Package org.biojava.nbio.ws.alignment.qblast

Class NCBIQBlastOutputProperties

java.lang.Object

org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties

All Implemented Interfaces:

Serializable, RemotePairwiseAlignmentOutputProperties

public class NCBIQBlastOutputProperties
extends Object
implements RemotePairwiseAlignmentOutputProperties

This class wraps a QBlast output parameter Map by adding several convenient parameter addition methods. Other QBlast URL API parameters should be added using setOutputOption(BlastOutputParameterEnum, String)

Author:

Sylvain Foisy, Diploide BioIT, Gediminas Rimsa

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
NCBIQBlastOutputProperties()	This constructor builds the parameters for the output of the GET command sent to the QBlast service with default values:

Method Summary

Modifier and Type	Method	Description
int	getAlignmentNumber()
String	getAlignmentOutputFormat()
int	getDescriptionNumber()
String	getOutputFormat()
String	getOutputOption(String key)	This method forwards to getOutputOption(BlastOutputParameterEnum).
String	getOutputOption(BlastOutputParameterEnum key)	Gets the value of specified parameter or null if it is not set
Set<String>	getOutputOptions()	Gets output parameters, which are currently set
void	removeOutputOption(BlastOutputParameterEnum key)	Removes given parameter
void	setAlignmentNumber(int number)	Set the number of alignments to fetch
void	setAlignmentOutputFormat(BlastOutputAlignmentFormatEnum alignmentFormat)	Sets the alignment output format to get from the QBlast service
void	setDescriptionNumber(int number)	Sets the number of descriptions to fetch
void	setOutputFormat(BlastOutputFormatEnum formatType)	Sets the stream output format to get from the QBlast service
void	setOutputOption(String key, String val)	This method forwards to setOutputOption(BlastOutputParameterEnum, String).
void	setOutputOption(BlastOutputParameterEnum key, String value)	Sets the value of specified output parameter

Methods inherited from class java.lang.Object

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

Constructor Details

NCBIQBlastOutputProperties

public NCBIQBlastOutputProperties()

This constructor builds the parameters for the output of the GET command sent to the QBlast service with default values:

 FORMAT_TYPE = XML;
 ALIGNMENT_VIEW = Pairwise;
 DESCRIPTIONS = 100;
 ALIGNMENTS = 100;
 

Method Details

getOutputOption

public String getOutputOption(String key)

This method forwards to getOutputOption(BlastOutputParameterEnum). Consider using it instead.

Specified by:

getOutputOption in interface RemotePairwiseAlignmentOutputProperties

Parameters:

key - :a String with the required key for this map.

Returns:

a String with the value associated with this key

setOutputOption

public void setOutputOption(String key,
 String val)

This method forwards to setOutputOption(BlastOutputParameterEnum, String). Consider using it instead.

Specified by:

setOutputOption in interface RemotePairwiseAlignmentOutputProperties

Parameters:

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

val - :the actual value matched to key

getOutputOption

public String getOutputOption(BlastOutputParameterEnum key)

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

setOutputOption

public void setOutputOption(BlastOutputParameterEnum key,
 String value)

Sets the value of specified output parameter

getOutputOptions

public Set<String> getOutputOptions()

Gets output parameters, which are currently set

Specified by:

getOutputOptions in interface RemotePairwiseAlignmentOutputProperties

Returns:

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

removeOutputOption

public void removeOutputOption(BlastOutputParameterEnum key)

Removes given parameter

getOutputFormat

public String getOutputFormat()

Returns:

stream output format - a String with the value of key FORMAT_TYPE

setOutputFormat

public void setOutputFormat(BlastOutputFormatEnum formatType)

Sets the stream output format to get from the QBlast service

If HTML format is selected, also adds the following parameters (which are removed if another output format is chosen):

 NOHEADER = true;
 SHOW_OVERVIEW = false;
 SHOW_LINKOUT = false;
 

Parameters:

formatType - : one of the output format types defined in enum

getAlignmentOutputFormat

public String getAlignmentOutputFormat()

Returns:

alignment output format - a String with the value of key ALIGNMENT_VIEW

setAlignmentOutputFormat

public void setAlignmentOutputFormat(BlastOutputAlignmentFormatEnum alignmentFormat)

Sets the alignment output format to get from the QBlast service

Parameters:

alignmentFormat - : one of available alignment types

getDescriptionNumber

public int getDescriptionNumber()

Returns:

number of descriptions fetched - an int with the value of the key DESCRIPTIONS

setDescriptionNumber

public void setDescriptionNumber(int number)

Sets the number of descriptions to fetch

Parameters:

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

getAlignmentNumber

public int getAlignmentNumber()

Returns:

number of alignments fetched - an int with the value of the key ALIGNMENTS

setAlignmentNumber

public void setAlignmentNumber(int number)

Set the number of alignments to fetch

Parameters:

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