Uses of Class
procope.methods.interologs.Sequences

Packages that use Sequences
procope.methods.interologs   
procope.methods.interologs.blast   
procope.tools   
 

Uses of Sequences in procope.methods.interologs
 

Methods in procope.methods.interologs that return Sequences
static Sequences FASTAParser.loadSequences(File file)
          Loads sequences from a given multi-FASTA file
static Sequences FASTAParser.loadSequences(InputStream input)
          Loads sequences from a given InputStream, requires multi-FASTA format data
static Sequences FASTAParser.loadSequences(String file)
          Loads sequences from a given multi-FASTA file
 

Methods in procope.methods.interologs with parameters of type Sequences
 void Sequences.addAll(Sequences toAdd)
          Adds all sequences of another Sequences object to this set.
 

Uses of Sequences in procope.methods.interologs.blast
 

Constructors in procope.methods.interologs.blast with parameters of type Sequences
BlastBBHAlignmentLengthConstraint(Sequences sequencePool, float minAlign)
          Create new alignment length object.
 

Uses of Sequences in procope.tools
 

Methods in procope.tools that return Sequences
 Sequences SequenceAligner.getSequencePool()
           
 

Methods in procope.tools with parameters of type Sequences
 void SequenceAligner.addToSequencePool(Sequences sequences)
          Add a set of sequences to the sequence pool of this aligner.