info.bioinfweb.commons.bio.biojava3.alignment

Class SimpleAlignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

java.lang.Object

info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment<S,C>

All Implemented Interfaces:

Alignment<S,C>

public class SimpleAlignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>
extends java.lang.Object
implements Alignment<S,C>

Default implementation of Alignment.

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
SimpleAlignment()

Method Summary

Modifier and Type	Method and Description
void	add(int index, java.lang.String name, S sequence)
void	add(java.lang.String name, S sequence)
void	addAllCharSets(java.util.Collection<CharSet> collection)
void	addCharSet(CharSet charSet)
java.util.Map<java.lang.String,S>	asMap() Returns this alignment as a map with sequence names as keys and sequences as values.
void	clear()
boolean	containsAllNames(java.util.Collection<?> c)
boolean	containsName(java.lang.String name)
boolean	equals(java.lang.Object other) Checks if this alignment contains the same sequences (name and sequence) and the same character sets (names and positions) as the specified one.
java.util.Map<java.lang.String,CharSet>	getCharSets()
S	getSequence(int index)
S	getSequence(java.lang.String name)
int	indexByName(java.lang.String name)
boolean	isEmpty()
int	maxSequenceLength()
void	moveAllCharSetPositions(int start, int offset) Moves all contained character sets by the specified offset.
java.lang.String	nameByIndex(int index)
java.util.Iterator<java.lang.String>	nameIterator()
S	remove(int index)
boolean	remove(java.lang.String name)
void	renameSequence(java.lang.String currentName, java.lang.String newName)
void	renameSequences(UniqueNameMap nameMap) Changes the sequence names in this alignment according to the parameters of the specified name map and stores in the old and new names in map.
void	replace(int index, S sequence)
void	replace(java.lang.String name, S sequence)
boolean	sequncesEqual(Alignment<?,?> other) Checks if this alignment contains the same sequences (name and sequence) as the specified one.
int	size()

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleAlignment

public SimpleAlignment()

Method Detail

getCharSets

public java.util.Map<java.lang.String,CharSet> getCharSets()

Specified by:

getCharSets in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

addCharSet

public void addCharSet(CharSet charSet)

Specified by:

addCharSet in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

addAllCharSets

public void addAllCharSets(java.util.Collection<CharSet> collection)

Specified by:

addAllCharSets in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

add

public void add(java.lang.String name,
                S sequence)

Specified by:

add in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

add

public void add(int index,
                java.lang.String name,
                S sequence)

Specified by:

add in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

replace

public void replace(java.lang.String name,
                    S sequence)

Specified by:

replace in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

replace

public void replace(int index,
                    S sequence)

Specified by:

replace in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

clear

public void clear()

Specified by:

clear in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

containsName

public boolean containsName(java.lang.String name)

Specified by:

containsName in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

containsAllNames

public boolean containsAllNames(java.util.Collection<?> c)

Specified by:

containsAllNames in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

getSequence

public S getSequence(int index)

Specified by:

getSequence in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

getSequence

public S getSequence(java.lang.String name)

Specified by:

getSequence in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

indexByName

public int indexByName(java.lang.String name)

Specified by:

indexByName in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

nameByIndex

public java.lang.String nameByIndex(int index)

Specified by:

nameByIndex in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

nameIterator

public java.util.Iterator<java.lang.String> nameIterator()

Specified by:

nameIterator in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

remove

public S remove(int index)

Specified by:

remove in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

remove

public boolean remove(java.lang.String name)

Specified by:

remove in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

size

public int size()

Specified by:

size in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

maxSequenceLength

public int maxSequenceLength()

Specified by:

maxSequenceLength in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

moveAllCharSetPositions

public void moveAllCharSetPositions(int start,
                                    int offset)

Moves all contained character sets by the specified offset.

Specified by:

moveAllCharSetPositions in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

See Also:

NonOverlappingIntervalList.movePositions(int, int)

renameSequence

public void renameSequence(java.lang.String currentName,
                           java.lang.String newName)

Specified by:

renameSequence in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

renameSequences

public void renameSequences(UniqueNameMap nameMap)

Changes the sequence names in this alignment according to the parameters of the specified name map and stores in the old and new names in map. (Previous contents of the map are deleted.)

Specified by:

renameSequences in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

asMap

public java.util.Map<java.lang.String,S> asMap()

Returns this alignment as a map with sequence names as keys and sequences as values. Note that the returned map is read only. (It might throw an exception if modifying methods are called.)

Specified by:

asMap in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

See Also:

Alignment.asMap()

sequncesEqual

public boolean sequncesEqual(Alignment<?,?> other)

Checks if this alignment contains the same sequences (name and sequence) as the specified one. (Ambiguity codes are not checked for equivalence. Character sets are not taken into account.)

Specified by:

sequncesEqual in interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

Parameters:

other -

Returns:

equals

public boolean equals(java.lang.Object other)

Checks if this alignment contains the same sequences (name and sequence) and the same character sets (names and positions) as the specified one. (Ambiguity codes are not checked for equivalence.)

Overrides:

equals in class java.lang.Object

See Also:

Object.equals(java.lang.Object)