Class AbstractULAlignment.SubULAlignment

    • Constructor Detail

      • SubULAlignment

        protected SubULAlignment​(java.util.Set<java.lang.String> labels,
                                 Location loc)
                          throws java.lang.IndexOutOfBoundsException
        Throws:
        java.lang.IndexOutOfBoundsException
    • Method Detail

      • 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
      • 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
      • listIntersection

        protected java.util.List<java.lang.String> listIntersection​(java.util.List<java.lang.String> s1,
                                                                    java.util.List<java.lang.String> s2)
      • labelsAt

        public java.util.List<java.lang.String> labelsAt​(int column)
                                                  throws java.lang.IndexOutOfBoundsException
        Description copied from interface: UnequalLengthAlignment
        Returns a list labels, of all seqs that cover that column
        Specified by:
        labelsAt in interface UnequalLengthAlignment
        Throws:
        java.lang.IndexOutOfBoundsException
      • 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)
                        throws java.util.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:
        java.util.NoSuchElementException - if there is no row for 'label'
      • symbolAt

        public Symbol symbolAt​(int column)
                        throws java.util.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:
        java.util.NoSuchElementException
      • 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'
      • 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 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