de.bioforscher.singa.structure.algorithms.superimposition.consensus

Class ConsensusAlignment

java.lang.Object

de.bioforscher.singa.structure.algorithms.superimposition.consensus.ConsensusAlignment

public class ConsensusAlignment
extends Object

A consensus alignment of same-sized StructuralMotifs can be used to cluster them according their geometric similarity in a multi-structure alignment manner as described in:

to be published

NOTE: Copies of given StructuralMotifs will be used, so original structures are not altered.

Author:

fk

Method Summary

Modifier and Type	Method and Description
List<Double>	getAlignmentTrace()
List<BinaryTree<ConsensusContainer>>	getClusters()
double	getConsensusScore() Returns the consensus score of this ConsensusAlignment, i.e.
List<BinaryTree<ConsensusContainer>>	getConsensusTrees() Returns all trees that were constructed during this alignment.
double	getNormalizedConsensusScore() Returns the consensus score normalized by number of iterations and the size of the input structures:
BinaryTree<ConsensusContainer>	getTopConsensusTree() Returns the top-level tree of this consensus alignment.
void	writeClusters(Path outputPath) Writes the created clusters to the specified Path.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getAlignmentTrace

public List<Double> getAlignmentTrace()

getClusters

public List<BinaryTree<ConsensusContainer>> getClusters()

writeClusters

public void writeClusters(Path outputPath)
                   throws IOException

Writes the created clusters to the specified Path.

Parameters:

outputPath - the desired output Path

Throws:

IOException - If the path cannot be written to.

getTopConsensusTree

public BinaryTree<ConsensusContainer> getTopConsensusTree()

Returns the top-level tree of this consensus alignment.

Returns:

the top-level tree

getConsensusTrees

public List<BinaryTree<ConsensusContainer>> getConsensusTrees()

Returns all trees that were constructed during this alignment.

Returns:

all trees that were constructed

getConsensusScore

public double getConsensusScore()

Returns the consensus score of this ConsensusAlignment, i.e. the sum of all closest pairs RMSD values.

Returns:

The consensus score

getNormalizedConsensusScore

public double getNormalizedConsensusScore()

Returns the consensus score normalized by number of iterations and the size of the input structures:

Returns:

The normalized consensus score.