java.io.Serializable
, RemotePairwiseAlignmentOutputProperties
public class NCBIQBlastOutputProperties extends java.lang.Object implements RemotePairwiseAlignmentOutputProperties
Map
by adding several convenient parameter addition methods. Other
QBlast URL API parameters should be added using setOutputOption(BlastOutputParameterEnum, String)
Constructor | Description |
---|---|
NCBIQBlastOutputProperties() |
This constructor builds the parameters for the output of the GET command sent to the QBlast service with default
values:
|
Modifier and Type | Method | Description |
---|---|---|
int |
getAlignmentNumber() |
|
java.lang.String |
getAlignmentOutputFormat() |
|
int |
getDescriptionNumber() |
|
java.lang.String |
getOutputFormat() |
|
java.lang.String |
getOutputOption(java.lang.String key) |
This method forwards to
getOutputOption(BlastOutputParameterEnum) . |
java.lang.String |
getOutputOption(BlastOutputParameterEnum key) |
Gets the value of specified parameter or
null if it is not set |
java.util.Set<java.lang.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(java.lang.String key,
java.lang.String val) |
This method forwards to
setOutputOption(BlastOutputParameterEnum, String) . |
void |
setOutputOption(BlastOutputParameterEnum key,
java.lang.String value) |
Sets the value of specified output parameter
|
public NCBIQBlastOutputProperties()
FORMAT_TYPE = XML; ALIGNMENT_VIEW = Pairwise; DESCRIPTIONS = 100; ALIGNMENTS = 100;
public java.lang.String getOutputOption(java.lang.String key)
getOutputOption(BlastOutputParameterEnum)
. Consider using it instead.getOutputOption
in interface RemotePairwiseAlignmentOutputProperties
key
- :a String with the required key for this map.public void setOutputOption(java.lang.String key, java.lang.String val)
setOutputOption(BlastOutputParameterEnum, String)
. Consider using it instead.setOutputOption
in interface RemotePairwiseAlignmentOutputProperties
key
- :the key use to designate the value to be storedval
- :the actual value matched to keypublic java.lang.String getOutputOption(BlastOutputParameterEnum key)
null
if it is not setpublic void setOutputOption(BlastOutputParameterEnum key, java.lang.String value)
public java.util.Set<java.lang.String> getOutputOptions()
getOutputOptions
in interface RemotePairwiseAlignmentOutputProperties
Set
with all keys held in this instance of the objectpublic void removeOutputOption(BlastOutputParameterEnum key)
public java.lang.String getOutputFormat()
public void setOutputFormat(BlastOutputFormatEnum formatType)
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;
formatType
- : one of the output format types defined in enumpublic java.lang.String getAlignmentOutputFormat()
public void setAlignmentOutputFormat(BlastOutputAlignmentFormatEnum alignmentFormat)
alignmentFormat
- : one of available alignment typespublic int getDescriptionNumber()
public void setDescriptionNumber(int number)
number
- : an int with the required number of descriptions to fetchpublic int getAlignmentNumber()
public void setAlignmentNumber(int number)
number
- : an int with the required number of alignments to fetch