- canvas - Variable in class org.biolegato.sequence.canvas.SequenceList
-
Canvas object which owns this SequenceList instance.
- changeCase() - Method in interface org.biolegato.sequence.canvas.SequenceCanvasObject
-
Changes the case of the currently selected sequence.
- changeCase() - Method in class org.biolegato.sequence.canvas.SequenceList
-
Changes the case of the currently selected sequence.
- changeCase() - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Changes the case of the currently selected sequence.
- changeCaseAction - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
-
The "Change case" menu item action.
- changePosition(boolean, int, int) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Updates/moves the cursor to a new position.
- CHAR_MASK_FILTER - Static variable in class org.biolegato.sequence.canvas.ColourMask
-
The colour mask file reader for GDE's position-based colour mask files.
- clearSelection() - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Clears the current text selection (does NOT delete any text).
- clone() - Method in class org.biolegato.sequence.data.Seq
-
Clones the current sequence object.
- col - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
-
The current column number/X-coordinate of the text caret cursor.
- ColourMask - Class in org.biolegato.sequence.canvas
-
Colour mask support file
- ColourMask(ColourMask.MaskType, String, Color[]) - Constructor for class org.biolegato.sequence.canvas.ColourMask
-
Creates a new instance of a colour mask
- ColourMask.MaskType - Enum in org.biolegato.sequence.canvas
-
The type of mask defined by the colour mask class
(i.e.
- colourMasks - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
-
The list of all colour masks loaded in the system.
- colWidth - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
-
The width of each column in the text area.
- contentsChanged(ListDataEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
This method is called when a field in a sequence is modified.
- convertFrom(Dataset, Scanner, int, int) - Method in class org.biolegato.sequence.data.DataFormat
-
Converts a string from the given file format into the BioLegato
internal format.
- convertSequence(Dataset, Scanner, int, int, boolean) - Method in class org.biolegato.sequence.data.DataFormat
-
Converts a single sequence from a scanner into BioLegato.
- convertSequence(Dataset, Scanner, int, int, boolean) - Method in class org.biolegato.sequence.data.FastAFile
-
Translates a single sequence from a scanner into BioLegato
- convertSequence(Dataset, Scanner, int, int, boolean) - Method in class org.biolegato.sequence.data.GDEFile
-
Translates a single sequence from a scanner into BioLegato
- convertSequence(Dataset, Scanner, int, int, boolean) - Method in class org.biolegato.sequence.data.GDEFlatfile
-
Translates a single sequence from a scanner into BioLegato
- convertSequence(Dataset, Scanner, int, int, boolean) - Method in class org.biolegato.sequence.data.GenBankFile2008
-
Converts a single sequence from a scanner into BioLegato
- convertTo(Appendable, Dataset, int) - Method in class org.biolegato.sequence.data.DataFormat
-
Converts data from the BioLegato's sequence canvas internal format
to the given file format specified by the DataFormat object.
- convertTo(Appendable, Dataset, int, int, int) - Method in class org.biolegato.sequence.data.DataFormat
-
Converts data from the BioLegato's sequence canvas internal format
to the given file format.
- convertTo(Appendable, Seq, int, int) - Method in class org.biolegato.sequence.data.DataFormat
-
Converts data from the BioLegato's sequence canvas internal format
to the given file format.
- convertTo(Appendable, Seq, int, int) - Method in class org.biolegato.sequence.data.FastAFile
-
Translates data from the BioLegato's sequence canvas internal format to
the given file format.
- convertTo(Appendable, Seq, int, int) - Method in class org.biolegato.sequence.data.GDEFile
-
Translates data from the BioLegato's sequence canvas internal format to
the given file format.
- convertTo(Appendable, Seq, int, int) - Method in class org.biolegato.sequence.data.GDEFlatfile
-
Translates data from the BioLegato's sequence canvas internal format to
the given file format.
- convertTo(Appendable, Seq, int, int) - Method in class org.biolegato.sequence.data.GenBankFile2008
-
Converts data from the BioLegato's sequence canvas internal format to
the given file format.
