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:
-
Constructor Summary
ConstructorsConstructorDescriptionThis constructor build the parameters for the default output of the GET command sent to the QBlast service. -
Method Summary
Modifier and TypeMethodDescriptionint
A method that simply returns the number of alignments fetched with this RemoteQBlastOutputProperties object.Method that returns the alignment output format for this actual RemoteQBlastOutputProperties objectint
A method that simply returns the number of descriptions fetched with this RemoteQBlastOutputProperties object.Simply returns stream output format for the actual RemoteQBlastOutputProperties objectMethod that returns any value associated to any key for this RemoteQBlastOutputProperties object.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
This method is use to set the alignment output format to get from the QBlast servicevoid
setDescriptionNumber
(int i) A method to set the number of descriptions to fetch to the GET command.void
This method is use to set the stream output format to get from the QBlast servicevoid
setOutputOption
(String o, String v) Method to set the value for a specific output parameter using a key to store in a map.
-
Constructor Details
-
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 Details
-
getOutputFormat
Simply returns stream output format for the actual RemoteQBlastOutputProperties object- Returns:
- a String with the value of key FORMAT_TYPE.
-
setOutputFormat
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
Method that returns the alignment output format for this actual RemoteQBlastOutputProperties object- Returns:
- a String with the value of key ALIGNMENT_VIEW
-
setAlignmentOutputFormat
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
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
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
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
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
Method that returns any value associated to any key for this RemoteQBlastOutputProperties object.- Specified by:
getOutputOption
in interfaceRemotePairwiseAlignmentOutputProperties
- 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
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 interfaceRemotePairwiseAlignmentOutputProperties
- Parameters:
o
- :the key use to designate the value to be storedv
- :the actual value matched to key
-
getOutputOptions
Description copied from interface:RemotePairwiseAlignmentOutputProperties
Method to get all keys to the information stored in this object.- Specified by:
getOutputOptions
in interfaceRemotePairwiseAlignmentOutputProperties
- Returns:
- a
Set
with all keys held in this instance of the object
-