info.bioinfweb.commons.bio.biojava3.alignment.template

Interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

All Known Implementing Classes:

SimpleAlignment

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

Classes implementing this interface represent an aligned set of sequences. Additionally the alignment can be annotated by character sets as defined in the Nexus format.

Although this interface is based on BioJava 3, it differs from Profile since alignment gaps are treated the same way as nucleotides here. (Note that a compound set allowing gaps must be use for this to work.) In the future there might be an alternative version extending Profile.

Author:

Ben Stöver

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()
void	clear()
boolean	containsAllNames(java.util.Collection<?> c)
boolean	containsName(java.lang.String name)
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)
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)
void	replace(int index, S sequence)
void	replace(java.lang.String name, S sequence)
boolean	sequncesEqual(Alignment<?,?> other)
int	size()

Method Detail

getCharSets

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

addCharSet

void addCharSet(CharSet charSet)

addAllCharSets

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

add

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

add

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

replace

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

replace

void replace(int index,
             S sequence)

clear

void clear()

containsName

boolean containsName(java.lang.String name)

containsAllNames

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

getSequence

S getSequence(int index)

getSequence

S getSequence(java.lang.String name)

indexByName

int indexByName(java.lang.String name)

nameByIndex

java.lang.String nameByIndex(int index)

isEmpty

boolean isEmpty()

nameIterator

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

remove

S remove(int index)

remove

boolean remove(java.lang.String name)

size

int size()

maxSequenceLength

int maxSequenceLength()

moveAllCharSetPositions

void moveAllCharSetPositions(int start,
                             int offset)

renameSequence

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

renameSequences

void renameSequences(UniqueNameMap nameMap)

asMap

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

sequncesEqual

boolean sequncesEqual(Alignment<?,?> other)