procope.methods.interologs.blast
Class BlastHits

java.lang.Object
  procope.methods.interologs.blast.BlastHits

All Implemented Interfaces:

Iterable<BlastHit>

public class BlastHits
extends Object
implements Iterable<BlastHit>

Represents an immutable list of BLAST hits which are normally parsed from a BLAST result file. Contains methods for the detection of best hits and bidirectional best hits.

Author:

Jan Krumsiek

Constructor Summary

BlastHits(Collection<BlastHit> hits)
Creates a new BLAST hits object from a given list of hits.

Method Summary

Collection<Integer>	getAllHitIDs() Returns al ist of all proteins which were hit at least once in the database.
Collection<Integer>	getAllQueryIDs() Returns a list of all proteins used as query in this BLAST result
Collection<BlastHit>	getBestHits(Integer queryID) Returns all best hits for a given query.
ProteinNetwork	getBidirectionalBestHits(BlastHits backward, BlastBBHConstraints constraints) Calculate bidirectional best hits (BBHs).
BlastHit	getHit(int query, int hit) Retrieves a specific BLAST hit from the result.
Collection<BlastHit>	getHitsPerQuery(int queryID) Returns all hits for a given query protein
int	getNumberOfHits() Returns the number of hits in this BLAST result
Iterator<BlastHit>	iterator() Returns an iterator over all BLAST hits contained in this set

Methods inherited from class java.lang.Object

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

Constructor Detail

BlastHits

public BlastHits(Collection<BlastHit> hits)

Creates a new BLAST hits object from a given list of hits.

Parameters:

hits - the BLAST hits list with which the object is initialized

Method Detail

iterator

public Iterator<BlastHit> iterator()

Returns an iterator over all BLAST hits contained in this set

Specified by:

iterator in interface Iterable<BlastHit>

getHitsPerQuery

public Collection<BlastHit> getHitsPerQuery(int queryID)

Returns all hits for a given query protein

Parameters:

queryID - the protein used as query in the BLAST run

Returns:

all hits for the given query

getBestHits

public Collection<BlastHit> getBestHits(Integer queryID)

Returns all best hits for a given query. A best hit is a hit in the BLAST result with the best score for that query. Eventual multiple best always have the same score.

Parameters:

queryID - the query protein for which the best hits will be retrieved

Returns:

list of best hits for that query

getAllQueryIDs

public Collection<Integer> getAllQueryIDs()

Returns a list of all proteins used as query in this BLAST result

Returns:

list of all query proteins

getAllHitIDs

public Collection<Integer> getAllHitIDs()

Returns al ist of all proteins which were hit at least once in the database.

Returns:

list of all hit proteins

getNumberOfHits

public int getNumberOfHits()

Returns the number of hits in this BLAST result

Returns:

number of hits in the list

getBidirectionalBestHits

public ProteinNetwork getBidirectionalBestHits(BlastHits backward,
                                               BlastBBHConstraints constraints)

Calculate bidirectional best hits (BBHs). A BBH is contained of two proteins which mutually identify each other as the best-scoring blast hit in the database. The calculation if BBHs requires another BLAST result in the backward direction (query as database and database as query).

Note: If proteins have multiple best hits there might be more than one BBH associated with a single protein.

Parameters:

backward - BLAST result which should have used the query of this result as the database and the database of this result as the query

constraints - constraints for filtering BBHs or null if all identified BBHs should be returned

Returns:

bipartite network containing one edge for each identified BBH.

getHit

public BlastHit getHit(int query,
                       int hit)

Retrieves a specific BLAST hit from the result.

Parameters:

query - query protein

hit - hit (database) protein

Returns:

the hit if it exists or null if not