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:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
RemoteQBlastAlignmentProperties()

Method Summary

Modifier and Type	Method	Description
String	getAlignmentOption(String key)	Method that returns the value associated with the key given in parameter.
Set<String>	getAlignmentOptions()	Method to get all keys to the information stored in this object.
String	getBlastAdvancedOptions()	Simply return the string given as argument via setBlastAdvancedOptions
String	getBlastDatabase()	This method returns the value of the database used for this particular blast run.
String	getBlastProgram()	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	setBlastDatabase(String db)	This method set the database to be use with blastall
void	setBlastProgram(String program)	This method set the program to be use with blastall.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RemoteQBlastAlignmentProperties

public RemoteQBlastAlignmentProperties()

Method Detail

getBlastProgram

public String 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

public String 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

public String getBlastAdvancedOptions()

Simply return the string given as argument via setBlastAdvancedOptions

Returns:

advanced :the string with the advanced options

getAlignmentOption

public String getAlignmentOption(String key)
                          throws BioException

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

public Set<String> 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