Package 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:

Alignment, UnequalLengthAlignment, 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.alignment.Alignment

Alignment.SymbolListIterator

Field Summary

Fields inherited from interface org.biojava.bio.alignment.Alignment

CONTENT

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SubULAlignment(Set<String> labels, Location loc)

Method Summary

Modifier and Type	Method	Description
Alphabet	getAlphabet()
List<String>	getLabels()
List<String>	labelsAt(int column)	Returns a list labels, of all seqs that cover that column
List<String>	labelsInRange(Location loc)	Returns list of all the labels that intersect that range
int	length()
protected List<String>	listIntersection(List<String> s1, List<String> s2)
Location	locInAlignment(Object label)	The location of an individual SymbolList relative to overall Alignment
Alignment	subAlignment(Set<String> labels, Location loc)
Symbol	symbolAt(int column)
Symbol	symbolAt(String label, int column)
SymbolList	symbolListForLabel(String label)
Iterator<SymbolList>	symbolListIterator()

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.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.symbol.SymbolList

edit, iterator, seqString, subList, subStr, toList

Constructor Details

SubULAlignment

protected SubULAlignment(Set<String> labels,
 Location loc)
                  throws IndexOutOfBoundsException

Throws:

IndexOutOfBoundsException

Method Details

length

public int length()

Specified by:

length in interface SymbolList

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<String> labels,
 Location loc)
                       throws NoSuchElementException

Specified by:

subAlignment in interface Alignment

Throws:

NoSuchElementException

listIntersection

protected List<String> listIntersection(List<String> s1,
 List<String> s2)

labelsAt

public List<String> 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<String> 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<String> getLabels()

Specified by:

getLabels in interface Alignment

symbolAt

public Symbol symbolAt(String label,
 int column)
                throws NoSuchElementException

Specified by:

symbolAt in interface Alignment

Throws:

NoSuchElementException

symbolAt

public Symbol symbolAt(int column)
                throws NoSuchElementException

Specified by:

symbolAt in interface SymbolList

Throws:

NoSuchElementException

symbolListForLabel

public SymbolList symbolListForLabel(String label)
                              throws NoSuchElementException

Specified by:

symbolListForLabel in interface Alignment

Throws:

NoSuchElementException

getAlphabet

public Alphabet getAlphabet()

Specified by:

getAlphabet in interface SymbolList

symbolListIterator

public Iterator<SymbolList> symbolListIterator()

Specified by:

symbolListIterator in interface Alignment