Package jebl.evolution.sequences

Class CanonicalSequence

java.lang.Object
jebl.evolution.sequences.CanonicalSequence
All Implemented Interfaces:
Comparable, Sequence, Attributable
public class CanonicalSequence extends Object implements Sequence
A default implementation of the Sequence interface that converts sequence characters to States such that calling getString() will always return uppercase residues with nucleotide U residues converted to T
Version:
$Id: BasicSequence.java 641 2007-02-16 11:56:21Z rambaut $
Author:
Andrew Rambaut, Alexei Drummond

  • Constructor Details

    • CanonicalSequence

      public CanonicalSequence(SequenceType sequenceType, Taxon taxon, CharSequence sequenceString)
      Creates a sequence with a name corresponding to the taxon name. Use CharSequence so both a String and a StringBuilder are fine
      Parameters:
      taxon -
      sequenceString -

    • CanonicalSequence

      public CanonicalSequence(SequenceType sequenceType, Taxon taxon, State[] states)
      Creates a sequence with a name corresponding to the taxon name
      Parameters:
      sequenceType -
      taxon -
      states -

  • Method Details

    • getSequenceType

      public SequenceType getSequenceType()
      Specified by:
      getSequenceType in interface Sequence
      Returns:
      the type of symbols that this sequence is made up of.

    • getString

      public String getString()
      Specified by:
      getString in interface Sequence
      Returns:
      a string representing the sequence of symbols.

    • getCleanString

      public String getCleanString()

    • getStates

      public State[] getStates()
      Specified by:
      getStates in interface Sequence
      Returns:
      an array of state objects.

    • getStateIndices

      public byte[] getStateIndices()
      Specified by:
      getStateIndices in interface Sequence
      Returns:
      an array of state indices.

    • getState

      public State getState(int site)
      Specified by:
      getState in interface Sequence
      Returns:
      the state at site.

    • getLength

      public int getLength()
      Returns the length of the sequence
      Specified by:
      getLength in interface Sequence
      Returns:
      the length

    • getTaxon

      public Taxon getTaxon()
      Specified by:
      getTaxon in interface Sequence
      Returns:
      that taxon that this sequence represents (primarily used to match sequences with tree nodes)

    • compareTo

      public int compareTo(Object o)
      Sequences are compared by their taxa
      Specified by:
      compareTo in interface Comparable
      Parameters:
      o - another sequence
      Returns:
      an integer

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • setAttribute

      public void setAttribute(String name, Object value)
      Description copied from interface: Attributable
      Sets an named attribute for this object.
      Specified by:
      setAttribute in interface Attributable
      Parameters:
      name - the name of the attribute.
      value - the new value of the attribute.

    • getAttribute

      public Object getAttribute(String name)
      Specified by:
      getAttribute in interface Attributable
      Parameters:
      name - the name of the attribute of interest, or null if the attribute doesn't exist.
      Returns:
      an object representing the named attributed for this object.

    • removeAttribute

      public void removeAttribute(String name)
      Specified by:
      removeAttribute in interface Attributable
      Parameters:
      name - name of attribute to remove

    • getAttributeNames

      public Set<String> getAttributeNames()
      Specified by:
      getAttributeNames in interface Attributable
      Returns:
      an array of the attributeNames that this object has.

    • getAttributeMap

      public Map<String,Object> getAttributeMap()
      Description copied from interface: Attributable
      Gets the entire attribute map.
      Specified by:
      getAttributeMap in interface Attributable
      Returns:
      an unmodifiable map