public interface MultipleAlignmentEnsemble extends ScoresCache
MultipleAlignment
s that share the same structures (Atoms)
and creation properties (algorithm, version, creation time, etc.).
This class is the top level of the hierarchy and allows the storage of a set of alignment alternatives created by a multiple structure alignment algorithm, so that only one object is returned with more than one alignment option.
Modifier and Type | Method and Description |
---|---|
void |
addMultipleAlignment(MultipleAlignment alignment)
Add a new MultipleAlignment to the end of the ensemble and set its
parent ensemble to this.
|
void |
clear()
Clear scores and other properties which depend on the specific alignment.
|
MultipleAlignmentEnsemble |
clone()
Creates and returns an identical copy of this ensemble, including a deep
clone of all constituent alignments.
|
java.lang.String |
getAlgorithmName()
Returns the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
|
int |
getAlignmentNum()
Return the number of alternative alignments stored in the Ensemble.
|
java.util.List<Atom[]> |
getAtomArrays()
Get an array of representative atoms for each structure (CA atoms for proteins).
|
java.lang.Long |
getCalculationTime()
public
Returns the running time of the structure alignment calculation, in milliseconds.
|
java.util.List<Matrix> |
getDistanceMatrix()
Returns the List containing the interatomic distance Matrix of each structure.
|
java.lang.Long |
getIoTime()
Returns the io time for this object, in milliseconds.
|
java.util.List<MultipleAlignment> |
getMultipleAlignments()
Returns the List of MultipleAlignments in the MultipleAlignmentEnsemble object.
|
java.util.List<java.lang.String> |
getStructureNames()
Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
|
java.lang.String |
getVersion()
Returns the version of the algorithm used to generate the MultipleAlignment objects.
|
void |
setAlgorithmName(java.lang.String algorithmName)
Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
|
void |
setAtomArrays(java.util.List<Atom[]> atomArrays)
Sets the List of Atom arrays.
|
void |
setCalculationTime(java.lang.Long millis)
Set the time needed to calculate this alignment
|
void |
setIoTime(java.lang.Long millis)
Set the IO time to load this object
|
void |
setMultipleAlignments(java.util.List<MultipleAlignment> multipleAlignments)
Set the List of MultipleAlignments in the MultipleAlignmentEnsemble object.
|
void |
setStructureNames(java.util.List<java.lang.String> structureNames)
Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
|
void |
setVersion(java.lang.String version)
Sets the version of the algorithm used to generate the MultipleAlignment objects.
|
int |
size()
Returns the number of aligned structures in the MultipleAlignments.
|
getScore, getScores, putScore
MultipleAlignmentEnsemble clone()
java.lang.String getAlgorithmName()
setAlgorithmName(String)
void setAlgorithmName(java.lang.String algorithmName)
algorithmName
- name of the algorithm.getAlgorithmName()
java.lang.String getVersion()
setVersion(String)
void setVersion(java.lang.String version)
version
- the version of the algorithm.getVersion()
java.util.List<java.lang.String> getStructureNames()
The names are structure identifiers of the structures. They are in the same order as in the alignment Blocks (same index number for same structure).
setStructureNames(List)
,
getAtomArrays()
void setStructureNames(java.util.List<java.lang.String> structureNames)
The names are structure identifiers of the structures.
structureNames
- names of the structures, structure identifiersgetStructureNames()
,
setAtomArrays(List)
java.util.List<Atom[]> getAtomArrays()
Atoms should be unrotated. Thus, to obtain a superimposed set of structures, each atom array should be cloned and then rotated according to the transformation matrix.
If atoms have not previously been set using setAtomArrays(List)
,
attempts to load representative atoms based on getStructureNames()
.
If it fails to load the Atoms it gives a NullPointerException before returning null.
setAtomArrays(List)
void setAtomArrays(java.util.List<Atom[]> atomArrays)
setStructureNames(List)
Setting the atom arrays to null will cause them to be automatically
regenerated based on getStructureNames()
during the next call to
getAtomArrays()
atomArrays
- the List of representative (C-alpha) atom arraysgetAtomArrays()
,
setStructureNames(List)
int getAlignmentNum()
size()
java.util.List<Matrix> getDistanceMatrix()
#updateDistanceMatrix()
java.util.List<MultipleAlignment> getMultipleAlignments()
#setMultipleAlignments()
,
#getOptimalMultipleAlignment()
void setMultipleAlignments(java.util.List<MultipleAlignment> multipleAlignments)
List
- of MultipleAlignments that are part of the ensemble.getMultipleAlignments()
,
#getOptimalMultipleAlignment()
void addMultipleAlignment(MultipleAlignment alignment)
alignment
- int size()
getStructureNames()
,
getAtomArrays()
java.lang.Long getIoTime()
void setIoTime(java.lang.Long millis)
millis
- java.lang.Long getCalculationTime()
getIoTime()L
void setCalculationTime(java.lang.Long millis)
millis
- void clear()
This can free memory and ensures consistency for cached variables.