Package pal.alignment

Class AlignmentReaders.PhylipClustalAlignment

java.lang.Object
pal.alignment.AlignmentReaders.PhylipClustalAlignment
All Implemented Interfaces:
Serializable, Alignment, IdGroup
Enclosing class:
AlignmentReaders
public static class AlignmentReaders.PhylipClustalAlignment extends Object
See Also:

  • Constructor Details

    • PhylipClustalAlignment

      public PhylipClustalAlignment(String[] names, String[] sequences, DataType dt)

  • Method Details

    • getData

      public char getData(int seq, int site)
      sequence alignment at (sequence, site)
      Specified by:
      getData in interface Alignment

    • getSiteCount

      public int getSiteCount()
      Specified by:
      getSiteCount in interface Alignment
      Returns:
      number of sites for each sequence in this alignment

    • getSequenceCount

      public int getSequenceCount()
      Description copied from interface: Alignment
      Return number of sequences in this alignment
      Specified by:
      getSequenceCount in interface Alignment

    • getDataType

      public DataType getDataType()
      Description copied from interface: Alignment
      Return DataType of this alignment.
      Specified by:
      getDataType in interface Alignment

    • setDataType

      public void setDataType(DataType dataType)

    • getAlignedSequenceString

      public String getAlignedSequenceString(int sequence)
      Description copied from interface: Alignment
      Returns string representation of single sequence in alignment with gap characters included.
      Specified by:
      getAlignedSequenceString in interface Alignment

    • getFrequency

      public double[] getFrequency()

    • setFrequency

      public void setFrequency(double[] frequencies)

    • getIdCount

      public int getIdCount()
      Description copied from interface: IdGroup
      Returns the number of identifiers in this group
      Specified by:
      getIdCount in interface IdGroup

    • getIdentifier

      public Identifier getIdentifier(int i)
      Description copied from interface: IdGroup
      Returns the ith identifier.
      Specified by:
      getIdentifier in interface IdGroup

    • setIdentifier

      public void setIdentifier(int i, Identifier id)
      Description copied from interface: IdGroup
      Sets the ith identifier.
      Specified by:
      setIdentifier in interface IdGroup

    • whichIdNumber

      public int whichIdNumber(String s)
      Description copied from interface: IdGroup
      returns the index of the identifier with the given name.
      Specified by:
      whichIdNumber in interface IdGroup

    • toString

      public String toString()
      Overrides:
      toString in class Object