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	SeqWrap.getSequence() Retrieves the wrapped sequence object.
Sequence	SeqDoc.getSequence(int lineNumber) Retrieves a sequence object from the SeqDoc specified by its line number.
Sequence[]	SeqDoc.getSequences(int[] lineNumbers) Calls getSequence multiple times for multiple line numbers.
Sequence	SeqWrap.subseq(int start) Extracts a portion of the wrapper's sequence.
Sequence	SeqWrap.subseq(int start, int end) Extracts a portion of the wrapper's sequence.

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

void	SeqDoc.addSequence(int lineNumber, Sequence seq) Adds a sequence to the document.
void	SeqDoc.addSequence(Sequence seq) Adds a sequence to the end of the data container.
void	SeqDoc.addSequences(int lineNumber, Sequence[] sequenceList) Adds an array of sequences to a data container at position "lineNumber".
void	SeqDoc.addSequences(Sequence[] sequenceList) Adds an array of sequences to the end of the data container.
boolean	SeqDoc.insert(int offset, 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	SeqWrap.sequenceChanged(Sequence sequence, java.lang.String key) Handles changes to the inner sequence.
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

SeqWrap(int offset, Sequence seq)
Creates a new instance of SeqWrap.

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 with parameters of type Sequence

void	SequenceListener.sequenceChanged(Sequence sequence, java.lang.String key) This method is called when a field in a sequence is modified.

Uses of Sequence in org.biolegato.core.main

Fields in org.biolegato.core.main declared as Sequence

protected Sequence[]

ProgramWindow.clipboard Global clipboard used for copy, cut, and paste

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

Sequence[]	ProgramWindow.getAllData() Returns the complete contents of the data in the canvas.
Sequence[]	ProgramWindow.getClipboard() Obtains the current contents of the clipboard.
Sequence[]	ProgramWindow.getData() Returns the current/selected data in the canvas.

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

void	ProgramWindow.addData(Sequence[] dataAdd) Adds the data to the canvas.
void	ProgramWindow.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.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.