Class SimpleAlignment

All Implemented Interfaces:
Serializable, Alignment, SymbolList, Changeable
Direct Known Subclasses:
AlignmentPair

public class SimpleAlignment extends AbstractSymbolList implements Alignment, Serializable
A simple implementation of an Alignment.

This is a simple-stupid implementation that is made from a set of same-lengthed SymbolList objects each with an associated label. It does not handle differently lengthed sequences and doesn't contain any gap-editing concepts.

Author:
Matthew Pocock, Greg Cox, Nimesh Singh
See Also:
  • Constructor Details

  • Method Details

    • finalize

      protected void finalize() throws Throwable
      Overrides:
      finalize in class Object
      Throws:
      Throwable
    • 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
    • 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
    • symbolAt

      public Symbol symbolAt(int index)
      Description copied from interface: SymbolList
      Return the symbol at index, counting from 1.
      Specified by:
      symbolAt in interface SymbolList
      Parameters:
      index - the offset into this SymbolList
      Returns:
      the Symbol at that index
    • 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)
      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
    • subAlignment

      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
    • symbolListForLabel

      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'
    • 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
    • getScore

      public int getScore()
      Returns:
    • setScore

      public void setScore(int score)
      Parameters:
      score -