|
BioLegato 0.7.3 GDE plugin | |||||||||
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| Uses of Cell in org.biolegato.gdesupport.canvas |
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| Methods in org.biolegato.gdesupport.canvas that return Cell | |
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static Cell[] |
GDECanvas.getClipboard()
Obtains the current contents of the clipboard (null if empty). |
Cell[] |
GDECanvas.getData()
Returns the current/selected data in the canvas. |
Cell[] |
GDECanvasObject.getData()
Used to obtain all of the text selected within the document. |
Cell[] |
ClipboardWrapper.toArray()
Dumps the data contained within the clipboard wrapper |
| Methods in org.biolegato.gdesupport.canvas with parameters of type Cell | |
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static void |
GDECanvas.setClipboard(Cell[] copy)
Changes the current contents of the clipboard. |
| Constructors in org.biolegato.gdesupport.canvas with parameters of type Cell | |
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ClipboardWrapper(Cell[] cellArray)
Creates a new instance of ClipboardWrapper |
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| Uses of Cell in org.biolegato.gdesupport.canvas.colourmap |
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| Methods in org.biolegato.gdesupport.canvas.colourmap with parameters of type Cell | |
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void |
CharacterColourMap.regularDrawString(BLTextArea ta,
java.awt.Graphics gfx,
int xstart,
int ystart,
Cell seq,
char[] array,
int pstart,
int pend)
Draws a sequence mapping the appropriate colours to each character rendered |
abstract void |
ColourMap.regularDrawString(BLTextArea ta,
java.awt.Graphics gfx,
int xstart,
int ystart,
Cell seq,
char[] array,
int pstart,
int pend)
Draws an unselected sequence while mapping the appropriate colours to each character rendered. |
void |
MonochromeColourMap.regularDrawString(BLTextArea ta,
java.awt.Graphics gfx,
int xstart,
int ystart,
Cell seq,
char[] array,
int pstart,
int pend)
Draws a sequence mapping the appropriate colours to each character rendered. |
void |
PositionColourMap.regularDrawString(BLTextArea ta,
java.awt.Graphics gfx,
int xstart,
int ystart,
Cell seq,
char[] array,
int pstart,
int pend)
Draws a sequence mapping the appropriate colours to each character rendered |
java.lang.String |
ColourMap.safesubstring(Cell seq,
int pstart,
int pend)
Ensures all substrings do not excees the start or end of the sequence |
void |
ColourMap.selectDrawString(BLTextArea ta,
java.awt.Graphics gfx,
int xstart,
int ystart,
Cell seq,
char[] drawArray,
int pstart,
int pend)
Draws a selected sequence while mapping the appropriate colours to each character rendered. |
| Uses of Cell in org.biolegato.gdesupport.canvas.data |
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| Methods in org.biolegato.gdesupport.canvas.data that return Cell | |
|---|---|
Cell |
Dataset.get(int y)
Retrieves a sequence object from the Dataset specified by its line number. |
Cell |
GDEModel.get(int number)
Retrieves a sequence object from the Dataset specified by its line line. |
Cell[] |
Dataset.toArray()
Converts the Dataset into a sequence array representation |
Cell[] |
GDEModel.toArray()
|
| Methods in org.biolegato.gdesupport.canvas.data with parameters of type Cell | |
|---|---|
boolean |
Dataset.addRow(int y,
Cell seq)
Adds a sequence to the data container. |
boolean |
GDEModel.addSequence(int y,
Cell seq)
Adds a sequence to the data container. |
void |
GDEModel.addSequences(Cell[] list)
|
void |
DatasetListener.sequenceAdded(Dataset source,
int index,
Cell sequence)
This method is called when a sequence is added to a Dataset. |
void |
GDEModelListener.sequenceAdded(GDEModel source,
int index,
Cell sequence)
This method is called when a sequence is added to a Dataset. |
void |
CellListener.sequenceChanged(Cell sequence,
java.lang.String key)
This method is called when a field in a sequence is modified. |
void |
Dataset.sequenceChanged(Cell sequence,
java.lang.String key)
Called when a field in a sequence is modified. |
void |
GDEModel.sequenceChanged(Cell sequence,
java.lang.String key)
Called when a field in a sequence is modified. |
void |
DatasetListener.sequenceChanged(Dataset source,
int index,
Cell sequence,
java.lang.String key)
This method is called when a field in a sequence is modified. |
void |
GDEModelListener.sequenceChanged(GDEModel source,
int index,
Cell sequence,
java.lang.String key)
This method is called when a field in a sequence is modified. |
void |
DatasetListener.sequenceRemoved(Dataset source,
int index,
Cell sequence)
This method is called when a sequence is removed from the Dataset class. |
void |
GDEModelListener.sequenceRemoved(GDEModel source,
int index,
Cell sequence)
This method is called when a sequence is removed from the Dataset class. |
| Constructors in org.biolegato.gdesupport.canvas.data with parameters of type Cell | |
|---|---|
Dataset(Cell[] row)
Creates a new instance of Dataset using the existing sequence list |
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| Uses of Cell in org.biolegato.gdesupport.canvas.list |
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| Methods in org.biolegato.gdesupport.canvas.list that return Cell | |
