Class AbstractULAlignment.SubULAlignment

Method Details

• length

  public int length()

  Description copied from interface: SymbolList

  The number of symbols in this SymbolList.

  Specified by:

  length in interface SymbolList

  Returns:

  the length

• locInAlignment

  public Location locInAlignment(Object label)

  The location of an individual SymbolList relative to overall Alignment

  Specified by:

  locInAlignment in interface UnequalLengthAlignment

• subAlignment

  public Alignment subAlignment(Set<String> labels, Location loc) throws NoSuchElementException

  Description copied from interface: Alignment

  Make a view onto this alignment.

  If labels is null, then each label will be kept. Otherwise, only those in labels will be kept. If loc is null, then the entire length of the alignment will be kept. If loc is not null, then only the columns within the location will be kept.

  Specified by:

  subAlignment in interface Alignment

  Parameters:

  labels - the Set of sequences to include by label

  loc - the Location to include

  Returns:

  a sub Alignment

  Throws:

  NoSuchElementException - if labels contains any item that is not a label

• listIntersection

  protected List<String> listIntersection(List<String> s1, List<String> s2)

• labelsAt

  public List<String> labelsAt(int column) throws IndexOutOfBoundsException

  Description copied from interface: UnequalLengthAlignment

  Returns a list labels, of all seqs that cover that column

  Specified by:

  labelsAt in interface UnequalLengthAlignment

  Throws:

  IndexOutOfBoundsException

• labelsInRange

  public List<String> labelsInRange(Location loc) throws IndexOutOfBoundsException

  Description copied from interface: UnequalLengthAlignment

  Returns list of all the labels that intersect that range

  Specified by:

  labelsInRange in interface UnequalLengthAlignment

  Throws:

  IndexOutOfBoundsException

• getLabels

  public List<String> getLabels()

  Description copied from interface: Alignment

  The list of SymbolLists in the alignment.

  The index in the list is the same as the index in the alignment. Each SymbolList object will only be in the alignment once. However, a single underlying SymbolList may have more than one view within an alignment, each represented by a different GappedSymbolList.

  Specified by:

  getLabels in interface Alignment

  Returns:

  the List of all SymbolLists in the alignment

• symbolAt

  public Symbol symbolAt(String label, int column) throws NoSuchElementException

  Description copied from interface: Alignment

  Retrieve a symbol by label and column.

  Specified by:

  symbolAt in interface Alignment

  Parameters:

  label - the SymbolList to retrieve from

  column - the index of the column to retrieve

  Returns:

  the symbol in the symbol list associated with the label at the given column

  Throws:

  NoSuchElementException - if there is no row for 'label'

• symbolAt

  public Symbol symbolAt(int column) throws NoSuchElementException

  Description copied from interface: SymbolList

  Return the symbol at index, counting from 1.

  Specified by:

  symbolAt in interface SymbolList

  Parameters:

  column - the offset into this SymbolList

  Returns:

  the Symbol at that index

  Throws:

  NoSuchElementException

• symbolListForLabel

  public SymbolList symbolListForLabel(String label) throws NoSuchElementException

  Description copied from interface: Alignment

  Retrieve a single row of the alignment by label.

  Specified by:

  symbolListForLabel in interface Alignment

  Parameters:

  label - the object from which to retrieve the symbol list

  Returns:

  a SymbolList that contains each token in a row of the alignment

  Throws:

  NoSuchElementException - if there is no row for 'label'

• getAlphabet

  public Alphabet getAlphabet()

  Description copied from interface: SymbolList

  The alphabet that this SymbolList is over.

  Every symbol within this SymbolList is a member of this alphabet. alphabet.contains(symbol) == true for each symbol that is within this sequence.

  Specified by:

  getAlphabet in interface SymbolList

  Returns:

  the alphabet

• symbolListIterator

  public Iterator<SymbolList> symbolListIterator()

  Description copied from interface: Alignment

  Creates an Iterator over the SymbolLists in the alignment. This should be similar to iterating over the labels and then fetching each SymbolList, but the order is not guaranteed to be the same.

  Specified by:

  symbolListIterator in interface Alignment

  Returns:

  an Iterator