Package org.biojavax.bio.alignment.blast

Class RemoteQBlastOutputProperties

java.lang.Object

org.biojavax.bio.alignment.blast.RemoteQBlastOutputProperties

All Implemented Interfaces:

Serializable, RemotePairwiseAlignmentOutputProperties

public class RemoteQBlastOutputProperties
extends Object
implements RemotePairwiseAlignmentOutputProperties

The actual implementation of the RemotePairwiseAlignmentOutputProperties interface for the QBlast service. The constructor for this class builds an object with default format values. Any modification will either use the generic method setOutputOption method or use the wrapper methods that are actually build around the generic method.

Since:

1.8

Author:

Sylvain Foisy, Diploide BioIT

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
RemoteQBlastOutputProperties()	This constructor build the parameters for the default output of the GET command sent to the QBlast service.

Method Summary

Modifier and Type	Method	Description
int	getAlignmentNumber()	A method that simply returns the number of alignments fetched with this RemoteQBlastOutputProperties object.
String	getAlignmentOutputFormat()	Method that returns the alignment output format for this actual RemoteQBlastOutputProperties object
int	getDescriptionNumber()	A method that simply returns the number of descriptions fetched with this RemoteQBlastOutputProperties object.
String	getOutputFormat()	Simply returns stream output format for the actual RemoteQBlastOutputProperties object
String	getOutputOption(String o)	Method that returns any value associated to any key for this RemoteQBlastOutputProperties object.
Set<String>	getOutputOptions()	Method to get all keys to the information stored in this object.
void	setAlignmentNumber(int i)	A method to set the number of alignments to fetch to the GET command.
void	setAlignmentOutputFormat(RemoteQBlastOutputFormat rf)	This method is use to set the alignment output format to get from the QBlast service
void	setDescriptionNumber(int i)	A method to set the number of descriptions to fetch to the GET command.
void	setOutputFormat(RemoteQBlastOutputFormat rf)	This method is use to set the stream output format to get from the QBlast service
void	setOutputOption(String o, String v)	Method to set the value for a specific output parameter using a key to store in a map.

Methods inherited from class java.lang.Object

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

Constructor Detail

RemoteQBlastOutputProperties

public RemoteQBlastOutputProperties()

This constructor build the parameters for the default output of the GET command sent to the QBlast service. Here are the default values: FORMAT_TYPE = Text; ALIGNMENT_VIEW = Pairwise DESCRIPTIONS = 100; ALIGNMENTS = 100;

Method Detail

getOutputFormat

public String getOutputFormat()

Simply returns stream output format for the actual RemoteQBlastOutputProperties object

Returns:

a String with the value of key FORMAT_TYPE.

setOutputFormat

public void setOutputFormat(RemoteQBlastOutputFormat rf)
                     throws BioException

This method is use to set the stream output format to get from the QBlast service

Parameters:

rf - :an enum from RemoteQBlastOutputFormat

Throws:

BioException - if the enum is neither of RemoteQBlastOutputFormat.TEXT/XML/HTML

getAlignmentOutputFormat

public String getAlignmentOutputFormat()

Method that returns the alignment output format for this actual RemoteQBlastOutputProperties object

Returns:

a String with the value of key ALIGNMENT_VIEW

setAlignmentOutputFormat

public void setAlignmentOutputFormat(RemoteQBlastOutputFormat rf)
                              throws BioException

This method is use to set the alignment output format to get from the QBlast service

Parameters:

rf - :an enum from RemoteQBlastOutputFormat

Throws:

BioException - if the enum is neither of RemoteQBlastOutputFormat.PAIRWISE/QUERY_ANCHORED/QUERY_ANCHORED_NO_IDENTITIES/FLAT_QUERY_ANCHORED FLAT_QUERY_ANCHORED_NO_IDENTITIES/TABULAR

getDescriptionNumber

public int getDescriptionNumber()

A method that simply returns the number of descriptions fetched with this RemoteQBlastOutputProperties object.

Returns:

an int with the value of the key DESCRIPTIONS

setDescriptionNumber

public void setDescriptionNumber(int i)

A method to set the number of descriptions to fetch to the GET command.

Parameters:

i - :an int with the required number of descriptions to fetch.

getAlignmentNumber

public int getAlignmentNumber()

A method that simply returns the number of alignments fetched with this RemoteQBlastOutputProperties object.

Returns:

an int with the value of the key ALIGNMENTS.

setAlignmentNumber

public void setAlignmentNumber(int i)

A method to set the number of alignments to fetch to the GET command.

Parameters:

i - :an int with the required number of alignments to fetch.

getOutputOption

public String getOutputOption(String o)
                       throws BioException

Method that returns any value associated to any key for this RemoteQBlastOutputProperties object.

Specified by:

getOutputOption in interface RemotePairwiseAlignmentOutputProperties

Parameters:

o - :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.

setOutputOption

public void setOutputOption(String o,
                            String v)

Description copied from interface: RemotePairwiseAlignmentOutputProperties

Method to set the value for a specific output parameter using a key to store in a map.

Specified by:

setOutputOption in interface RemotePairwiseAlignmentOutputProperties

Parameters:

o - :the key use to designate the value to be stored

v - :the actual value matched to key

getOutputOptions

public Set<String> getOutputOptions()

Description copied from interface: RemotePairwiseAlignmentOutputProperties

Method to get all keys to the information stored in this object.

Specified by:

getOutputOptions in interface RemotePairwiseAlignmentOutputProperties

Returns:

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