Method Detail

• getIdentifier

  java.lang.String getIdentifier​(int row)

• setIdentifier

  void setIdentifier​(int row,
                     java.lang.String identifier)

• getLength

  int getLength()

• getNumberOfSequences

  int getNumberOfSequences()

• getResidueAt

  char getResidueAt​(int row,
                    int col)

• isGapAt

  boolean isGapAt​(int row,
                  int col)

• getColumnAt

  java.util.List<java.lang.Character> getColumnAt​(int col)

• getSequence

  MolecularSequence getSequence​(java.lang.String id)

• getSequence

  MolecularSequence getSequence​(int row)

• asSequenceList

  java.util.List<MolecularSequence> asSequenceList()

• getSequenceAsString

  java.lang.StringBuffer getSequenceAsString​(int row)

• getType

  MolecularSequence.TYPE getType()

• setResidueAt

  void setResidueAt​(int row,
                    int col,
                    char residue)

• write

  void write​(java.io.Writer w,
             Msa.MSA_FORMAT format)
      throws java.io.IOException

  Throws:

  java.io.IOException