org.biopax.paxtools.pattern

Class Pattern

java.lang.Object

org.biopax.paxtools.pattern.Pattern

public class Pattern
extends Object

A pattern is a list of mapped constraints.

Author:

Ozgun Babur

Field Summary

Fields

Modifier and Type	Field and Description
protected List<MappedConst>	constraints List of mapped constraints.
protected Map<String,Integer>	labelMap Indexes in a pattern can be labeled using this map.
protected int	lastIndex How many elements are there in a pattern match.
protected Class<? extends BioPAXElement>	startingClass Class of the first elements to match with this pattern.

Constructor Summary

Constructors

Constructor and Description
Pattern(Class<? extends BioPAXElement> startingClass, Constraint firstConstraint, String... label) Constructor with the first constraint and labels it uses.
Pattern(Class<? extends BioPAXElement> startingClass, String label) Constructor with a label for the element at index 0.

Method Summary

Modifier and Type	Method and Description
void	add(Constraint constr, String... label) Creates a mapped constraint with the given generative constraint and the indexes it applies.
void	add(Pattern p) Appends the constraints in the parameter pattern to the desired location.
List<MappedConst>	getConstraints() Getter for the constraint list.
Class<? extends BioPAXElement>	getStartingClass() Gets the type of the initial element.
boolean	hasLabel(int index) Checks if the given location has a label.
boolean	hasLabel(String labelText) Checks if the label is already in use.
int	indexOf(String labelText) Gets the index of the given label.
void	insertPointConstraint(Constraint con, int... ind) A point constraint deals with only one element in a match, checks its validity.
void	label(String labelText, int index) Puts the given label for the given index.
void	optimizeConstraintOrder()
void	removeLastConstraint() Removes the last constraint added to the pattern.
int	size() Gets the element size of the pattern.
void	updateLabel(String oldLabel, String newLabel) Changes a label.

Methods inherited from class java.lang.Object

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

Field Detail

lastIndex

protected int lastIndex

How many elements are there in a pattern match.

startingClass

protected Class<? extends BioPAXElement> startingClass

Class of the first elements to match with this pattern.

constraints

protected List<MappedConst> constraints

List of mapped constraints.

labelMap

protected Map<String,Integer> labelMap

Indexes in a pattern can be labeled using this map.

Constructor Detail

Pattern

public Pattern(Class<? extends BioPAXElement> startingClass,
               Constraint firstConstraint,
               String... label)

Constructor with the first constraint and labels it uses. This constructor is good for patterns with a single constraint.

Parameters:

startingClass - type of initial element

firstConstraint - first constraint

label - labels for the constraint

Pattern

public Pattern(Class<? extends BioPAXElement> startingClass,
               String label)

Constructor with a label for the element at index 0.

Parameters:

startingClass - type of the initial element

label - a label for the initial element

Method Detail

removeLastConstraint

public void removeLastConstraint()

Removes the last constraint added to the pattern.

optimizeConstraintOrder

public void optimizeConstraintOrder()

add

public void add(Constraint constr,
                String... label)

Creates a mapped constraint with the given generative constraint and the indexes it applies. Also labels the last given index.

Parameters:

constr - constraint to add

label - a label for the last of the given indices

add

public void add(Pattern p)

Appends the constraints in the parameter pattern to the desired location. Indexes in the constraint mappings are translated so that 0 is translated to ind0, and others are translated to orig + indAppend - 1. All slots of this pattern should already be full before calling this method. This method makes room for the new variables. Labels in the parameter pattern is transferred to this pattern. If there are equivalent labels, then these slots are mapped.

Parameters:

p - the parameter pattern

insertPointConstraint

public void insertPointConstraint(Constraint con,
                                  int... ind)

A point constraint deals with only one element in a match, checks its validity. This method injects the parameter constraint multiple times among the list of mapped constraints, to the specified indexes.

Parameters:

con - constraint to add

ind - indices to add this point constraint

getConstraints

public List<MappedConst> getConstraints()

Getter for the constraint list.

Returns:

constraints

size

public int size()

Gets the element size of the pattern.

Returns:

size inferred from lastIndex

getStartingClass

public Class<? extends BioPAXElement> getStartingClass()

Gets the type of the initial element.

Returns:

type of first element in a match

label

public void label(String labelText,
                  int index)

Puts the given label for the given index.

Parameters:

labelText - the label

index - index to label

hasLabel

public boolean hasLabel(String labelText)

Checks if the label is already in use.

Parameters:

labelText - label to check

Returns:

true if label exists

hasLabel

public boolean hasLabel(int index)

Checks if the given location has a label.

Parameters:

index - index to check

Returns:

true if a label exists for the given index

indexOf

public int indexOf(String labelText)

Gets the index of the given label. The label must exist, otherwise a runtime exception is thrown.

Parameters:

labelText - label to check

Returns:

index of the label

updateLabel

public void updateLabel(String oldLabel,
                        String newLabel)

Changes a label. The oldLabel has to be an existing label and new label has to be a new label.

Parameters:

oldLabel - label to update

newLabel - updated label