Interface Alignment

All Superinterfaces:
Changeable, SymbolList
All Known Subinterfaces:
ARAlignment, StatePath, UnequalLengthAlignment
All Known Implementing Classes:
AbstractULAlignment, AbstractULAlignment.SubULAlignment, AlignmentPair, FlexibleAlignment, RelabeledAlignment, SimilarityPairFeature.EmptyPairwiseAlignment, SimpleAlignment, SimpleStatePath

public interface Alignment extends SymbolList
An alignment containing multiple SymbolLists.

The alignment can be thought of as a rectangular array of Symbols. Each row is indexed by a label and each column is indexed by offset (counting from 1).

Alternatively, it can be thought of as a SymbolList where each Symbol is a list of Symbols in that column.

To create gapped alignments, use SymbolLists with gaps. The most flexible way to do this will be to leverage GappedSymbolList objects.

Since:
1.1
Author:
Matthew Pocock, Nimesh Singh
  • Field Details

    • CONTENT

      static final ChangeType CONTENT
      Signals that SymbolLists will be added to or removed from an alignment. The ChangeEvent will record Object[] { label, symbolList } in previous if it is being removed, in current if it is being added and in both if the SymbolList for a given name is swapped.
  • Method Details

    • getLabels

      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.

      Returns:
      the List of all SymbolLists in the alignment
    • symbolAt

      Symbol symbolAt(String label, int column) throws NoSuchElementException
      Retrieve a symbol by label and column.
      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'
    • symbolListForLabel

      Retrieve a single row of the alignment by label.
      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'
    • subAlignment

      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.

      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
    • symbolListIterator

      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.
      Returns:
      an Iterator