Class SequenceDBSearchResult

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.search.SequenceDBSearchResult
All Implemented Interfaces:
Annotatable, SeqSimilaritySearchResult, Changeable

Deprecated.
SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.
SequenceDBSearchResult objects represent a result of a search of a SymbolList against the sequences within a SequenceDB object. The core data (query sequence, database, search parameters, hits) have accessors, while supplementary data are stored in the Annotation object. Supplementary data are typically the more loosely formatted details which vary from one search program to another (and between versions of those programs).
Since:
1.1
Author:
Keith James, Matthew Pocock
See Also:
  • Field Details

  • Constructor Details

    • SequenceDBSearchResult

      public SequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation)
      Deprecated.
      Creates a new SequenceDBSearchResult.
      Parameters:
      querySequence - a Sequence.
      sequenceDB - a SequenceDB.
      searchParameters - a Map.
      hits - a List.
      annotation - an Annotation.
  • Method Details

    • getQuerySequence

      Deprecated.
      Description copied from interface: SeqSimilaritySearchResult
      Returns the query sequence which was used to perform the search.
      Specified by:
      getQuerySequence in interface SeqSimilaritySearchResult
      Returns:
      the Sequence object used to search the SequenceDB. Never returns null.
    • getSequenceDB

      Deprecated.
      Description copied from interface: SeqSimilaritySearchResult
      Returns the sequence database against which the search was performed.
      Specified by:
      getSequenceDB in interface SeqSimilaritySearchResult
      Returns:
      the SequenceDB object against which the search was carried out. Never returns null.
    • getSearchParameters

      Deprecated.
      Description copied from interface: SeqSimilaritySearchResult
      Returns the search parameters used in the search that produced this search result.
      Specified by:
      getSearchParameters in interface SeqSimilaritySearchResult
      Returns:
      the (immutable) search parameter Map object. May return null.
    • getHits

      public List getHits()
      Deprecated.
      Description copied from interface: SeqSimilaritySearchResult
      Return all hits in this sequence similarity search result. The hits are sorted from best to worst.
      Specified by:
      getHits in interface SeqSimilaritySearchResult
      Returns:
      an (immutable) List of SeqSimilaritySearchHit objects containing all hits in the search result. Never returns null but may return an empty list.
    • getAnnotation

      Deprecated.
      getAnnotation returns the Annotation associated with this hit.
      Specified by:
      getAnnotation in interface Annotatable
      Returns:
      an Annotation.
    • equals

      public boolean equals(Object other)
      Deprecated.
      Overrides:
      equals in class Object
    • hashCode

      public int hashCode()
      Deprecated.
      Overrides:
      hashCode in class Object
    • toString

      public String toString()
      Deprecated.
      Overrides:
      toString in class Object
    • getChangeSupport

      Deprecated.
      Description copied from class: AbstractChangeable
      Called to retrieve the ChangeSupport for this object.

      Your implementation of this method should have the following structure:

       ChangeSupport cs = super.getChangeSupport(ct);
      
       if(someForwarder == null invalid input: '&'invalid input: '&' ct.isMatching(SomeInterface.SomeChangeType)) {
         someForwarder = new ChangeForwarder(...
      
         this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
       }
      
       return cs;
       
      It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register invalid input: '&' unregister the forwarder in the code that does the ChangeEvent handling in setter methods.
      Overrides:
      getChangeSupport in class AbstractChangeable