Uses of Class
org.biolegato.core.data.sequence.Sequence

Packages that use Sequence

org.biolegato.core.data.seqdoc
org.biolegato.core.data.sequence
org.biolegato.core.main
org.biolegato.core.plugintypes

Uses of Sequence in org.biolegato.core.data.seqdoc

Methods in org.biolegato.core.data.seqdoc that return Sequence

Sequence	SeqDoc.getLine(int y) Retrieves a sequence object from the SeqDoc specified by its line number.
Sequence[]	SeqDoc.toArray() Converts the SeqDoc into a sequence array representation

Methods in org.biolegato.core.data.seqdoc with parameters of type Sequence

boolean	SeqDoc.addSequence(int y, Sequence seq) Adds a sequence to the data container.
int	SeqDoc.indexOf(Sequence seq) Retrieves the line number for a sequence object in the SeqDoc.
boolean	SeqDoc.insert(int x, int y, Sequence[] sequences) Inserts sequences at a specific offset in the document.
void	SeqDocListener.sequenceAdded(SeqDoc source, int index, Sequence sequence) This method is called when a sequence is added to a SeqDoc.
void	SeqDocListener.sequenceChanged(SeqDoc source, int index, Sequence sequence, java.lang.String key) This method is called when a field in a sequence is modified.
void	SeqDoc.sequenceChanged(Sequence sequence, java.lang.String key) Called when a field in a sequence is modified.
void	SeqDocListener.sequenceRemoved(SeqDoc source, int index, Sequence sequence) This method is called when a sequence is removed from the SeqDoc class.

Constructors in org.biolegato.core.data.seqdoc with parameters of type Sequence

SeqDoc(Sequence[] sequenceList)
Creates a new instance of SeqDoc using the existing sequence list

Uses of Sequence in org.biolegato.core.data.sequence

Methods in org.biolegato.core.data.sequence that return Sequence

Sequence	Sequence.subseq(int start) Extracts a portion of the current sequence.
Sequence	Sequence.subseq(int start, int end) Extracts a portion of the current sequence.

Methods in org.biolegato.core.data.sequence that return types with arguments of type Sequence

static java.util.LinkedList<Sequence>

Sequence.getgroup(java.lang.Integer groupNumber)

Methods in org.biolegato.core.data.sequence with parameters of type Sequence

static void	Sequence.group(Sequence[] sequences)
void	SequenceListener.sequenceChanged(Sequence sequence, java.lang.String key) This method is called when a field in a sequence is modified.
static void	Sequence.ungroup(Sequence[] sequences)

Uses of Sequence in org.biolegato.core.main

Methods in org.biolegato.core.main that return Sequence

static Sequence[]	BLMain.getAllData() Returns the complete contents of the data in the canvas.
static Sequence[]	BLMain.getClipboard() Obtains the current contents of the clipboard (null if empty).
static Sequence[]	BLMain.getData() Returns the current/selected data in the canvas.

Methods in org.biolegato.core.main with parameters of type Sequence

static void	BLMain.addData(Sequence[] dataAdd) Adds the data to the canvas.
static void	BLMain.setClipboard(Sequence[] copy) Changes the current contents of the clipboard.

Uses of Sequence in org.biolegato.core.plugintypes

Methods in org.biolegato.core.plugintypes that return Sequence

static Sequence[]	DataFormat.auto(java.io.BufferedReader data) Used to auto-detect and parse data into BioLegato sequence objects.
static Sequence[]	DataFormat.auto(java.io.File file) Used to auto-detect and parse files into BioLegato sequence objects.
static Sequence[]	DataFormat.auto(java.io.InputStream stream) Used to auto-detect and parse an input stream's data into BioLegato sequence objects.
Sequence[]	DataCanvas.getAllData() Returns the complete contents of the data in the canvas.
Sequence[]	DataCanvas.getData() Returns the current/selected data in the canvas.
Sequence[]	DataFormat.readFile(java.io.File file) Reads a file's contained sequences using the file filter's translation.
abstract Sequence[]	DataFormat.translateFrom(java.io.BufferedReader data) Translates a string from the given file format into the BioLegato internal format.

Methods in org.biolegato.core.plugintypes with parameters of type Sequence

abstract java.lang.String	DataFormat.translateTo(Sequence data) Translates a string from the BioLegato internal format to the given file format.
void	DataFormat.writeFile(java.io.File file, Sequence[] data) Writes a list of sequences to a file.