org.biojava3.ws.alignment.qblast
Class NCBIQBlastOutputProperties

java.lang.Object
  extended by org.biojava3.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
NCBIQBlastOutputProperties()
          This constructor builds the parameters for the output of the GET command sent to the QBlast service with default values:
 
Method Summary
 int getAlignmentNumber()
           
 String getAlignmentOutputFormat()
           
 int getDescriptionNumber()
           
 String getOutputFormat()
           
 String getOutputOption(BlastOutputParameterEnum key)
          Gets the value of specified parameter or null if it is not set
 String getOutputOption(String key)
          This method forwards to getOutputOption(BlastOutputParameterEnum).
 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

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

 void setOutputOption(BlastOutputParameterEnum key, String value)
          Sets the value of specified output parameter
 void setOutputOption(String key, String val)
          This method forwards to setOutputOption(BlastOutputParameterEnum, String).
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

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 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