Class BiojavaSequence

java.lang.Object
net.bioclipse.core.domain.BioObject
net.bioclipse.biojava.domain.BiojavaSequence
All Implemented Interfaces:
net.bioclipse.core.domain.IBioObject, net.bioclipse.core.domain.ISequence, org.eclipse.core.runtime.IAdaptable
Direct Known Subclasses:
BiojavaDNA, BiojavaProtein

public class BiojavaSequence extends net.bioclipse.core.domain.BioObject implements net.bioclipse.core.domain.ISequence
Author:
jonalv, olas
  • Constructor Details

    • BiojavaSequence

      public BiojavaSequence(org.biojava.bio.seq.Sequence sequence)
      Create a BiojavaSequence from a Sequence.
      Parameters:
      sequence - sequence to create the object from
    • BiojavaSequence

      public BiojavaSequence()
  • Method Details

    • getPlainSequence

      public String getPlainSequence()
      Specified by:
      getPlainSequence in interface net.bioclipse.core.domain.ISequence
    • toFasta

      public String toFasta()
      Convert RichSequence to FASTA and return as String.
      Specified by:
      toFasta in interface net.bioclipse.core.domain.ISequence
    • getParsedResource

      public Object getParsedResource()
      Returns the RichSequence
      Specified by:
      getParsedResource in interface net.bioclipse.core.domain.ISequence
    • setRichSequence

      public void setRichSequence(org.biojavax.bio.seq.RichSequence richSequence)
    • getName

      public String getName()
      Specified by:
      getName in interface net.bioclipse.core.domain.ISequence
    • getAdapter

      public Object getAdapter(Class adapter)
      Specified by:
      getAdapter in interface org.eclipse.core.runtime.IAdaptable
      Overrides:
      getAdapter in class net.bioclipse.core.domain.BioObject