collectSelectedRows(JTable restable, |
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int[] selectedRows, List<SequenceI> selectedSeqsToView); |
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@param |
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@return |
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public abstract List<FilterOption> getAvailableFilterOptions( |
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String VIEWS_FILTER); |
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@param |
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@return |
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| 96.3% |
Uncovered Elements: 1 (27) |
Complexity: 9 |
Complexity Density: 0.47 |
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public static StructureChooserQuerySource getQuerySourceFor(... |
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SequenceI[] selectedSeqs) |
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{ |
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ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource(); |
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boolean hasUniprot = false, hasCanonical = false; |
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boolean hasNA = false, hasProtein = false; |
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int protWithoutUni = 0; |
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int protWithoutCanon = 0; |
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for (SequenceI seq : selectedSeqs) |
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{ |
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hasNA |= !seq.isProtein(); |
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hasProtein |= seq.isProtein(); |
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if (seq.isProtein()) |
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{ |
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int refsAvailable = ThreeDBStructureChooserQuerySource |
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.checkUniprotRefs(seq.getDBRefs()); |
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if (refsAvailable > -2) |
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{ |
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if (refsAvailable > -1) |
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{ |
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8 |
hasCanonical = true; |
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} |
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else |
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{ |
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protWithoutCanon++; |
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} |
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hasUniprot = true; |
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} |
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else |
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{ |
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protWithoutUni++; |
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} |
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} |
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} |
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65 |
if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0 |
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&& protWithoutUni == 0) |
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{ |
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return tdbSource; |
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} |
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return new PDBStructureChooserQuerySource(); |
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} |
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@param |
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@return |
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public abstract boolean needsRefetch(FilterOption selectedFilterOpt); |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
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public void updateAvailableFilterOptions(String VIEWS_FILTER,... |
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List<FilterOption> xtantOptions, Collection<FTSData> lastFTSData) |
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{ |
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} |
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} |