Interface Blat

All Known Implementing Classes:
ShellDelegatingBlat
public interface Blat

  • Field Details

    • DEFAULT_BLAT_SCORE_THRESHOLD

      static final double DEFAULT_BLAT_SCORE_THRESHOLD
      This value is basically a threshold fraction of aligned bases in the query. Hits below this score are simply not reported. BlatResult has implementation of score computation.
      See Also:

  • Method Details

    • blatQuery

      List<BlatResult> blatQuery(BioSequence b) throws IOException
      Run a BLAT search using the gfClient.
      Parameters:
      b - The genome is inferred from the Taxon held by the sequence.
      Returns:
      Collection of BlatResult objects.
      Throws:
      IOException - when there are IO problems.

    • blatQuery

      List<BlatResult> blatQuery(BioSequence b, Taxon taxon, boolean sensitive) throws IOException
      Run a BLAT search using the gfClient.
      Parameters:
      b - The genome is inferred from the Taxon held by the sequence.
      taxon - taxon
      sensitive - if true use the more sensitive gfServer, if available.
      Returns:
      Collection of BlatResult objects.
      Throws:
      IOException - when there are IO problems.

    • blatQuery

      Map<BioSequence, List<BlatResult>> blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon) throws IOException
      Parameters:
      sequences - The genome is inferred from the Taxon held by the sequence.
      sensitive - if true use the more sensitive gfServer, if available.
      taxon - The taxon whose database will be searched.
      Returns:
      map of the input sequences to a corresponding collection of blat result(s)
      Throws:
      IOException - when there are IO problems.

    • blatQuery

      Map<BioSequence, List<BlatResult>> blatQuery(Collection<BioSequence> sequences, Taxon taxon) throws IOException
      Throws:
      IOException

    • setBlatScoreThreshold

      void setBlatScoreThreshold(double blatScoreThreshold)
      Set the blat score threshold to use.

      Defaults to DEFAULT_BLAT_SCORE_THRESHOLD.