Package org.snpeff.interval

Class Chromosome

java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Chromosome
All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, TxtSerializable
public class Chromosome extends Marker
Interval for the whole chromosome If a SNP has no 'ChromosomeInterval' => it is outside the chromosome => Invalid
Author:
pcingola
See Also:

  • Constructor Details

    • Chromosome

      public Chromosome()

    • Chromosome

      public Chromosome(Genome parent, int start, int end, String id)

  • Method Details

    • compare

      public static int compare(String chr1, String chr2)
      Compare chromosome names

    • number

      public static int number(String chrName)
      Convert to chromosome number (return '0' if it cannot be converted)

    • simpleName

      public static String simpleName(String chrName)
      Simplify chromosome name

    • cloneShallow

      public Chromosome cloneShallow()
      Description copied from class: Marker
      Perform a shallow clone
      Overrides:
      cloneShallow in class Marker

    • compareChromoName

      public int compareChromoName(Interval interval)
      Compare only chromosome's name

    • detectCircular

      public boolean detectCircular()
      Is this a circular chromosome? See if any exon has evidence of 'circular coordinates'
      Returns:

    • getCodonTable

      public CodonTable getCodonTable()

    • getDnaSequence

      public DnaSequence getDnaSequence()

    • getSequence

      public String getSequence()

    • isCircular

      public boolean isCircular()
      Description copied from class: Interval
      Is this interval part of a circular chromosome and it spans the 'chromosome zero / chromosome end' line?
      Overrides:
      isCircular in class Interval

    • isMt

      public boolean isMt()
      Is this a mitochondrial chromosome? Note: This is a wild guess just by looking at the name

    • isShowWarningIfParentDoesNotInclude

      protected boolean isShowWarningIfParentDoesNotInclude()
      Description copied from class: Marker
      Show an error if parent does not include child?
      Overrides:
      isShowWarningIfParentDoesNotInclude in class Marker

    • serializeParse

      public void serializeParse(MarkerSerializer markerSerializer)
      Parse a line from a serialized file
      Specified by:
      serializeParse in interface TxtSerializable
      Overrides:
      serializeParse in class Marker

    • serializeSave

      public String serializeSave(MarkerSerializer markerSerializer)
      Description copied from class: Marker
      Create a string to serialize to a file
      Specified by:
      serializeSave in interface TxtSerializable
      Overrides:
      serializeSave in class Marker

    • setCircular

      public void setCircular(boolean circular)

    • setLength

      public void setLength(int len)

    • setSequence

      public void setSequence(String sequenceStr)
      Set sequence for this chromosome
      Parameters:
      sequenceStr -

    • toString

      public String toString()
      Overrides:
      toString in class Marker