Package org.biojavax.bio.alignment.blast
Class RemoteQBlastAlignmentProperties
java.lang.Object
org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties
- All Implemented Interfaces:
Serializable
,RemotePairwiseAlignmentProperties
public class RemoteQBlastAlignmentProperties
extends Object
implements 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:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetAlignmentOption
(String key) Method that returns the value associated with the key given in parameter.Method to get all keys to the information stored in this object.Simply return the string given as argument via setBlastAdvancedOptionsThis method returns the value of the database used for this particular blast run.This method returns the value of the program used for this particular blast run.void
setAdvancedOptions
(String aStr) This method is to be used if a request is to use non-default values at submission.void
setAlignementOption
(String key, String val) Method to set the value for a specific alignment parameter using a key to store in a map.void
This method set the database to be use with blastallvoid
setBlastProgram
(String program) This method set the program to be use with blastall.
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Constructor Details
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RemoteQBlastAlignmentProperties
public RemoteQBlastAlignmentProperties()
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Method Details
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getBlastProgram
This method returns the value of the program used for this particular blast run.- Returns:
- program :the name of the blastall program used.
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setBlastProgram
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
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getBlastDatabase
This method returns the value of the database used for this particular blast run.- Returns:
- db :the name of the database used
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setBlastDatabase
This method set the database to be use with blastall- Parameters:
db
- :a valid name to a NCBI Blastable database
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setAdvancedOptions
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.
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getBlastAdvancedOptions
Simply return the string given as argument via setBlastAdvancedOptions- Returns:
- advanced :the string with the advanced options
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getAlignmentOption
Description copied from interface:RemotePairwiseAlignmentProperties
Method that returns the value associated with the key given in parameter.- Specified by:
getAlignmentOption
in interfaceRemotePairwiseAlignmentProperties
- 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.
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setAlignementOption
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 interfaceRemotePairwiseAlignmentProperties
- Parameters:
key
- :the key use to designate the value to be storedval
- :the actual value matched to key
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getAlignmentOptions
Description copied from interface:RemotePairwiseAlignmentProperties
Method to get all keys to the information stored in this object.- Specified by:
getAlignmentOptions
in interfaceRemotePairwiseAlignmentProperties
- Returns:
- a
Set
with all keys held in this instance of the object
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