org.molgenis.genomebrowser.meta.GenomeBrowserSettings Maven / Gradle / Ivy

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package org.molgenis.genomebrowser.meta;

import java.util.stream.Stream;
import java.util.stream.StreamSupport;
import javax.annotation.Nullable;
import org.molgenis.data.Entity;
import org.molgenis.data.meta.model.Attribute;
import org.molgenis.data.meta.model.EntityType;
import org.molgenis.data.support.StaticEntity;
import org.molgenis.genomebrowser.GenomeBrowserTrack;

public class GenomeBrowserSettings extends StaticEntity {
  public GenomeBrowserSettings(Entity entity) {
    super(entity);
  }

  public GenomeBrowserSettings(EntityType entityType) {
    super(entityType);
  }

  public GenomeBrowserSettings(String identifier, EntityType entityType) {
    super(identifier, entityType);
  }

  public String getIdentifier() {
    return getString(GenomeBrowserSettingsMetadata.IDENTIFIER);
  }

  public void setIdentifier(String identifier) {
    set(GenomeBrowserSettingsMetadata.IDENTIFIER, identifier);
  }

  public String getLabel() {
    return getString(GenomeBrowserSettingsMetadata.LABEL);
  }

  public void setLabel(String label) {
    set(GenomeBrowserSettingsMetadata.LABEL, label);
  }

  public Attribute getLabelAttr() {
    return getEntity(GenomeBrowserSettingsMetadata.LABEL_ATTR, Attribute.class);
  }

  public void setLabelAttr(Attribute labelAttr) {
    set(GenomeBrowserSettingsMetadata.LABEL_ATTR, labelAttr);
  }

  public EntityType getEntity() {
    return getEntity(GenomeBrowserSettingsMetadata.ENTITY, EntityType.class);
  }

  public void setEntity(EntityType entity) {
    set(GenomeBrowserSettingsMetadata.ENTITY, entity);
  }

  public TrackType getTrackType() {
    String string = getString(GenomeBrowserSettingsMetadata.TRACK_TYPE);
    return string != null ? TrackType.valueOf(string.toUpperCase()) : null;
  }

  public void setTrackType(TrackType trackType) {
    set(GenomeBrowserSettingsMetadata.TRACK_TYPE, trackType.toString().toUpperCase());
  }

  public Stream getMolgenisReferenceTracks() {
    return StreamSupport.stream(
            getEntities(
                    GenomeBrowserSettingsMetadata.MOLGENIS_REFERENCE_TRACKS,
                    GenomeBrowserSettings.class)
                .spliterator(),
            false)
        .map(settings -> GenomeBrowserTrack.create(settings));
  }

  public void setMolgenisReferenceTracks(GenomeBrowserSettings molgenisReferenceTracks) {
    set(GenomeBrowserSettingsMetadata.MOLGENIS_REFERENCE_TRACKS, molgenisReferenceTracks);
  }

  public MolgenisReferenceMode getMolgenisReferenceMode() {
    String string = getString(GenomeBrowserSettingsMetadata.MOLGENIS_REFERENCES_MODE);
    return string != null
        ? MolgenisReferenceMode.valueOf(
            getString(GenomeBrowserSettingsMetadata.MOLGENIS_REFERENCES_MODE).toUpperCase())
        : null;
  }

  public void setMolgenisReferenceMode(MolgenisReferenceMode mode) {
    set(GenomeBrowserSettingsMetadata.MOLGENIS_REFERENCES_MODE, mode.toString().toUpperCase());
  }

  public GenomeBrowserAttributes getGenomeBrowserAttrs() {
    return getEntity(
        GenomeBrowserSettingsMetadata.GENOME_BROWSER_ATTRS, GenomeBrowserAttributes.class);
  }

  public void setGenomeBrowserAttrs(GenomeBrowserAttributes genomeBrowserAttrs) {
    set(GenomeBrowserSettingsMetadata.GENOME_BROWSER_ATTRS, genomeBrowserAttrs);
  }

  @Nullable
  public String getActions() {
    return getString(GenomeBrowserSettingsMetadata.ACTIONS);
  }

  public void setActions(String actions) {
    set(GenomeBrowserSettingsMetadata.ACTIONS, actions);
  }

  @Nullable
  public String getAttrs() {
    return getString(GenomeBrowserSettingsMetadata.ATTRS);
  }

  public void setAttrs(String attrs) {
    set(GenomeBrowserSettingsMetadata.ATTRS, attrs);
  }

  @Nullable
  public String getScoreAttr() {
    return getString(GenomeBrowserSettingsMetadata.SCORE_ATTR);
  }

  public void setScoreAttr(String scoreAttr) {
    set(GenomeBrowserSettingsMetadata.SCORE_ATTR, scoreAttr);
  }

  @Nullable
  public String getExonKey() {
    return getString(GenomeBrowserSettingsMetadata.EXON_KEY);
  }

  public void setExonKey(String exonKe) {
    set(GenomeBrowserSettingsMetadata.EXON_KEY, exonKe);
  }

  public enum TrackType {
    VARIANT,
    NUMERIC,
    EXON
  }

  public enum MolgenisReferenceMode {
    ALL,
    NONE,
    CONFIGURED
  }
}