public interface Alignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>
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
.
Modifier and Type | Method and Description |
---|---|
void |
add(int index,
String name,
S sequence) |
void |
add(String name,
S sequence) |
void |
addAllCharSets(Collection<CharSet> collection) |
void |
addCharSet(CharSet charSet) |
Map<String,S> |
asMap() |
void |
clear() |
boolean |
containsAllNames(Collection<?> c) |
boolean |
containsName(String name) |
Map<String,CharSet> |
getCharSets() |
S |
getSequence(int index) |
S |
getSequence(String name) |
int |
indexByName(String name) |
boolean |
isEmpty() |
int |
maxSequenceLength() |
void |
moveAllCharSetPositions(int start,
int offset) |
String |
nameByIndex(int index) |
Iterator<String> |
nameIterator() |
S |
remove(int index) |
boolean |
remove(String name) |
void |
renameSequence(String currentName,
String newName) |
void |
renameSequences(UniqueNameMap nameMap) |
void |
replace(int index,
S sequence) |
void |
replace(String name,
S sequence) |
boolean |
sequncesEqual(Alignment<?,?> other) |
int |
size() |
Map<String,CharSet> getCharSets()
void addCharSet(CharSet charSet)
void addAllCharSets(Collection<CharSet> collection)
void clear()
boolean containsName(String name)
boolean containsAllNames(Collection<?> c)
S getSequence(int index)
S getSequence(String name)
int indexByName(String name)
String nameByIndex(int index)
boolean isEmpty()
Iterator<String> nameIterator()
int size()
int maxSequenceLength()
void moveAllCharSetPositions(int start, int offset)
void renameSequence(String currentName, String newName)
void renameSequences(UniqueNameMap nameMap)
boolean sequncesEqual(Alignment<?,?> other)