Class SimpleAlignment

  • All Implemented Interfaces:
    java.io.Serializable, Alignment, SymbolList, Changeable
    Direct Known Subclasses:
    AlignmentPair

    public class SimpleAlignment
    extends AbstractSymbolList
    implements Alignment, java.io.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:
    Serialized Form
    • Constructor Detail

      • SimpleAlignment

        public SimpleAlignment​(java.util.Map<java.lang.String,​SymbolList> labelToResList)
                        throws java.lang.IllegalArgumentException
        Generate an alignment from a list of SymbolLists.

        The SymbolLists must all be of the same length.

        Parameters:
        labelToResList - the label-to-symbol list mapping
        Throws:
        java.lang.IllegalArgumentException - if the SymbolLists are not the same length
    • Method Detail

      • finalize

        protected void finalize()
                         throws java.lang.Throwable
        Overrides:
        finalize in class java.lang.Object
        Throws:
        java.lang.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

        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
      • 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 java.util.List<java.lang.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​(java.lang.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

        public Alignment subAlignment​(java.util.Set<java.lang.String> labels,
                                      Location loc)
                               throws java.util.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:
        java.util.NoSuchElementException - if labels contains any item that is not a label
      • symbolListForLabel

        public SymbolList symbolListForLabel​(java.lang.String label)
                                      throws java.util.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:
        java.util.NoSuchElementException - if there is no row for 'label'
      • symbolListIterator

        public java.util.Iterator<SymbolListsymbolListIterator()
        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 -