de.julielab.geneexpbase.genemodel.SpeciesCandidates Maven / Gradle / Ivy

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package de.julielab.geneexpbase.genemodel;

import de.julielab.java.utilities.spanutils.OffsetMap;
import org.apache.commons.lang3.Range;

import java.util.Collections;
import java.util.HashSet;
import java.util.Set;

public class SpeciesCandidates implements Cloneable {

    private OffsetMap titleCandidates;
    private Set meshCandidates;
    private OffsetMap textCandidates;

    public SpeciesCandidates(OffsetMap titleCandidates, Set meshCandidates,
                             OffsetMap textCandidates) {
        this.titleCandidates = titleCandidates;
        this.meshCandidates = meshCandidates;
        this.textCandidates = textCandidates;
    }

    /**
     * If the textCandidates include species mentions for the title,
     * this constructor will automatically derive the title species IDs.
     *
     * @param titleBegin
     * @param titleEnd
     * @param meshCandidates
     * @param textCandidates
     */
    public SpeciesCandidates(int titleBegin, int titleEnd, Set meshCandidates,
                             OffsetMap textCandidates) {
        this.textCandidates = textCandidates;
        if (null == textCandidates)
            this.textCandidates = OffsetMap.emptyOffsetMap();
        this.titleCandidates = new OffsetMap(this.textCandidates.restrictTo(Range.between(titleBegin, titleEnd)));
        this.meshCandidates = meshCandidates;
    }

    @Override
    protected SpeciesCandidates clone() {
        OffsetMap titleCandidates = this.titleCandidates != null ? new OffsetMap<>(this.titleCandidates) : OffsetMap.emptyOffsetMap();
        Set meshCandidates = this.meshCandidates != null ? new HashSet<>(this.meshCandidates) : Collections.emptySet();
        OffsetMap textCandidates = this.textCandidates != null ? new OffsetMap<>(this.textCandidates) : OffsetMap.emptyOffsetMap();
        return new SpeciesCandidates(titleCandidates, meshCandidates, textCandidates);
    }

    public OffsetMap getAllMentionCandidates() {
        OffsetMap allMentionCandidates = new OffsetMap<>();
        if (titleCandidates != null)
            allMentionCandidates.putAll(titleCandidates);
        if (textCandidates != null)
            allMentionCandidates.putAll(textCandidates);
        return allMentionCandidates;
    }

    public OffsetMap getTitleCandidates() {
        return titleCandidates;
    }

    public void setTitleCandidates(OffsetMap titleCandidates) {
        this.titleCandidates = titleCandidates;
    }

    public Set getMeshCandidates() {
        return meshCandidates;
    }

    public void setMeshCandidates(Set meshCandidates) {
        this.meshCandidates = meshCandidates;
    }

    public OffsetMap getTextCandidates() {
        return textCandidates;
    }

    public void setTextCandidates(OffsetMap textCandidates) {
        this.textCandidates = textCandidates;
    }
}