Uses of Class
data.Sequences

Packages that use Sequences
data   
methods.interologs.blast   
tools   
 

Uses of Sequences in data
 

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

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

Uses of Sequences in methods.interologs.blast
 

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

Uses of Sequences in tools
 

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

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