info.bioinfweb.libralign.alignmentarea.order

Class SequenceOrder

java.lang.Object

info.bioinfweb.libralign.alignmentarea.order.SequenceOrder

public class SequenceOrder
extends java.lang.Object

Manages the ordering of the sequences displayed by AlignmentArea.

Since:

0.0.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
SequenceOrder(AlignmentArea owner) Crates a new instance of this class and loads the names from the underlying data source of the specified owner, if it has a data source.

Method Summary

Modifier and Type	Method and Description
SequenceOrderType	getOrderType()
AlignmentArea	getOwner()
java.lang.String	idByIndex(int index) Returns the unique identifier of the sequence displayed at the specified index
java.util.Iterator<java.lang.String>	idIterator() Returns an iterator over all IDs contained in this order.
int	indexByID(java.lang.String id) Returns the display index of the sequence with the specified ID.
int	moveSequence(int index, int offset) Moves a sequence to a new position.
void	refreshFromSource()
void	setAlphabeticalSequenceOrder(boolean ascending) Sorts the sequences by their name.
void	setSourceSequenceOrder() Sorts the sequences by their occurrence in the source data.

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceOrder

public SequenceOrder(AlignmentArea owner)

Crates a new instance of this class and loads the names from the underlying data source of the specified owner, if it has a data source.

The initial order the determined by the oder in the data source.

Parameters:

owner - the alignment view objects the returned instance should be used for

Method Detail

getOwner

public AlignmentArea getOwner()

getOrderType

public SequenceOrderType getOrderType()

indexByID

public int indexByID(java.lang.String id)

Returns the display index of the sequence with the specified ID.

Parameters:

id - the unique identifier of the sequence

Returns:

the index of the sequence (The first sequence has the index 0.)

idByIndex

public java.lang.String idByIndex(int index)

Returns the unique identifier of the sequence displayed at the specified index

Parameters:

index - the index of the sequence (The first sequence has the index 0.)

Returns:

the ID of the sequence in the data source

Throws:

java.lang.IndexOutOfBoundsException - if the specified index is below 0 or greater or equal to number of sequences.

refreshFromSource

public void refreshFromSource()

setSourceSequenceOrder

public void setSourceSequenceOrder()

Sorts the sequences by their occurrence in the source data.

This method can also be used to refresh the sequence names if the data source changed.

setAlphabeticalSequenceOrder

public void setAlphabeticalSequenceOrder(boolean ascending)

Sorts the sequences by their name.

Parameters:

ascending - Specify true here, if you want the sequences to have an ascending alphabetical order and false for a descending order.

moveSequence

public int moveSequence(int index,
                        int offset)

Moves a sequence to a new position. All other sequences are moved by one position accordingly.

If the index + offset is lower than 0 the sequence if moved to the beginning, if the result greater than the index of the last element in the list, the sequence is moved to the end.

Parameters:

index - the index of the sequence to be moved (The first sequence has the index 0.)

offset - the number of positions to move the sequence (Can be positive or negative.)

Returns:

the new index the specified sequence has after the move operation

idIterator

public java.util.Iterator<java.lang.String> idIterator()

Returns an iterator over all IDs contained in this order.

Returns:

an unmodifiable iterator object