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 parameterMap
by adding several convenient parameter addition methods. Other QBlast URL API parameters should be added usingsetOutputOption(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
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getAlignmentNumber()
String
getAlignmentOutputFormat()
int
getDescriptionNumber()
String
getOutputFormat()
String
getOutputOption(String key)
This method forwards togetOutputOption(BlastOutputParameterEnum)
.String
getOutputOption(BlastOutputParameterEnum key)
Gets the value of specified parameter ornull
if it is not setSet<String>
getOutputOptions()
Gets output parameters, which are currently setvoid
removeOutputOption(BlastOutputParameterEnum key)
Removes given parametervoid
setAlignmentNumber(int number)
Set the number of alignments to fetchvoid
setAlignmentOutputFormat(BlastOutputAlignmentFormatEnum alignmentFormat)
Sets the alignment output format to get from the QBlast servicevoid
setDescriptionNumber(int number)
Sets the number of descriptions to fetchvoid
setOutputFormat(BlastOutputFormatEnum formatType)
Sets the stream output format to get from the QBlast servicevoid
setOutputOption(String key, String val)
This method forwards tosetOutputOption(BlastOutputParameterEnum, String)
.void
setOutputOption(BlastOutputParameterEnum key, String value)
Sets the value of specified output parameter
-
-
-
Constructor Detail
-
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 Detail
-
getOutputOption
public String getOutputOption(String key)
This method forwards togetOutputOption(BlastOutputParameterEnum)
. Consider using it instead.- Specified by:
getOutputOption
in interfaceRemotePairwiseAlignmentOutputProperties
- 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 tosetOutputOption(BlastOutputParameterEnum, String)
. Consider using it instead.- Specified by:
setOutputOption
in interfaceRemotePairwiseAlignmentOutputProperties
- Parameters:
key
- :the key use to designate the value to be storedval
- :the actual value matched to key
-
getOutputOption
public String getOutputOption(BlastOutputParameterEnum key)
Gets the value of specified parameter ornull
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 interfaceRemotePairwiseAlignmentOutputProperties
- 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 IfHTML
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
-
-