## org.biojava.bio.alignment
Class AbstractULAlignment.SubULAlignment

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.symbol.AbstractSymbolList
              org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment

All Implemented Interfaces:
  UnequalLengthAlignment, Alignment, SymbolList, Changeable

Enclosing class:
  AbstractULAlignment

    public class AbstractULAlignment.SubULAlignment

extends AbstractSymbolList
implements UnequalLengthAlignment

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList
`AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater`

Nested classes/interfaces inherited from interface org.biojava.bio.symbol.Alignment
`Alignment.SymbolListIterator`

Field Summary

Fields inherited from interface org.biojava.bio.symbol.Alignment
`CONTENT`

Fields inherited from interface org.biojava.bio.symbol.SymbolList
`EDIT, EMPTY_LIST`

Constructor Summary
`protected` `AbstractULAlignment.SubULAlignment(Set labels, Location loc)`

Method Summary
`Alphabet` `getAlphabet()` The alphabet that this SymbolList is over.
`List` `getLabels()` The list of SymbolLists in the alignment.
`List` `labelsAt(int column)` Returns a list labels, of all seqs that cover that column
`List` `labelsInRange(Location loc)` Returns list of all the labels that intersect that range
`int` `length()` The number of symbols in this SymbolList.
`protected List` `listIntersection(List s1, List s2)`
`Location` `locInAlignment(Object label)` The location of an individual SymbolList relative to overall Alignment
`Alignment` `subAlignment(Set labels, Location loc)` Make a view onto this alignment.
`Symbol` `symbolAt(int column)` Return the symbol at index, counting from 1.
`Symbol` `symbolAt(Object label, int column)` Retrieve a symbol by label and column.
`SymbolList` `symbolListForLabel(Object label)` Retrieve a single row of the alignment by label.
`Iterator` `symbolListIterator()` Creates an Iterator over the SymbolLists in the alignment.

Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList
`edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString`

Methods inherited from class org.biojava.utils.AbstractChangeable
`addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from class java.lang.Object
`clone, finalize, getClass, notify, notifyAll, wait, wait, wait`

Methods inherited from interface org.biojava.bio.symbol.SymbolList
`edit, iterator, seqString, subList, subStr, toList`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Constructor Detail

### AbstractULAlignment.SubULAlignment

    protected AbstractULAlignment.SubULAlignment(Set labels,
                                                 Location loc)
                                          throws IndexOutOfBoundsException

Throws:
  `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

### 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 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 listIntersection(List s1,
                                    List s2)

### labelsAt

    public List 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 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 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(Object 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(Object 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 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