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allow to specify number of candidates for db filter
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@mfleisch
mfleisch committed Aug 19, 2023
1 parent dc81efa commit c868f09
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Showing 4 changed files with 89 additions and 26 deletions.
22 changes: 17 additions & 5 deletions sirius_cli/src/main/java/de/unijena/bioinf/projectspace/Instance.java
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Original file line number Diff line number Diff line change
Expand Up @@ -142,11 +142,23 @@ public final synchronized Optional<FormulaResult> loadTopFormulaResult(List<Clas

@SafeVarargs
private Optional<FormulaResult> getTop(List<? extends SScored<FormulaResult, ? extends FormulaScore>> sScoreds, Class<? extends DataAnnotation>... components) {
if (sScoreds.isEmpty()) return Optional.empty();
else {
FormulaResult candidate = sScoreds.get(0).getCandidate();
return loadFormulaResult(candidate.getId(), components);
}
if (sScoreds.isEmpty())
return Optional.empty();

FormulaResult candidate = sScoreds.get(0).getCandidate();
return loadFormulaResult(candidate.getId(), components);
}


@SafeVarargs
public final synchronized List<? extends SScored<FormulaResult, ? extends FormulaScore>> loadTopKFormulaResults(int k, List<Class<? extends FormulaScore>> rankingScoreTypes, Class<? extends DataAnnotation>... components) {
return getTopK(k, loadFormulaResults(rankingScoreTypes), components);
}

@SafeVarargs
private List<? extends SScored<FormulaResult, ? extends FormulaScore>> getTopK(int k, List<? extends SScored<FormulaResult, ? extends FormulaScore>> sScoreds, Class<? extends DataAnnotation>... components) {
return sScoreds.stream().limit(k).peek(ss -> loadFormulaResult(ss.getCandidate().getId(), components)
.ifPresent(r -> ss.getCandidate().setAnnotationsFrom(r))).toList();
}

@SafeVarargs
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16 changes: 12 additions & 4 deletions sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/dialogs/CompoundFilterOptionsDialog.java
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ public class CompoundFilterOptionsDialog extends JDialog implements ActionListen

final SearchTextField searchField;
final JTextField searchFieldDialogCopy;
final JSpinner minMzSpinner, maxMzSpinner, minRtSpinner, maxRtSpinner, minConfidenceSpinner, maxConfidenceSpinner;
final JSpinner minMzSpinner, maxMzSpinner, minRtSpinner, maxRtSpinner, minConfidenceSpinner, maxConfidenceSpinner, candidateSpinner;
public final JCheckboxListPanel<PrecursorIonType> adductOptions;
JButton discard, apply, reset;
JCheckBox invertFilter;
Expand Down Expand Up @@ -200,9 +200,15 @@ public CompoundFilterOptionsDialog(MainFrame owner, SearchTextField searchField,
{
searchDBList = new JCheckboxListPanel<>(new DBSelectionList(), "Hit in structure DB");
smallParameters.add(searchDBList);
searchDBList.remove(searchDBList.buttons);
searchDBList.checkBoxList.uncheckAll();
if (filterModel.isDbFilterEnabled()) //null check
searchDBList.checkBoxList.checkAll(filterModel.getDbFilter());
candidateSpinner = makeSpinner(1, 1, 100, 1);
smallParameters.addNamed("Candidates to check: ", candidateSpinner);

if (filterModel.isDbFilterEnabled()) { //null check
searchDBList.checkBoxList.checkAll(filterModel.getDbFilter().getDbs());
candidateSpinner.setValue(filterModel.getDbFilter().getNumOfCandidates());
}
}

smallParameters.add(new JXTitledSeparator("Filter options"));
Expand Down Expand Up @@ -300,7 +306,8 @@ private void applyToModel(@NotNull CompoundFilterModel filterModel) {
)
);

filterModel.setDbFilter(searchDBList.checkBoxList.getCheckedItems());
filterModel.setDbFilter(new CompoundFilterModel.DbFilter(searchDBList.checkBoxList.getCheckedItems(),
((SpinnerNumberModel) candidateSpinner.getModel()).getNumber().intValue()));

saveTextFilter();
}
Expand Down Expand Up @@ -371,6 +378,7 @@ private void resetSpinnerValues() {
maxRtSpinner.setValue(filterModel.getMaxRt());
minConfidenceSpinner.setValue(filterModel.getMinConfidence());
maxConfidenceSpinner.setValue(filterModel.getMaxConfidence());
candidateSpinner.setValue(1);
}

public double getMinMz() {
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32 changes: 27 additions & 5 deletions sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/utils/CompoundFilterMatcher.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,13 +20,15 @@

