Package pal.alignment

Class SimpleAlignment

java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.SimpleAlignment
All Implemented Interfaces:
Serializable, Alignment, IdGroup, Report
Direct Known Subclasses:
MultiLocusAnnotatedAlignment, SimpleAnnotatedAlignment

public class SimpleAlignment extends AbstractAlignment
An alignment class that can be efficiently constructed from an array of strings.
Version:
$Id: SimpleAlignment.java,v 1.26 2003/08/16 23:48:26 matt Exp $
Author:
Alexei Drummond
See Also:
  • Constructor Details

    • SimpleAlignment

      public SimpleAlignment()
      parameterless constructor.
    • SimpleAlignment

      public SimpleAlignment(Alignment a)
      Clone constructor.
    • SimpleAlignment

      public SimpleAlignment(Alignment a, LabelMapping lm)
      Clone constructor.
    • SimpleAlignment

      public SimpleAlignment(Alignment a, int sequenceToIgnore)
      Clone constructor.
      Parameters:
      sequenceToIgnore - Will not copy across specified sequence
    • SimpleAlignment

      public SimpleAlignment(Identifier[] ids, String[] sequences, String gaps, DataType dt)
    • SimpleAlignment

      public SimpleAlignment(IdGroup ids, String[] sequences, DataType dt)
    • SimpleAlignment

      public SimpleAlignment(IdGroup ids, String[] sequences, String gaps, DataType dt)
    • SimpleAlignment

      public SimpleAlignment(Identifier[] ids, String[] sequences, DataType dt)
    • SimpleAlignment

      public SimpleAlignment(IdGroup group, char[][] cSequences, DataType dt)
      Parameters:
      cSequences - sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]
    • SimpleAlignment

      public SimpleAlignment(IdGroup group, DataType dt, int[][] sSequences)
      Parameters:
      cSequences - sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]
    • SimpleAlignment

      public SimpleAlignment(IdGroup group, char[][] cSequences, String gaps, DataType dt)
      Parameters:
      cSequences - sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]
    • SimpleAlignment

      public SimpleAlignment(Identifier id, String sequence, DataType dataType)
      Constructor taking single identifier and sequence.
    • SimpleAlignment

      public SimpleAlignment(Alignment a, Alignment b, String guide1, String guide2, char gap)
      This constructor combines to alignments given two guide strings.
  • Method Details