org.biojava.nbio.ws.alignment

Interface RemotePairwiseAlignmentProperties

All Superinterfaces:

java.io.Serializable

All Known Implementing Classes:

NCBIQBlastAlignmentProperties

public interface RemotePairwiseAlignmentProperties
extends java.io.Serializable

RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties. Ideally, one would extend this class if creating a service by creating wrapper methods that actually call either getAlignementOption or setAlignementOption with specific values for parameter names and checking values for options. For an example, go see NCBIQBlastProperties

Since:

Biojava 3

Author:

Sylvain Foisy, Diploide BioIT

Field Summary

Fields

Modifier and Type	Field and Description
static long	serialVersionUID

Method Summary

Modifier and Type	Method and Description
java.lang.String	getAlignmentOption(java.lang.String key) Method that returns the value associated with the key given in parameter.
java.util.Set<java.lang.String>	getAlignmentOptions() Method to get all keys to the information stored in this object.
void	setAlignementOption(java.lang.String key, java.lang.String val) Method to set the value for a specific alignment parameter using a key to store in a map.

Field Detail

serialVersionUID

static final long serialVersionUID

See Also:

Constant Field Values

Method Detail

getAlignmentOption

java.lang.String getAlignmentOption(java.lang.String key)
                             throws java.lang.Exception

Method that returns the value associated with the key given in parameter.

Parameters:

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

Returns:

a String with the value associated with this key

Throws:

java.lang.Exception - if key is not in the map of output options.

setAlignementOption

void setAlignementOption(java.lang.String key,
                         java.lang.String val)

Method to set the value for a specific alignment parameter using a key to store in a map.

Parameters:

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

val - :the actual value matched to key

getAlignmentOptions

java.util.Set<java.lang.String> getAlignmentOptions()

Method to get all keys to the information stored in this object.

Returns:

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