import ca.odell.glazedlists.matchers.Matcher;
import de.unijena.bioinf.ChemistryBase.algorithm.scoring.SScored;
import de.unijena.bioinf.ChemistryBase.algorithm.scoring.Scored;
import de.unijena.bioinf.ChemistryBase.chem.FormulaConstraints;
import de.unijena.bioinf.ChemistryBase.chem.PrecursorIonType;
import de.unijena.bioinf.ChemistryBase.chem.RetentionTime;
import de.unijena.bioinf.ChemistryBase.ms.lcms.CoelutingTraceSet;
import de.unijena.bioinf.ChemistryBase.ms.lcms.LCMSPeakInformation;
import de.unijena.bioinf.GibbsSampling.ZodiacScore;
import de.unijena.bioinf.chemdb.ChemDBs;
import de.unijena.bioinf.chemdb.CompoundCandidate;
import de.unijena.bioinf.elgordo.LipidSpecies;
import de.unijena.bioinf.fingerid.blast.FBCandidates;
import de.unijena.bioinf.fingerid.blast.TopCSIScore;
Expand All @@ -38,6 +40,7 @@
import de.unijena.bioinf.sirius.scores.SiriusScore;
import org.jetbrains.annotations.NotNull;

import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.Set;
Expand Down Expand Up @@ -121,18 +124,37 @@ private boolean matchesLipidFilter(InstanceBean item, CompoundFilterModel filter
}

private boolean matchesDBFilter(InstanceBean item, CompoundFilterModel filterModel) {
long requestFilter = filterModel.getDbFilterBits();
final int k;
final long requestFilter;
if (filterModel.isDbFilterEnabled()) {
k = filterModel.getDbFilter().getNumOfCandidates();
requestFilter = filterModel.getDbFilter().getDbFilterBits();
} else {
k = 1;
requestFilter = 0;
}

FBCandidates candidates = item.loadTopFormulaResult(List.of(TopCSIScore.class), FBCandidates.class)
.flatMap(i -> i.getAnnotation(FBCandidates.class)).orElse(null);
final List<Scored<CompoundCandidate>> candidates;
switch (k) {
case 0 -> {
return false;
}
case 1 -> candidates = item.loadTopFormulaResult(List.of(TopCSIScore.class), FBCandidates.class)
.flatMap(i -> i.getAnnotation(FBCandidates.class).map(FBCandidates::getResults))
.map(s -> s.stream().limit(k).toList()).orElse(null);
default -> candidates = item.loadTopKFormulaResults(k, List.of(TopCSIScore.class), FBCandidates.class)
.stream().filter(i -> i.getCandidate().hasAnnotation(FBCandidates.class))
.flatMap(i -> i.getCandidate().getAnnotation(FBCandidates.class)
.map(FBCandidates::getResults).stream().flatMap(Collection::stream)).limit(k).toList();
}

if (candidates == null)
if (candidates == null || candidates.isEmpty())
return false;

if (requestFilter == 0)
return true;

return candidates.getResults().stream().map(SScored::getCandidate).anyMatch(c -> ChemDBs.inFilter(c.getBitset(), requestFilter));
return candidates.stream().map(SScored::getCandidate).anyMatch(c -> ChemDBs.inFilter(c.getBitset(), requestFilter));
}

private boolean matchesElementFilter(InstanceBean item, CompoundFilterModel filterModel) {
Expand Down
45 changes: 33 additions & 12 deletions sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/utils/CompoundFilterModel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -58,8 +58,7 @@ public class CompoundFilterModel implements SiriusPCS {
private ElementFilter elementFilter = ElementFilter.disabled();

@Nullable
private List<CustomDataSources.Source> dbFilter;

private DbFilter dbFilter;

/*
min/max possible values
Expand Down Expand Up @@ -131,24 +130,17 @@ public void setLipidFilter(LipidFilter value) {
pcs.firePropertyChange("setLipidFilter", oldValue, value);
}

public void setDbFilter(@Nullable List<CustomDataSources.Source> dbFilter) {
public void setDbFilter(@Nullable DbFilter dbFilter) {
this.dbFilter = dbFilter;
}

@Nullable
public List<CustomDataSources.Source> getDbFilter() {
public DbFilter getDbFilter() {
return dbFilter;
}

public long getDbFilterBits() {
if (dbFilter == null || dbFilter.isEmpty())
return 0;
return dbFilter.stream().
mapToLong(CustomDataSources.Source::flag).reduce((a, b) -> a | b).orElse(0);
}

public boolean isDbFilterEnabled() {
return dbFilter != null && !dbFilter.isEmpty();
return dbFilter != null && !dbFilter.dbs.isEmpty();
}

public boolean isElementFilterEnabled() {
Expand Down Expand Up @@ -343,6 +335,35 @@ public enum LipidFilter {
KEEP_ALL_COMPOUNDS, ANY_LIPID_CLASS_DETECTED, NO_LIPID_CLASS_DETECTED
}

public static class DbFilter {
final List<CustomDataSources.Source> dbs;
final int numOfCandidates;

public DbFilter(List<CustomDataSources.Source> dbs) {
this(dbs, 5);

}
public DbFilter(List<CustomDataSources.Source> dbFilter, int numOfCandidates) {
this.dbs = dbFilter;
this.numOfCandidates = numOfCandidates;
}

public long getDbFilterBits() {
if (dbs == null || dbs.isEmpty())
return 0;
return dbs.stream().
mapToLong(CustomDataSources.Source::flag).reduce((a, b) -> a | b).orElse(0);
}

public int getNumOfCandidates() {
return numOfCandidates;
}

public List<CustomDataSources.Source> getDbs() {
return dbs;
}
}

public static class ElementFilter {
@NotNull
final FormulaConstraints constraints;
Expand Down

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