Class Chromosome

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.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:
    Serialized Form
    • Constructor Detail

      • Chromosome

        public Chromosome()
      • Chromosome

        public Chromosome​(Genome parent,
                          int start,
                          int end,
                          java.lang.String id)
    • Method Detail

      • compare

        public static int compare​(java.lang.String chr1,
                                  java.lang.String chr2)
        Compare chromosome names
      • number

        public static int number​(java.lang.String chrName)
        Convert to chromosome number (return '0' if it cannot be converted)
      • simpleName

        public static java.lang.String simpleName​(java.lang.String chrName)
        Simplify chromosome name
      • compareChromoName

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

        public CodonTable getCodonTable()
      • getSequence

        public java.lang.String getSequence()
      • 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
      • setLength

        public void setLength​(int len)
      • setSequence

        public void setSequence​(java.lang.String sequenceStr)
        Set sequence for this chromosome
        Parameters:
        sequenceStr -