Class Marker

Method Details

• adjust

  protected void adjust(Marker child)

  Adjust [start,end] to include child

• apply

  public Marker apply(Variant variant)

  Apply a variant to a marker.

  Calculate a the result of a marker, such that newMarker = marker.apply( variant ) variant = Diff( newMarker , marker ) // Differences in sequence

  Note: This method may return: - The same marker (this) when genetic coordinates remain unchanged - 'null' if the whole marker is removed by the variant (e.g. a deletion spanning the whole marker)

  For these reasons, the method should never be invoked directly. This is why the method is 'private' and 'final'

  Returns:

  The marker result after applying variant

• applyDel

  protected Marker applyDel(Variant variant)

  Apply a Variant to a marker. Variant is a deletion

• applyDup

  protected Marker applyDup(Variant variant)

  Apply a Variant to a marker. Variant is a duplication

• applyIns

  protected Marker applyIns(Variant variant)

  Apply a Variant to a marker. Variant is an insertion

• applyMixed

  protected Marker applyMixed(Variant variant)

  Apply a mixed variant Note: MIXED variant is interpreted as "MNP + InDel"

• clone

  public Marker clone()

  Overrides:

  clone in class Interval

• cloneShallow

  public Marker cloneShallow()

  Perform a shallow clone

• codonTable

  public CodonTable codonTable()

  Get a suitable codon table

• compareTo

  public int compareTo(Interval i2)

  Compare by start and end

  Specified by:

  compareTo in interface Comparable<Interval>

  Overrides:

  compareTo in class Interval

• compareToPos

  public int compareToPos(Interval i2)

  Compare genomic coordinates

• distance

  public int distance(Marker interval)

  How far apart are these intervals?

  Returns:

  Distance or -1 if they are not comparable (i.e. different chromosomes)

• distanceBases

  public int distanceBases(List<? extends Marker> markers, boolean fromEnd)

  Distance from the beginning/end of a list of intervals, until this SNP It count the number of bases in 'markers'

• getParent

  public Marker getParent()

  Overrides:

  getParent in class Interval

• getType

  public EffectType getType()

• idChain

  public String idChain()

• idChain

  public String idChain(String separatorBetween, String separatorWithin, boolean useGeneId)

• idChain

  public String idChain(String separatorBetween, String separatorWithin, boolean useGeneId, VariantEffect varEff)

  A list of all IDs and parent IDs until chromosome

• includes

  public boolean includes(Marker marker)

  Is 'interval' completely included in 'this'?

  Returns:

  return true if 'this' includes 'interval'

• intersect

  public Marker intersect(Marker marker)

  Intersect of two markers

  Returns:

  A new marker which is the intersect of the two

• isAdjustIfParentDoesNotInclude

  protected boolean isAdjustIfParentDoesNotInclude(Marker parent)

  Adjust parent if it does not include child?

• isDeferredAnalysis

  public boolean isDeferredAnalysis()

  Deferred analysis markers must be analyzed after 'standard' ones because their impact depends on other results For instance, a NextProt marker's impact would be different if the variant is synonymous or non-synonymous

• isShowWarningIfParentDoesNotInclude

  protected boolean isShowWarningIfParentDoesNotInclude()

  Show an error if parent does not include child?

• minus

  public Markers minus(Marker interval)

  Return the difference between two markers

  Parameters:

  interval -

  Returns:

  A set of 'markers'. Note that the result can have zero, one or two markers

• query

  public Markers query(IntervalForest intervalForest)

  Return a collection of intervals that intersect this marker

• query

  public Markers query(Marker marker)

  Query all genomic regions that intersect 'marker' (this makes sense in Gene, Transcript, Exon, etc.)

• readTxt

  public void readTxt(String line, int lineNum, Genome genome, int positionBase)

  Parse a line (form a file) Format: "chromosome \t start \t end \t id \n"

• serializeParse

  public void serializeParse(MarkerSerializer markerSerializer)

  Parse a line from a serialized file

  Specified by:

  serializeParse in interface TxtSerializable

• serializeSave

  public String serializeSave(MarkerSerializer markerSerializer)

  Create a string to serialize to a file

  Specified by:

  serializeSave in interface TxtSerializable

• shouldApply

  public boolean shouldApply(Variant variant)

  True if the variant should be applied to the marker

• toString

  public String toString()

  Overrides:

  toString in class Interval

• union

  public Marker union(Marker m)

  Union of two markers

  Returns:

  A new marker which is the union of the two

• variantEffect

  public boolean variantEffect(Variant variant, VariantEffects variantEffects)

  Calculate the effect of this variant

• variantEffectNonRef

  public boolean variantEffectNonRef(Variant variant, VariantEffects variantEffects)

  Calculate the effect of this variant

  Parameters:

  variantEndPoint - : Before analyzing results, we have to change markers using variantrRef to create a new reference 'on the fly'