Uses of Class
methods.interologs.blast.BlastHits

Packages that use BlastHits
methods.interologs   
methods.interologs.blast   
 

Uses of BlastHits in methods.interologs
 

Constructors in methods.interologs with parameters of type BlastHits
EvalueInterologScorer(BlastHits forward, BlastHits backward)
          Creates a new e-value interolog scorer from the given BLAST results.
 

Uses of BlastHits in methods.interologs.blast
 

Methods in methods.interologs.blast that return BlastHits
static BlastHits BlastHitFileParser.parseBlastHits(File hitfile)
          Parse BLAST hits from a given BLAST hit file in tabular format.
static BlastHits BlastHitFileParser.parseBlastHits(File hitfile, String organism1, String organism2)
          Parse BLAST hits from a given BLAST hit file in tabular format.
static BlastHits BlastHitFileParser.parseBlastHits(InputStream input)
          Parse BLAST hits from a given input stream.
static BlastHits BlastHitFileParser.parseBlastHits(InputStream input, String organism1, String organism2)
          Parse BLAST hits from a given input stream.
static BlastHits BlastHitFileParser.parseBlastHits(String hitfile)
          Parse BLAST hits from a given BLAST hit file in tabular format.
static BlastHits BlastHitFileParser.parseBlastHits(String hitfile, String organism1, String organism2)
          Parse BLAST hits from a given BLAST hit file in tabular format.
 

Methods in methods.interologs.blast with parameters of type BlastHits
 ProteinNetwork BlastHits.getBidirectionalBestHits(BlastHits backward, BlastBBHConstraints constraints)
          Calculate bidirectional best hits (BBHs).