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Cell[] |
GDEList.getData()
Returns the currently selected data in the list. |
| Methods in org.biolegato.gdesupport.canvas.list with parameters of type Cell | |
|---|---|
void |
SequenceListModel.sequenceAdded(GDEModel source,
int index,
Cell sequence)
Passes any sequence additions to the data listeners. |
void |
SequenceListModel.sequenceChanged(GDEModel source,
int index,
Cell sequence,
java.lang.String key)
Passes any sequence modifications to the data listeners. |
void |
SequenceListModel.sequenceRemoved(GDEModel source,
int index,
Cell sequence)
Passes any sequence deletions to the data listeners. |
| Constructors in org.biolegato.gdesupport.canvas.list with parameters of type Cell | |
|---|---|
GDESequenceWindow(GDEModel datamodel,
javax.swing.JFrame window,
Cell[] sequences)
Creates a window for editing the properties of a given array of sequences. |
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| Uses of Cell in org.biolegato.gdesupport.canvas.textarea |
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| Methods in org.biolegato.gdesupport.canvas.textarea that return Cell | |
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Cell[] |
BLTextArea.getData()
Used to obtain all of the text selected within the document. |
| Methods in org.biolegato.gdesupport.canvas.textarea with parameters of type Cell | |
|---|---|
boolean |
GDETextArea.getProtectAlignment(Cell seq,
java.lang.String text)
Checks a string against a sequence's alignment gap protection settings. |
boolean |
GDETextArea.getProtectAmbiguous(Cell seq,
java.lang.String text)
Checks a string against a sequence's ambiguous character protection settings. |
boolean |
GDETextArea.getProtectUnambiguous(Cell seq,
java.lang.String text)
Checks a string against a sequence's unambiguous character protection settings. |
boolean |
BLTextArea.insert(int col,
int y,
Cell[] data)
Inserts an array of sequences into the textarea's underlying Dataset |
boolean |
GDETextArea.isProtectionsOn(Cell seq,
java.lang.String text)
Checks a string against all of a sequence's protection settings. |
void |
BLTextArea.sequenceAdded(GDEModel source,
int index,
Cell sequence)
Called when a sequence is added to a Dataset. |
void |
BLTextArea.sequenceChanged(GDEModel source,
int index,
Cell sequence,
java.lang.String key)
Called when a field in a sequence is modified. |
void |
BLTextArea.sequenceRemoved(GDEModel source,
int index,
Cell sequence)
Called when a sequence is removed from a Dataset. |
Undoable |
UndoableGDETextArea.uinsert(int x,
int y,
Cell[] sequences)
Inserts an array of sequences into the textarea's underlying SeqDoc |
| Uses of Cell in org.biolegato.gdesupport.canvas.undo |
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| Constructors in org.biolegato.gdesupport.canvas.undo with parameters of type Cell | |
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UndoRowDeletion(GDEModel source,
int lineNumber,
Cell deleted)
Creates a new instance of UndoRowDeletion |
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| Uses of Cell in org.biolegato.gdesupport.formats |
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| Methods in org.biolegato.gdesupport.formats that return Cell | |
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static Cell[] |
DataFormat.auto(java.io.BufferedReader data)
Used to auto-detect and parse data into BioLegato sequence objects. |
static Cell[] |
DataFormat.auto(java.io.File file)
Used to auto-detect and parse files into BioLegato sequence objects. |
static Cell[] |
DataFormat.auto(java.io.InputStream stream)
Used to auto-detect and parse an input stream's data into BioLegato sequence objects. |
Cell[] |
DataFormat.readFile(java.io.File file)
Reads a file's contained sequences using the file filter's translation. |
abstract Cell[] |
DataFormat.translateFrom(java.io.BufferedReader data)
Translates a string from the given file format into the BioLegato internal format. |
Cell[] |
FastAFile.translateFrom(java.io.BufferedReader data)
Translates data in the FastA file format to sequence objecte |
Cell[] |
GDEFile.translateFrom(java.io.BufferedReader data)
Translates data in the GDE file format to sequence objecte |
Cell[] |
GDEFlatfile.translateFrom(java.io.BufferedReader data)
Translates data in the GDE flat file format to sequence objecte |
Cell[] |
GenBankFile2008.translateFrom(java.io.BufferedReader data)
Translates data in the GenBank file format to sequence objecte |
| Methods in org.biolegato.gdesupport.formats with parameters of type Cell | |
|---|---|
abstract java.lang.String |
DataFormat.translateTo(Cell data)
Translates a string from the BioLegato internal format to the given file format. |
java.lang.String |
FastAFile.translateTo(Cell seq)
Translates a sequence into the FastA file format. |
java.lang.String |
GDEFile.translateTo(Cell seq)
Translates a sequence into the GDE file format. |
java.lang.String |
GDEFlatfile.translateTo(Cell seq)
Translates a sequence into the GDE flat file format. |
java.lang.String |
GenBankFile2008.translateTo(Cell seq)
Translates a sequence into the GenBank file format. |
void |
DataFormat.writeFile(java.io.File file,
Cell[] rows)
Writes a list of sequences to a file. |
|
BioLegato 0.7.3 GDE plugin | |||||||||
| PREV NEXT | FRAMES NO FRAMES | |||||||||