Class NCBIQBlastAlignmentProperties

Method Details

• getAlignmentOption

  public String getAlignmentOption(String key)

  This method forwards to getAlignmentOption(BlastAlignmentParameterEnum). Consider using it instead.

  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

• setAlignementOption

  public void setAlignementOption(String key, String val)

  This method forwards to setAlignmentOption(BlastAlignmentParameterEnum, String). Consider using it instead.

  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

  public Set<String> getAlignmentOptions()

  Gets parameters, which are currently set

  Specified by:

  getAlignmentOptions in interface RemotePairwiseAlignmentProperties

  Returns:

  a Set with all keys held in this instance of the object

• getAlignmentOption

  public String getAlignmentOption(BlastAlignmentParameterEnum key)

  Gets the value of specified parameter or null if it is not set.

• setAlignmentOption

  public void setAlignmentOption(BlastAlignmentParameterEnum key, String val)

  Sets the value of specified parameter

• removeAlignmentOption

  public void removeAlignmentOption(BlastAlignmentParameterEnum key)

  Removes given parameter

• getBlastProgram

  public BlastProgramEnum getBlastProgram()

  Returns:

  BlastProgramEnum used for blast run

• setBlastProgram

  public void setBlastProgram(BlastProgramEnum program)

  Sets the program to be used with blastall

  Parameters:

  program - : one of blastall programs

• getBlastDatabase

  public String getBlastDatabase()

  Returns:

  name of database used with blastall

• setBlastDatabase

  public void setBlastDatabase(String database)

  Sets the database to be used with blastall

  A list of available databases can be acquired by calling NCBIQBlastService#printRemoteBlastInfo()

  Blastall equivalent: -d

  Parameters:

  db - : a valid name to a NCBI blastable database

• getBlastExpect

  public double getBlastExpect()

  Returns:

  double value of EXPECT parameter used for blast run

• setBlastExpect

  public void setBlastExpect(double expect)

  Sets the EXPECT parameter to be use with blastall

  Example: if you want a EXPECT of 1e-10, pass Double.parseDouble("1e-10") as a parameter

  Blastall equivalent: -e

  Parameters:

  expect - : a double value of EXPECT parameter

• getBlastWordSize

  public int getBlastWordSize()

  Returns the value of the WORD_SIZE parameter used for this blast run

  Returns:

  int value of WORD_SIZE used by this search

  Throws:

  IllegalArgumentException - when program type is not set and program type is not supported

• setBlastWordSize

  public void setBlastWordSize(int word)

  Sets the WORD_SIZE parameter to be use with blastall

  WARNING!! At this point, the method does not verify the validity of your choice; for example, word size of greater than 5 with blastp returns error messages from QBlast. Word size range depends on the algorithm chosen.

  More at https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node74.html

  Blastall equivalent: -W

  Parameters:

  word - : an int used to set WORD_SIZE

• getBlastGapCreation

  public int getBlastGapCreation()

  Returns the value for the GAP_CREATION parameter (first half of GAPCOSTS parameter)

  Returns:

  an integer value for gap creation used by this search, -1 if not set or not a number

• getBlastGapExtension

  public int getBlastGapExtension()

  Returns the value for the gap extension parameter (second half of GAPCOSTS parameter)

  Returns:

  an integer for the value for gap extension used by this search, -1 if not set or not a number

• getBlastGapCosts

  public String getBlastGapCosts()

  Returns the actual string for the GAPCOSTS parameter which is used to build the URL

  Returns:

  the string representation of the GAPCOSTS parameter formatted for the URL

• setBlastGapCosts

  public void setBlastGapCosts(int gapCreation, int gapExtension)

  Sets the GAPCOSTS parameter

  Parameters:

  gapCreation - integer to use as gap creation value

  gapExtension - integer to use as gap extension value

• getBlastMatrix

  public String getBlastMatrix()

  Returns the value of the specified substitution matrix

  Returns:

  matrix: the name of the specified substitution matrix

• setBlastMatrix

  public void setBlastMatrix(BlastMatrixEnum matrix)

  Sets the value for the MATRIX parameter to use for blastall

  Blastall equivalent: -M

  Parameters:

  matrix - : a String to use as gap creation value

  See Also:

  • BlastMatrixEnum

• setBlastFromToPosition

  public void setBlastFromToPosition(int start, int end)

  Sets the QUERY_FROM and QUERY_TO parameters to be use by blast. Do not use if you want to use the whole sequence.
  Blastall equivalent: -L

  Parameters:

  start - QUERY_FROM parameter

  end - QUERY_TO parameter

• getBlastFromPosition

  public int getBlastFromPosition()

  Returns:

  an integer value for the QUERY_FROM parameter

  See Also:

  • setBlastFromToPosition(int, int)

• getBlastToPosition

  public int getBlastToPosition()

  Returns:

  QUERY_TO parameter

  See Also:

  • setBlastFromToPosition(int, int)

• setBlastAdvancedOptions

  public void setBlastAdvancedOptions(String advancedOptions)

  This method is to be used if a request is to use non-default values at submission. Useful for the following blastall parameters:

  • -r: integer to reward for match. Default = 1
  • -q: negative integer for penalty to allow mismatch. Default = -3
  • -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 no moment is there any error checking on the use of these parameters by this class.

  Parameters:

  advancedOptions - : a String with any number of optional parameters with an associated value.

• getBlastAdvancedOptions

  public String getBlastAdvancedOptions()

  Returns:

  the String with the advanced options