Class Markers

Method Details

• readMarkers

  public static Markers readMarkers(String fileName)

  Read markers from a file Supported formats: BED, BigBed, VCF, TXT

• add

  public boolean add(Marker marker)

  Add an interval to the collection

  Specified by:

  add in interface Collection<Marker>

• add

  public Markers add(Markers markersToAdd)

  Add all intervals

• addAll

  public boolean addAll(Collection<? extends Marker> mm)

  Add all markers in this collection

  Specified by:

  addAll in interface Collection<Marker>

• clear

  public void clear()

  Specified by:

  clear in interface Collection<Marker>

• contains

  public boolean contains(Object o)

  Specified by:

  contains in interface Collection<Marker>

• containsAll

  public boolean containsAll(Collection<?> c)

  Specified by:

  containsAll in interface Collection<Marker>

• equals

  public boolean equals(Markers intervals)

  Are all intervals equal?

• get

  public Marker get(int i)

• getMarkers

  public List<Marker> getMarkers()

• getMedian

  public int getMedian()

  Calculate the median point in this set of markers

• getName

  public String getName()

• setName

  public void setName(String name)

• intersect

  public Markers intersect()

  Perform the intersection of all overlapping sub-intervals

  For each marker, calculate all overlapping markers and create a new marker that contains them all. Return a set of those new markers.

• intersect

  public Markers intersect(Marker marker)

  Intersection between 'marker' and all sub-intervals

• isEmpty

  public boolean isEmpty()

  Specified by:

  isEmpty in interface Collection<Marker>

• iterator

  public Iterator<Marker> iterator()

  Specified by:

  iterator in interface Collection<Marker>

  Specified by:

  iterator in interface Iterable<Marker>

• load

  public void load(String fileName)

• load

  public void load(String fileName, Genome genome)

• merge

  public Markers merge()

  Merge overlapping intervals This is the same as 'union()' method, but the algorithm is more efficient

• minus

  public Markers minus(Marker interval)

  Calculate 'set minus' using one interval

  Parameters:

  interval -

  Returns:

• minus

  public Markers minus(Markers intervals)

  Returns the result of this set minus 'intervals'

  WARNING: This method should only be used for debugging (or in very small collections) since it is extremely inefficient.

• rand

  public Interval rand()

  Return a random interval within this collection

• remove

  public boolean remove(Object o)

  Specified by:

  remove in interface Collection<Marker>

• removeAll

  public boolean removeAll(Collection<?> c)

  Specified by:

  removeAll in interface Collection<Marker>

• retainAll

  public boolean retainAll(Collection<?> c)

  Specified by:

  retainAll in interface Collection<Marker>

• save

  public void save(String fileName)

  Save to a file using a serializer

• save

  public void save(String fileName, String chr)

  Save to a file using a serializer Only save one chromosome ('chr') Note: This is used to save only markers related to one chromosome (e.g. when saving GenomicSequences)

• size

  public int size()

  Specified by:

  size in interface Collection<Marker>

• sort

  public Markers sort()

  Sort intervals

• sort

  public Markers sort(boolean byEnd, boolean reverse)

  Sort intervals

  Parameters:

  byEnd - : If true, sort by end. Otherwise sort by start

  reverse - : Reverse order

• toArray

  public Marker[] toArray()

  Specified by:

  toArray in interface Collection<Marker>

• toArray

  public <T> T[] toArray(T[] a)

  Specified by:

  toArray in interface Collection<Marker>

• toString

  public String toString()

  Overrides:

  toString in class Object

• toStringAsciiArt

  public String toStringAsciiArt(int maxLen)

  Show all intervals as an ASCII art

• toStringTxt

  public String toStringTxt()

• union

  public Markers union()

  Perform the union of all overlapping intervals

  For each marker, calculate all overlapping markers and create a new marker that contains them all. Return a set of those new markers.

• unique

  public Markers unique()

  Remove duplicated markers

  Returns:

  this object