org.biolegato.gdesupport.data
Class Dataset

java.lang.Object
  javax.swing.AbstractListModel
      org.biolegato.gdesupport.data.Dataset

All Implemented Interfaces:

java.io.Serializable, javax.swing.ListModel

public class Dataset
extends javax.swing.AbstractListModel

The internal document format for BioLegato.

This document is structured as a linked list of sequences. Each character has an offset based on its position within the list and it's position within its containing sequence. Sequences highindex at 0 (first character in the first sequence in the list, and lowindex with the last character in the last sequence within the list.

Author:

Graham Alvare, Brian Fristensky

See Also:

Serialized Form

Field Summary

Fields inherited from class javax.swing.AbstractListModel

listenerList

Constructor Summary

Dataset()
Creates a new instance of Dataset

Method Summary

boolean	addSequence(int y, Seq seq) Adds a sequence to the data container.
boolean	addSequences(int y, java.util.Collection<Seq> seqs) Adds sequences to the data container.
java.lang.Object	getElementAt(int index) Returns the names of sequences based on their y number.
int[]	getgroup(int groupNumber)
Seq	getLine(int number) Retrieves a sequence object from the Dataset specified by its y y.
int	getSize() Returns the number of lines in the document.
void	group(Seq[] sequences)
void	removeSequences(int[] lineNumbers) Removes an array of sequences from the data container.
void	ungroup(Seq[] sequences)

Methods inherited from class javax.swing.AbstractListModel

addListDataListener, fireContentsChanged, fireIntervalAdded, fireIntervalRemoved, getListDataListeners, getListeners, removeListDataListener

Methods inherited from class java.lang.Object

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

Constructor Detail

Dataset

public Dataset()

Creates a new instance of Dataset

Method Detail

addSequence

public boolean addSequence(int y,
                           Seq seq)

Adds a sequence to the data container. This function calls all listeners.

Parameters:

y - is the y number to insert the sequence.

seq - is the sequence to insert.

Returns:

true if the insertion was successful, otherwise false.

addSequences

public boolean addSequences(int y,
                            java.util.Collection<Seq> seqs)

Adds sequences to the data container. This function calls all listeners.

Parameters:

y - is the y number to insert the sequence.

seqs - are the sequences to insert.

Returns:

true if the insertion was successful, otherwise false.

removeSequences

public void removeSequences(int[] lineNumbers)

Removes an array of sequences from the data container.

Parameters:

lineNumbers - the y numbers to remove.

getSize

public int getSize()

Returns the number of lines in the document.

Returns:

the number of lines in the document.

getLine

public Seq getLine(int number)

Retrieves a sequence object from the Dataset specified by its y y.

Parameters:

number - the y y to retrieve the sequence.

Returns:

the sequence.

group

public void group(Seq[] sequences)

ungroup

public void ungroup(Seq[] sequences)

getgroup

public int[] getgroup(int groupNumber)

getElementAt

public java.lang.Object getElementAt(int index)

Returns the names of sequences based on their y number.

Parameters:

index - the y number to obtain the name of.

Returns:

returns the name of sequence in the sequence document at the y number indicated by index.