Package de.isas.mztab2.cvmapping

Class CvParameterLookupService

java.lang.Object

de.isas.mztab2.cvmapping.CvParameterLookupService

public class CvParameterLookupService
extends Object

Abstraction over OLSClient to autoconvert Terms to Parameters and to allow easy matching of Parameters against parent terms and their children.

Author:

nilshoffmann

Constructor Summary

Constructors

Constructor	Description
CvParameterLookupService()	Create a new instance of the lookup service with default OLS configuration.
CvParameterLookupService(uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient client)	Create a new instance of the lookup service with a custom OLSClient.
CvParameterLookupService(uk.ac.ebi.pride.utilities.ols.web.service.config.OLSWsConfig config)	Create a new instance of the lookup service with a custom OLSWsConfig configuration.

Method Summary

Modifier and Type	Method	Description
void	clearCaches()	Clears all query result caches (parent and child).
ParameterComparisonResult	isChildOfOrSame(Parameter parent, Parameter potentialChild)	Compares two parameters for their parent to child relationship.
List<Parameter>	resolveChildren(Parameter parameter)	Resolve all children of a parameter up to an arbitrary depth.
List<Parameter>	resolveChildren(Parameter parameter, int levels)	Resolve all children of a parameter up to a given maximum depth (1 meaning immediate children, -1 meaning all).
List<Parameter>	resolveParents(Parameter parameter)	Resolve all parents of parameter up to an arbitrary depth (actually height, since we go from bottom to top).
List<Parameter>	resolveParents(Parameter parameter, int levels)	Resolve all parents of a parameter up to a given maximum depth (1 meaning the immediate parents, -1 meaning all).

Methods inherited from class java.lang.Object

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

Constructor Detail

CvParameterLookupService

public CvParameterLookupService()

Create a new instance of the lookup service with default OLS configuration.

CvParameterLookupService

public CvParameterLookupService(uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient client)

Create a new instance of the lookup service with a custom OLSClient.

Parameters:

client - the custom OLS client

CvParameterLookupService

public CvParameterLookupService(uk.ac.ebi.pride.utilities.ols.web.service.config.OLSWsConfig config)

Create a new instance of the lookup service with a custom OLSWsConfig configuration.

Parameters:

config - the custom configuration

Method Detail

clearCaches

public void clearCaches()

Clears all query result caches (parent and child).

resolveParents

public List<Parameter> resolveParents(Parameter parameter)
                               throws org.springframework.web.client.HttpClientErrorException

Resolve all parents of parameter up to an arbitrary depth (actually height, since we go from bottom to top). Use at your own risk, the OLS service may terminate your connection if the response is too large or takes too long.

Parameters:

parameter - the parameter to start from

Returns:

a list of all parent parameters for the given parameter

Throws:

org.springframework.web.client.HttpClientErrorException - on http related errors

resolveParents

public List<Parameter> resolveParents(Parameter parameter,
                                      int levels)
                               throws org.springframework.web.client.HttpClientErrorException

Resolve all parents of a parameter up to a given maximum depth (1 meaning the immediate parents, -1 meaning all).

Parameters:

parameter - the parameter to start from

levels - maximum levels to query

Returns:

a list of all parent parameters for the given parameter

Throws:

org.springframework.web.client.HttpClientErrorException - on http related errors

resolveChildren

public List<Parameter> resolveChildren(Parameter parameter,
                                       int levels)
                                throws org.springframework.web.client.HttpClientErrorException

Resolve all children of a parameter up to a given maximum depth (1 meaning immediate children, -1 meaning all).

Parameters:

parameter - the parameter to start from

levels - maximum levels to query

Returns:

a list of all child parameters for the given parameter

Throws:

org.springframework.web.client.HttpClientErrorException - on http related errors

resolveChildren

public List<Parameter> resolveChildren(Parameter parameter)
                                throws org.springframework.web.client.HttpClientErrorException

Resolve all children of a parameter up to an arbitrary depth. Use at your own risk, the OLS service may terminate your connection if the response is too large or takes too long.

Parameters:

parameter - the parameter to start from

Returns:

a list of all child parameters for the given parameter

Throws:

org.springframework.web.client.HttpClientErrorException - on http related errors

isChildOfOrSame

public ParameterComparisonResult isChildOfOrSame(Parameter parent,
                                                 Parameter potentialChild)
                                          throws org.springframework.web.client.HttpClientErrorException

Compares two parameters for their parent to child relationship. The result can be one of: IDENTICAL, if parent and potential child are the same node, CHILD_OF, if potentialChild is a child of parent (at least 1 level away), or NOT_RELATED, if there is no path from child to parent.

Parameters:

parent - the parent term to start from

potentialChild - the potential child term to check against parent

Returns:

the comparison result

Throws:

org.springframework.web.client.HttpClientErrorException - on http related errors