info.bioinfweb.libralign.dataarea

Class DataAreaList

java.lang.Object

info.bioinfweb.libralign.dataarea.DataAreaChangeEventList

info.bioinfweb.libralign.dataarea.DataAreaList

All Implemented Interfaces:

java.lang.Iterable<DataArea>, java.util.Collection<DataArea>, java.util.List<DataArea>

public class DataAreaList
extends DataAreaChangeEventList

A list of DataArea that are displayed at a specified position in an AlignmentArea. The oder of the list determines the display order, where the first element of the list is displayed top most.

Since:

0.0.0

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static int	INITIAL_LIST_SIZE

Constructor Summary

Constructors

Constructor and Description
DataAreaList(DataAreasModel owner, DataAreaListType listType) Creates a new instance of this class for lists containing data areas displayed above or underneath the alignment.
DataAreaList(DataAreasModel owner, DataAreaLocation location) Creates a new instance of this class representing a list of data areas attached to one sequence of the alignment.
DataAreaList(DataAreasModel owner, java.lang.String sequenceID) Creates a new instance of this class representing a list of data areas attached to one sequence of the alignment.

Method Summary

Modifier and Type	Method and Description
DataAreaLocation	getLocation() Returns the location the elements in this list have in the containing AlignmentArea.
double	getMaxLengthAfterEnd() Returns maximum space right of the alignment end that is needed by any currently visible data area in this list.
double	getMaxLengthBeforeStart() Returns maximum space left of the alignment start that is needed by any currently visible data area in this list.
DataAreasModel	getOwner()
int	getVisibleHeight() Calculates the sum of the heights of all visible data areas contained in this list.
java.util.Collection<DataArea>	setAllVisible(boolean visible) Fades all elements in this list in or out.
java.util.Iterator<DataArea>	visibleIterator() Returns an iterator that only iterates over the visible data areas.

Methods inherited from class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList

add, add, addAll, addAll, clear, contains, containsAll, get, getDataAreaList, getUnderlyingList, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.List

equals, hashCode, replaceAll, sort, spliterator

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Field Detail

INITIAL_LIST_SIZE

public static final int INITIAL_LIST_SIZE

See Also:

Constant Field Values

Constructor Detail

DataAreaList

public DataAreaList(DataAreasModel owner,
                    DataAreaListType listType)

Creates a new instance of this class for lists containing data areas displayed above or underneath the alignment.

Parameters:

owner - the parent element that will contain this list

listType - specifies if list represents data areas displayed above or underneath the alignment

Throws:

java.lang.IllegalArgumentException - if DataAreaListType.SEQUENCE is specified as listType

DataAreaList

public DataAreaList(DataAreasModel owner,
                    java.lang.String sequenceID)

Creates a new instance of this class representing a list of data areas attached to one sequence of the alignment.

The list type is automatically set to DataAreaListType.SEQUENCE.

Parameters:

owner - the parent element that will contain this list

sequenceID - the unique identifier of the sequence the contained data areas will be attached to

DataAreaList

public DataAreaList(DataAreasModel owner,
                    DataAreaLocation location)

Creates a new instance of this class representing a list of data areas attached to one sequence of the alignment.

Parameters:

owner - the parent element that will contain this list

location - the location this list will have in the alignment area

Method Detail

getOwner

public DataAreasModel getOwner()

getLocation

public DataAreaLocation getLocation()

Returns the location the elements in this list have in the containing AlignmentArea.

Returns:

the according location object

setAllVisible

public java.util.Collection<DataArea> setAllVisible(boolean visible)

Fades all elements in this list in or out.

Parameters:

visible - Specify true here, if you want the elements to be displayed, false otherwise.

Returns:

a collection containing all affected elements

See Also:

DataAreasModel.setSequenceDataAreasVisible(boolean)

visibleIterator

public java.util.Iterator<DataArea> visibleIterator()

Returns an iterator that only iterates over the visible data areas.

Returns:

an instance of DataAreaVisibleIterator

getVisibleHeight

public int getVisibleHeight()

Calculates the sum of the heights of all visible data areas contained in this list.

Returns:

an integer value greater of equal to zero

getMaxLengthBeforeStart

public double getMaxLengthBeforeStart()

Returns maximum space left of the alignment start that is needed by any currently visible data area in this list.

Returns:

an integer >= 0

getMaxLengthAfterEnd

public double getMaxLengthAfterEnd()

Returns maximum space right of the alignment end that is needed by any currently visible data area in this list.

Returns:

an integer >= 0