uk.ac.ebi.pride.utilities.pia.modeller.filter

Class AbstractFilter

java.lang.Object

uk.ac.ebi.pride.utilities.pia.modeller.filter.AbstractFilter

Direct Known Subclasses:

PeptideNrPSMsFilter, ProteinAccessionFilter, ProteinNrPSMsFilter, PSMAccessionsFilter, PSMDecoyFilter, PSMQValueFilter, PSMScoreFilter

public abstract class AbstractFilter
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
protected FilterComparator	comparator
protected boolean	negate

Constructor Summary

Constructors

Constructor and Description
AbstractFilter()

Method Summary

Methods

Modifier and Type	Method and Description
Object	doFileRefinement(Object o) performs the file refinement an the given object and returns the refined object.
FilterComparator	getFilterComparator() getter for the filter's comparator
abstract String	getFilteringName() returns the human readable name, which can be used in a drop-down menu (shorter than getName)
boolean	getFilterNegate() returns, whether this filter is negating or not
abstract FilterType	getFilterType() returns the type of the filter, i.e.
abstract Object	getFilterValue() returns the value, against which is filtered
abstract String	getName() returns the human readable long name of the filter
abstract Object	getObjectsValue(Object o) returns the value of the Object o, which will be used for filtering.
abstract String	getShortName() returns the machine readable name of the filter
boolean	newInferenceFor(Class c) Returns, whether a new inference on the level, where this filter is applied, is necessary.
boolean	satisfiesFilter(Object o) compares the given object and the filter value with the filter comparator and thus returns, whether the object satisfies the filter.
abstract boolean	supportsClass(Object c) Returns, whether the class of the given object is valid for an instance of this filter.
String	toString()
boolean	valueNeedsFileRefinement() returns true, if the objects need file refinement (e.g.

Methods inherited from class java.lang.Object

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

Field Detail

comparator

protected FilterComparator comparator

negate

protected boolean negate

Constructor Detail

AbstractFilter

public AbstractFilter()

Method Detail

getShortName

public abstract String getShortName()

returns the machine readable name of the filter

Returns:

getName

public abstract String getName()

returns the human readable long name of the filter

Returns:

getFilteringName

public abstract String getFilteringName()

returns the human readable name, which can be used in a drop-down menu (shorter than getName)

Returns:

getFilterValue

public abstract Object getFilterValue()

returns the value, against which is filtered

Returns:

getFilterType

public abstract FilterType getFilterType()

returns the type of the filter, i.e. the kind of comparison

Returns:

getFilterNegate

public boolean getFilterNegate()

returns, whether this filter is negating or not

Returns:

getFilterComparator

public FilterComparator getFilterComparator()

getter for the filter's comparator

Returns:

getObjectsValue

public abstract Object getObjectsValue(Object o)

returns the value of the Object o, which will be used for filtering.

Parameters:

o -

Returns:

valueNeedsFileRefinement

public boolean valueNeedsFileRefinement()

returns true, if the objects need file refinement (e.g. filtering the accessions).

Returns:

doFileRefinement

public Object doFileRefinement(Object o)

performs the file refinement an the given object and returns the refined object.

Returns:

newInferenceFor

public boolean newInferenceFor(Class c)

Returns, whether a new inference on the level, where this filter is applied, is necessary. As the reports are for each file separately, only the file's inference must be performed, where this filter was added. If false is returned, the result will be valid simply by filering the current report list.

Parameters:

c - one of the objects, the filter is performed on

Returns:

supportsClass

public abstract boolean supportsClass(Object c)

Returns, whether the class of the given object is valid for an instance of this filter.

Parameters:

c -

Returns:

satisfiesFilter

public boolean satisfiesFilter(Object o)

compares the given object and the filter value with the filter comparator and thus returns, whether the object satisfies the filter.

Parameters:

o -

Returns:

toString

public String toString()

Overrides:

toString in class Object