MultipleAlignment (biojava-structure 4.2.0 API)

All Superinterfaces:

ScoresCache

All Known Implementing Classes:

MultipleAlignmentImpl
```
public interface MultipleAlignment
extends ScoresCache
```
A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type.
Each alignment is described as a collection of:
- BlockSets that define the aligned positions and 3D superposition,
- Structure identifiers (i,e. Atom arrays, structure names),
- Creation properties (algorithm, version, etc).
A collection of MultipleAlignments that share the same structures and creation properties are part of the same MultipleAlignmentEnsemble. Every MultipleAlignment has a MultipleAlignmentEnsemble as its parent, which contains the shared meta-information.
Since:

4.1.0

Author:

Aleix Lafita, Spencer Bliven

Method Summary

Methods
Modifier 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 copy of all constituent BlockSets.
`List<Atom[]>`	`getAtomArrays()` Returns the array of Atoms for each structure from its parent Ensemble.
`Block`	`getBlock(int index)` Returns the Block with the specified index of the MultipleAlignment.
`List<Block>`	`getBlocks()` Convenience method to get a List of all Blocks from all BlockSets.
`BlockSet`	`getBlockSet(int index)` Returns the BlockSet with the specified index of the MultipleAlignment.
`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.
`StructureIdentifier`	`getStructureIdentifier(int index)` Returns the StructureIdentifier associated with the structure index from its parent Ensemble.
`int`	`length()` Returns the total number of aligned residues (columns) in the multiple alignment: the sum of all BlockSet lengths.
`void`	`setBlockSets(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.
`int`	`size()` Returns the number of aligned structures in the MultipleAlignment.
`String`	`toString()` Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores.

Methods inherited from interface org.biojava.nbio.structure.align.multiple.ScoresCache
getScore, getScores, putScore

- Method Detail
  - clone
```
MultipleAlignment clone()
```
    Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.
    
    Returns:
    MultipleAlignment identical copy of this object.
  - getEnsemble
```
MultipleAlignmentEnsemble getEnsemble()
```
    Returns the parent Ensemble of the MultipleAlignment. Returns null if there is no referenced object.
    
    Returns:
    MultipleAlignmentEnsemble the parent MultipleAlignment of the BlockSet, or null.
    See Also:
    setEnsemble(MultipleAlignmentEnsemble)
  - setEnsemble
```
void setEnsemble(MultipleAlignmentEnsemble parent)
```
    Set the back-reference to its parent Ensemble.
    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.
    
    Parameters:
    parent - the parent MultipleAlignmentEnsemble.
    See Also:
    getEnsemble()
  - getBlockSets
```
List<BlockSet> getBlockSets()
```
    Returns the BlockSet List of the multiple structure alignment. Initializes the variable if it is null.
    
    Returns:
    List of BlockSets that describe the aligned residues of all the structures.
    See Also:
    getBlocks(), setBlockSets(List)
  - getBlockSet
```
BlockSet getBlockSet(int index)
```
    Returns the BlockSet with the specified index of the MultipleAlignment. Throws an Exception if the index is out of bounds, like accessing a normal List.
    
    Parameters:
    index - of the BlockSet
    
    Returns:
    BlockSets at the specified index
    See Also:
    getBlocks(), getBlockSets()
  - setBlockSets
```
void setBlockSets(List<BlockSet> blockSets)
```
    Sets the List of BlockSet List of the specified alignment.
    
    Parameters:
    blockSets - the List of BlockSets that describe the aligned residues.
    See Also:
    getBlockSets()
  - getBlocks
```
List<Block> getBlocks()
```
    Convenience method to get a List of all Blocks from all BlockSets. Modifications of this List will not alter the MultipleAlignment, but modifications to the Blocks will.
    
    Returns:
    List of Blocks
    See Also:
    getBlockSets()
  - getBlock
```
Block getBlock(int index)
```
    Returns the Block with the specified index of the MultipleAlignment. Throws an Exception if the index is out of bounds, like accessing a normal List.
    
    Parameters:
    index - of the BlockSet
    
    Returns:
    Block at the specified index
    See Also:
    getBlocks(), getBlockSets()
  - getAtomArrays
```
List<Atom[]> getAtomArrays()
```
    Returns the array of Atoms for each structure from its parent Ensemble. Throws an Exception if the parent ensemble is null or the Atom variables are not previously set.
    
    Returns:
    List of Atom arrays
    See Also:
    getEnsemble()
  - getStructureIdentifier
```
StructureIdentifier getStructureIdentifier(int index)
```
    Returns the StructureIdentifier associated with the structure index from its parent Ensemble. Throws an Exception if the parent ensemble is null or the StructureIdentifiers are not previously set.
    
    Returns:
    StructureIdentifier
    See Also:
    getEnsemble()
  - size
```
int size()
```
    Returns the number of aligned structures in the MultipleAlignment.
    
    Returns:
    int number of aligned structures
    See Also:
    length(), getCoreLength()
  - length
```
int length()
```
    Returns the total number of aligned residues (columns) in the multiple alignment: the sum of all BlockSet lengths.
    
    Returns:
    int the total number of aligned residues in the alignment.
    See Also:
    getCoreLength(), size()
  - getCoreLength
```
int getCoreLength()
```
    Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all BlockSet core lengths.
    
    Returns:
    int the total number of aligned residues.
    See Also:
    length(), size()
  - clear
```
void clear()
```
    Clear scores and other properties which depend on the specific alignment. This frees memory and ensures consistency of the cached variables.
    Recursively clears member BlockSets.
  - toString
```
String toString()
```
    Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores. Can be used as a header for the differnt display options.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    String header summary of the MultipleAlignment

Interface MultipleAlignment

Method Summary

Methods inherited from interface org.biojava.nbio.structure.align.multiple.ScoresCache

Method Detail

clone

getEnsemble

setEnsemble

getBlockSets

getBlockSet

setBlockSets

getBlocks

getBlock

getAtomArrays

getStructureIdentifier

size

length

getCoreLength

clear

toString