Constructor Detail

• BasicMsa

  public BasicMsa(int rows,
                  int columns,
                  MolecularSequence.TYPE type)

Method Detail

• asSequenceList

  public java.util.List<MolecularSequence> asSequenceList()

  Specified by:

  asSequenceList in interface Msa

• getColumnAt

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

  Specified by:

  getColumnAt in interface Msa

• getIdentifier

  public java.lang.String getIdentifier(int row)

  Specified by:

  getIdentifier in interface Msa

• getLength

  public int getLength()

  Specified by:

  getLength in interface Msa

• getNumberOfSequences

  public int getNumberOfSequences()

  Specified by:

  getNumberOfSequences in interface Msa

• getResidueAt

  public char getResidueAt(int row,
                           int col)

  Specified by:

  getResidueAt in interface Msa

• getSequence

  public MolecularSequence getSequence(int row)

  Specified by:

  getSequence in interface Msa

• getSequence

  public MolecularSequence getSequence(java.lang.String id)

  Specified by:

  getSequence in interface Msa

• getSequenceAsString

  public java.lang.StringBuffer getSequenceAsString(int row)

  Specified by:

  getSequenceAsString in interface Msa

• getType

  public MolecularSequence.TYPE getType()

  Specified by:

  getType in interface Msa

• isGapAt

  public boolean isGapAt(int row,
                         int col)

  Specified by:

  isGapAt in interface Msa

• setIdentifier

  public void setIdentifier(int row,
                            java.lang.String id)

  Specified by:

  setIdentifier in interface Msa

• setResidueAt

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

  Specified by:

  setResidueAt in interface Msa

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object

• write

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

  Specified by:

  write in interface Msa

  Throws:

  java.io.IOException

• createInstance

  public static Msa createInstance(java.util.List<MolecularSequence> seqs)