Class RemoteQBlastAlignmentProperties

java.lang.Object
org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
All Implemented Interfaces:
Serializable, RemotePairwiseAlignmentProperties

This class implements RemotePairwiseAlignmentProperties by specifying several convenient methods used to wrap the addition of Blast alignment parameters.
Since:
1.8
Author:
Sylvain Foisy, Diploide BioIT
See Also:
  • Constructor Details

  • Method Details

    • getBlastProgram

      This method returns the value of the program used for this particular blast run.
      Returns:
      program :the name of the blastall program used.
    • setBlastProgram

      public void setBlastProgram(String program) throws BioException
      This method set the program to be use with blastall. This method does a validation before running on the valid blastall programs: blastn / blastp / blastx / tblastn / tblastx
      Parameters:
      program - : one of blastall programs
      Throws:
      BioException - if the named program is not a valid blastall options
    • getBlastDatabase

      This method returns the value of the database used for this particular blast run.
      Returns:
      db :the name of the database used
    • setBlastDatabase

      public void setBlastDatabase(String db)
      This method set the database to be use with blastall
      Parameters:
      db - :a valid name to a NCBI Blastable database
    • setAdvancedOptions

      public void setAdvancedOptions(String aStr)

      This method is to be used if a request is to use non-default values at submission. According to QBlast info, the accepted parameters for PUT requests are:

      • -G: cost to create a gap. Default = 5 (nuc-nuc) / 11 (protein) / non-affine for megablast
      • -E: Cost to extend a gap. Default = 2 (nuc-nuc) / 1 (protein) / non-affine for megablast
      • -r: integer to reward for match. Default = 1
      • -q: negative integer for penalty to allow mismatch. Default = -3
      • -e: expectation value. Default = 10.0
      • -W: word size. Default = 3 (proteins) / 11 (nuc-nuc) / 28 (megablast)
      • -y: dropoff for blast extensions in bits, using default if not specified. Default = 20 for blastn, 7 for all others (except megablast for which it is not applicable).
      • -X: X dropoff value for gapped alignment, in bits. Default = 30 for blastn/megablast, 15 for all others.
      • -Z: final X dropoff value for gapped alignement, in bits. Default = 50 for blastn, 25 for all others (except megablast for which it is not applicable)
      • -P: equals 0 for multiple hits 1-pass, 1 for single hit 1-pass. Does not apply to blastn ou megablast.
      • -A: multiple hits window size. Default = 0 (for single hit algorithm)
      • -I: number of database sequences to save hits for. Default = 500
      • -Y: effective length of the search space. Default = 0 (0 represents using the whole space)
      • -z: a real specifying the effective length of the database to use. Default = 0 (0 represents the real size)
      • -c: an integer representing pseudocount constant for PSI-BLAST. Default = 7
      • -F: any filtering directive

      WARNING!! This method is still very much in flux and might not work as expected...

      You have to be aware that at not moment is there any error checking on the use of these parameters by this class.

      Parameters:
      aStr - : a String with any number of optional parameters with an associated value.
    • getBlastAdvancedOptions

      Simply return the string given as argument via setBlastAdvancedOptions
      Returns:
      advanced :the string with the advanced options
    • getAlignmentOption

      Description copied from interface: RemotePairwiseAlignmentProperties
      Method that returns the value associated with the key given in parameter.
      Specified by:
      getAlignmentOption in interface RemotePairwiseAlignmentProperties
      Parameters:
      key - :a String with the required key for this map.
      Returns:
      a String with the value associated with this key
      Throws:
      BioException - if key is not in the map of output options.
    • setAlignementOption

      public void setAlignementOption(String key, String val)
      Description copied from interface: RemotePairwiseAlignmentProperties
      Method to set the value for a specific alignment parameter using a key to store in a map.
      Specified by:
      setAlignementOption in interface RemotePairwiseAlignmentProperties
      Parameters:
      key - :the key use to designate the value to be stored
      val - :the actual value matched to key
    • getAlignmentOptions

      Description copied from interface: RemotePairwiseAlignmentProperties
      Method to get all keys to the information stored in this object.
      Specified by:
      getAlignmentOptions in interface RemotePairwiseAlignmentProperties
      Returns:
      a Set with all keys held in this instance of the object