public interface BlockSet extends ScoresCache
Block
s.
It allows non-sequential alignments and circular permutations,
thanks to the multiple Block
format.
Every BlockSet has a unique transformation 4D matrix, which describes the 3D superimposition of the structures in this particular region of the alignment.
A collection of BlockSets, in a MultipleAlignment
, allows the description
of multiple alignments with various flexible parts.
Every BlockSet object is part of a MultipleAlignment
instance, its parent.
Modifier and Type | Method and Description |
---|---|
void |
clear()
Clear scores and other properties which depend on the specific alignment.
|
BlockSet |
clone()
Creates and returns an identical copy of this blockset, including a deep
clone of all constituent
Block s. |
java.util.List<Block> |
getBlocks()
Returns the List of alignment Blocks of the BlockSet.
|
int |
getCoreLength()
Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all Block core lengths.
|
MultipleAlignment |
getMultipleAlignment()
Returns the parent MultipleAlignment of the BlockSet.
|
java.util.List<Matrix4d> |
getTransformations()
Returns a transformation matrix for each structure giving the
3D superimposition information of the multiple structure alignment.
|
int |
length()
Returns the total number of aligned residues (columns) in the alignment: the sum of all Block lengths.
|
void |
setBlocks(java.util.List<Block> blocks)
Set the List of alignment Blocks of the BlockSet.
|
void |
setMultipleAlignment(MultipleAlignment parent)
Set the back-reference to its parent MultipleAlignment.
|
void |
setTransformations(java.util.List<Matrix4d> transformations)
Set a new superposition for the structures.
|
int |
size()
Returns the number of aligned structures in the BlockSet.
|
getScore, getScores, putScore
BlockSet clone()
Block
s.MultipleAlignment getMultipleAlignment()
setMultipleAlignment(MultipleAlignment)
void setMultipleAlignment(MultipleAlignment parent)
Neither removes this BlockSet from its previous alignment, if any, nor adds it to the new parent. Calling code should assure that links to and from the ensemble are consistent and free of memory leaks.
parent
- the parent MultipleAlignment.getMultipleAlignment()
java.util.List<Block> getBlocks()
setBlocks(List)
void setBlocks(java.util.List<Block> blocks)
Also calls Block.setBlockSet(BlockSet)
for each argument
blocks
- List of alignment Blocks.getBlocks()
java.util.List<Matrix4d> getTransformations()
void setTransformations(java.util.List<Matrix4d> transformations)
matrices
- int length()
#updateLength()
,
getCoreLength()
,
size()
,
#getBlockNum()
int getCoreLength()
int size()
length()
,
#getBlockNum()
void clear()
Recursively clears the memeber Blocks.