org.biojava.bio.alignment

Class AbstractULAlignment

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.alignment.AbstractULAlignment

All Implemented Interfaces:

UnequalLengthAlignment, Alignment, SymbolList, Changeable

Direct Known Subclasses:

FlexibleAlignment

public abstract class AbstractULAlignment
extends AbstractSymbolList
implements UnequalLengthAlignment

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	AbstractULAlignment.LeftRightLocationComparator Orders by location left to right.
class	AbstractULAlignment.SubULAlignment

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

Modifier and Type	Field and Description
protected Alphabet	alphabet

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

CONTENT

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

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor and Description
AbstractULAlignment()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	debug(String s)
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
Object	leftMost() leftMost and rightMost return labels.
SortedSet	orderedLables(Comparator comp)
Object	rightMost()
Alignment	subAlignment(Set labels, int min, int max) Retreives a subAlignment
Alignment	subAlignment(Set labels, Location loc) Retrieves a subalignment specified by the location.
Symbol	symbolAt(int index) this will return the ambiguity symbol associated with all symbols in that column
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.alignment.UnequalLengthAlignment

locInAlignment

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

getLabels, symbolAt, symbolListForLabel

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

edit, getAlphabet, iterator, length, seqString, subList, subStr, toList

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

alphabet

protected Alphabet alphabet

Constructor Detail

AbstractULAlignment

public AbstractULAlignment()

Method Detail

symbolAt

public Symbol symbolAt(int index)

this will return the ambiguity symbol associated with all symbols in that column

Specified by:

symbolAt in interface SymbolList

Parameters:

index - the offset into this SymbolList

Returns:

the Symbol at that index

labelsAt

public List labelsAt(int column)

Description copied from interface: UnequalLengthAlignment

Returns a list labels, of all seqs that cover that column

Specified by:

labelsAt in interface UnequalLengthAlignment

labelsInRange

public List labelsInRange(Location loc)

Description copied from interface: UnequalLengthAlignment

Returns list of all the labels that intersect that range

Specified by:

labelsInRange in interface UnequalLengthAlignment

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

debug

protected void debug(String s)

leftMost

public Object leftMost()

leftMost and rightMost return labels. If there are more than one that start at the same location it returns the longest, if they are the same length it returns the first one it found;

rightMost

public Object rightMost()

subAlignment

public Alignment subAlignment(Set labels,
                     Location loc)
                       throws IndexOutOfBoundsException

Retrieves a subalignment specified by the location.

WARNING: It is assumed that the location is contiguous. If the location is non-contiguous it may be preferable to use a block iterator to retrieve each sub location independently.

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:

IndexOutOfBoundsException

See Also:

subAlignment(Set labels, int min, int max)

subAlignment

public Alignment subAlignment(Set labels,
                     int min,
                     int max)
                       throws NoSuchElementException

Retreives a subAlignment

Parameters:

labels - the labels of the SymbolLists to be in the Alignment

min - the left most coordinate

max - the right most coordinate

Returns:

an Alignment

Throws:

NoSuchElementException - if one of the values in labels is not in the parent alignment

orderedLables

public SortedSet orderedLables(Comparator comp)