Method Detail

• getLength

  int getLength()

  Returns the length of the Sequence

• getCompoundAt

  C getCompoundAt​(int position)

  Returns the Compound at the given biological index

  Parameters:

  position - Biological index (1 to n)

  Returns:

  Compound at the specified position

• getIndexOf

  int getIndexOf​(C compound)

  Scans through the Sequence looking for the first occurrence of the given compound

  Parameters:

  compound - Compounds to look for

  Returns:

  Index of the first position of the compound in the sequence (1 to n)

• getLastIndexOf

  int getLastIndexOf​(C compound)

  Scans through the Sequence looking for the last occurrence of the given compound

  Parameters:

  compound - Compounds to look for

  Returns:

  Index of the last position of the compound in the sequence (1 to n)

• getSequenceAsString

  java.lang.String getSequenceAsString()

  Returns the String representation of the Sequence

• getAsList

  java.util.List<C> getAsList()

  Returns the Sequence as a List of compounds

• getSubSequence

  SequenceView<C> getSubSequence​(java.lang.Integer start,
                                 java.lang.Integer end)

  Returns a portion of the sequence from the different positions. This is indexed from 1

  Parameters:

  start - Biological index start; must be greater than 0

  end - Biological end; must be less than length + 1

  Returns:

  A SequenceView of the offset

• getCompoundSet

  CompoundSet<C> getCompoundSet()

  Gets the compound set used to back this Sequence

• countCompounds

  int countCompounds​(C... compounds)

  Returns the number of times we found a compound in the Sequence

  Parameters:

  compounds - Vargs of the compounds to count

  Returns:

  Number of times a compound was found

• getInverse

  SequenceView<C> getInverse()

  Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.