Package pal.alignment

Class SimpleAlignment

    • Constructor Detail

      • SimpleAlignment

        public SimpleAlignment()
        parameterless constructor.
      • SimpleAlignment

        public SimpleAlignment​(Alignment a)
        Clone constructor.
      • SimpleAlignment

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

        public SimpleAlignment​(Identifier[] ids,
                               java.lang.String[] sequences,
                               java.lang.String gaps,
                               DataType dt)
      • SimpleAlignment

        public SimpleAlignment​(IdGroup ids,
                               java.lang.String[] sequences,
                               DataType dt)
      • SimpleAlignment

        public SimpleAlignment​(IdGroup ids,
                               java.lang.String[] sequences,
                               java.lang.String gaps,
                               DataType dt)
      • SimpleAlignment

        public SimpleAlignment​(Identifier[] ids,
                               java.lang.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,
                               java.lang.String gaps,
                               DataType dt)
        Parameters:
        cSequences - sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]
      • SimpleAlignment

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

        public SimpleAlignment​(Alignment a,
                               Alignment b,
                               java.lang.String guide1,
                               java.lang.String guide2,
                               char gap)
        This constructor combines to alignments given two guide strings.