Uses of Class
methods.interologs.blast.BlastHit

Packages that use BlastHit
methods.interologs.blast   
 

Uses of BlastHit in methods.interologs.blast
 

Methods in methods.interologs.blast that return BlastHit
 BlastHit BlastHits.getHit(int query, int hit)
          Retrieves a specific BLAST hit from the result.
 

Methods in methods.interologs.blast that return types with arguments of type BlastHit
 Collection<BlastHit> BlastHits.getBestHits(Integer queryID)
          Returns all best hits for a given query.
 Collection<BlastHit> BlastHits.getHitsPerQuery(int queryID)
          Returns all hits for a given query protein
 Iterator<BlastHit> BlastHits.iterator()
          Returns an iterator over all BLAST hits contained in this set
 

Methods in methods.interologs.blast with parameters of type BlastHit
 boolean BlastBBHConstraints.acceptBBH(int protein1, int protein2, BlastHit forwardHit, BlastHit backwardHit)
          Function which is called by the BBH calculator to ask whether a given BBH is accepted or not.
 boolean BlastBBHAlignmentLengthConstraint.acceptBBH(int protein1, int protein2, BlastHit forwardHit, BlastHit backwardHit)
          Accepts a BBH if the give minimum fraction of both protein sequences is covered by the BLAST alignment.
 int BlastHit.compareTo(BlastHit o)
          Orders the hits by their hit ID.
 

Constructor parameters in methods.interologs.blast with type arguments of type BlastHit
BlastHits(Collection<BlastHit> hits)
          Creates a new BLAST hits object from a given list of hits.