info.bioinfweb.libralign.alignmentarea.paintsettings

Class TokenPainterList

java.lang.Object

info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterList

All Implemented Interfaces:

java.lang.Iterable<TokenPainter>

public class TokenPainterList
extends java.lang.Object
implements java.lang.Iterable<TokenPainter>

Manages a list of TokenPainters used by PaintSettings and AlignmentArea. For usual alignment models this list will contain only one token painter, but if an instance of ConcatenatedAlignmentModel is used, it will contain one token painter for each part model.

Note that ConcatenatedAlignmentModel is just a placeholder for future functionality in current versions of LibrAlign. See its documnentation for details.

Since:

0.4.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
TokenPainterList(PaintSettings owner) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
void	afterAlignmentModelChanged() This method is called by the owning alignment area to notify this object about a change of the associated alignment model.
TokenPainter	get(int index) Returns the painter at the specified index.
TokenPainterMap	getDefaultTokenMap() Returns the default token painter map that is used to paint tokens from the alignment model if no respective painter is defined in the list.
PaintSettings	getOwner() Returns the paint settings object containing this instance.
int	indexOf(TokenPainter painter) Returns the first index of the specified token painter in this list.
boolean	isEmpty() Checks whether this list contains any painters.
java.util.Iterator<TokenPainter>	iterator() Returns an unmodifiable iterator over all painter of this list.
TokenPainter	painterByColumn(int columnIndex) Returns the according painter to the specified column index.
TokenPainter	set(int index, TokenPainter painter) Replaces the painter at the specified position in this list with the specified new painter.
int	size() Returns the number of list elements in this instance.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

TokenPainterList

public TokenPainterList(PaintSettings owner)

Creates a new instance of this class.

Parameters:

owner - the paint settings object containing this instance

Method Detail

getOwner

public PaintSettings getOwner()

Returns the paint settings object containing this instance.

Returns:

the owning paint settings instance

get

public TokenPainter get(int index)

Returns the painter at the specified index. If no painter is defined for this index, a default painter from getDefaultTokenMap() is returned that best matches the alignment model at the specified index. If the index is out of range, a default model will anyway be returned.

Parameters:

index - the index of the painter to be returned (identical with the index of the alignment part model in ConcatenatedAlignmentModels)

Returns:

the best matching painter for the alignment model at the specified position (never null)

painterByColumn

public TokenPainter painterByColumn(int columnIndex)

Returns the according painter to the specified column index. If no painter is found, the default painter will be returned, even if the specified column does not exist in the associated model.

Parameters:

columnIndex - the index of the column that contains the token to be painted

Returns:

the associated painter or the default painter if no according painter is available

set

public TokenPainter set(int index,
                        TokenPainter painter)

Replaces the painter at the specified position in this list with the specified new painter.

Painters can also be set to null. In such cases the alignment area will use its default painter for the according column ranges.

Parameters:

index - the index of the painter to be replaced

painter - the new painter to be set

Returns:

the painter previously located at the specified position

Throws:

java.lang.IndexOutOfBoundsException - if the index is out of range (index < 0 || index >= size())

size

public int size()

Returns the number of list elements in this instance. (An entry in the list can either be a painter instance of null.)

Returns:

the length of this list

indexOf

public int indexOf(TokenPainter painter)

Returns the first index of the specified token painter in this list.

Parameters:

painter - the painter object to determine the index for

Returns:

the index of the first occurrence or -1 of the painter is not contained in this list

iterator

public java.util.Iterator<TokenPainter> iterator()

Returns an unmodifiable iterator over all painter of this list. (null elements can occur.)

Specified by:

iterator in interface java.lang.Iterable<TokenPainter>

Returns:

an iterator not supporting Iterator.remove()

isEmpty

public boolean isEmpty()

Checks whether this list contains any painters. A list with only null elements is not empty. A list with the length of 0 only specifying a default painter is considered empty.

Returns:

true if the list is empty, false otherwise

getDefaultTokenMap

public TokenPainterMap getDefaultTokenMap()

Returns the default token painter map that is used to paint tokens from the alignment model if no respective painter is defined in the list. See the documentation of TokenPainterMap for further details.

Returns:

the token painter map instance used by this i

afterAlignmentModelChanged

public void afterAlignmentModelChanged()

This method is called by the owning alignment area to notify this object about a change of the associated alignment model. This could either be that a different model was set or that changes inside a concatenated model happened.

This method is meant for internal use in LibrAlign and it should not be necessary to call it directly from external code.