public interface MultipleAlignment extends ScoresCache
Each alignment is described as a collection of:
BlockSet
s that define the aligned positions,
MultipleAlignmentEnsemble
.
Every MultipleAlignment has a MultipleAlignmentEnsemble
as its parent, which contains this informationModifier and Type | Method and Description |
---|---|
void |
clear()
Clear scores and other properties which depend on the specific alignment.
|
MultipleAlignment |
clone()
Creates and returns an identical copy of this alignment, including a deep
clone of all constituent blocks sets.
|
java.util.List<Block> |
getBlocks()
Convenience method to get a list of all blocks from all blocksets
|
java.util.List<BlockSet> |
getBlockSets()
Returns the BlockSet List of the multiple structure alignment.
|
int |
getCoreLength()
Returns the number of aligned residues (columns) without gaps in the alignment:
the sum of all BlockSet core lengths.
|
MultipleAlignmentEnsemble |
getEnsemble()
Returns the parent Ensemble of the MultipleAlignment.
|
java.util.List<Matrix4d> |
getTransformations()
Returns a transformation 4D 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 multiple alignment:
the sum of all BlockSet lengths.
|
void |
setBlockSets(java.util.List<BlockSet> blockSets)
Sets the List of BlockSet List of the specified alignment.
|
void |
setEnsemble(MultipleAlignmentEnsemble parent)
Set the back-reference to its parent Ensemble.
|
void |
setTransformations(java.util.List<Matrix4d> transformations)
Set a new superposition for the structures.
|
int |
size()
Returns the number of aligned structures in the MultipleAlignment.
|
java.lang.String |
toString()
Return a summary of the MultipleAlignment, containing the structures, the lengths and the
cached scores.
|
getScore, getScores, putScore
MultipleAlignment clone()
MultipleAlignmentEnsemble getEnsemble()
#setParent(MultipleAlignmentEnsemble)
void setEnsemble(MultipleAlignmentEnsemble parent)
Neither removes this alignment from its previous ensemble, 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 MultipleAlignmentEnsemble.getEnsemble()
java.util.List<BlockSet> getBlockSets()
#getBlockSetNum()
,
setBlockSets(List)
void setBlockSets(java.util.List<BlockSet> blockSets)
blockSets
- the List of BlockSets that describe the aligned residues.getBlockSets()
java.util.List<Block> getBlocks()
java.util.List<Matrix4d> getTransformations()
Individual BlockSets may override the transformation matrix for particular
substructures. Flexible alignments will generally return null from
this method, while rigid-body methods would typically store the global
matrices here and return null for BlockSet.getTransformations()
.
void setTransformations(java.util.List<Matrix4d> transformations)
This may trigger other properties to update which depend on the superposition. In particular, the list of scores should be reset by implementations after changing the transformation matrices.
matrices
- 4Djava.lang.IllegalArgumentException
- when the size of the alignment and the size of transformations do not match.int size()
length()
,
getCoreLength()
,
#getBlockSetNum()
int length()
#updateLength()
,
getCoreLength()
,
size()
,
#getBlockSetNum()
int getCoreLength()
void clear()
This frees memory and ensures consistency for cached variables.
java.lang.String toString()
toString
in class java.lang.Object