- copyAct - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
-
The "Copy" menu item action.
- copyClipboard() - Method in class org.biolegato.sequence.canvas.SequenceCanvas
-
Copies the currently selected sequences or text from the sequence canvas
to the clipboard.
- cursorChange(int, int) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
-
This method receives cursor updates for use in the status bar, and
updates the row and column number displayed in the sequence canvas's
status bar.
- cutAct - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
-
The "Cut" menu item action.
- DataFormat - Class in org.biolegato.sequence.data
-
Class to represent reading of data formats.
- DataFormat() - Constructor for class org.biolegato.sequence.data.DataFormat
-
Creates a new instance of DataFormat
- datamodel - Variable in class org.biolegato.sequence.canvas.SequenceList
-
Used for the relationship between the data model and the list.
- datamodel - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
-
This reference is used to connect the data model/Dataset sequence object
container to the text area.
- Dataset - Class in org.biolegato.sequence.data
-
The internal document format for BioLegato.
- Dataset(SequenceCanvas) - Constructor for class org.biolegato.sequence.data.Dataset
-
Creates a new instance of the Dataset object.
- DBL_CLICK_TIME - Static variable in class org.biolegato.sequence.canvas.SequenceList
-
The amount of time (ms) between clicks to be considered a double click.
- DEFAULT_FONT - Static variable in class org.biolegato.sequence.canvas.SequenceCanvas
-
The default font for the canvas (12pt monospaced).
- DEFAULT_MASK - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
-
The default colour mask for BioLegato.
- delete(int, int, int, int, boolean) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Deletes characters from the textarea's underlying Dataset
NOTE: deletions are performed in a sequential manner
- delete(int, int, int, boolean) - Method in class org.biolegato.sequence.data.Dataset
-
Deletes a portion of a sequence from the Dataset sequence object
container.
- deleteSelection() - Method in interface org.biolegato.sequence.canvas.SequenceCanvasObject
-
Cuts/deletes the content selected in the sequence canvas object.
- deleteSelection() - Method in class org.biolegato.sequence.canvas.SequenceList
-
Deletes the currently selected sequences.
- deleteSelection(boolean) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Deletes any text currently selected.
- deleteSelection() - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Deletes any text currently selected.
- detectType(StringBuffer) - Static method in class org.biolegato.sequence.data.Seq
-
This function detects the type of a sequence (RNA, DNA, or protein).
- display() - Method in class org.biolegato.sequence.canvas.SequenceCanvas
-
Displays the canvas.
- drawString(Graphics, char[], int, int, int, int) - Method in class org.biolegato.sequence.canvas.ColourMask
-
Draws a character string using the character colour coding specified by
the ColourMask object.
- GDE_MASK_FILTER - Static variable in class org.biolegato.sequence.canvas.ColourMask
-
The colour mask file reader for BioLegato's
character-based colour mask files.
- GDEFILE - Static variable in class org.biolegato.sequence.data.DataFormat
-
A static final object used for handling normal GDE files.
- GDEFile - Class in org.biolegato.sequence.data
-
This class acts as a parser/translator for standard GDE files.
- GDEFile() - Constructor for class org.biolegato.sequence.data.GDEFile
-
Creates a new instance of GDEFile
- GDEFLAT - Static variable in class org.biolegato.sequence.data.DataFormat
-
A static final object used for handling GDE flat-files.
- GDEFlatfile - Class in org.biolegato.sequence.data
-
This class acts as a parser/translator for GDE flat files.
- GDEFlatfile() - Constructor for class org.biolegato.sequence.data.GDEFlatfile
-
Creates a new instance of GDEFlatfile
- GENBANK - Static variable in class org.biolegato.sequence.data.DataFormat
-
A static final object used for handling GenBank files.
- GenBankFile2008 - Class in org.biolegato.sequence.data
-
This class acts as a parser/translator for GenBank files (using the file
specification current to 2008).
- GenBankFile2008() - Constructor for class org.biolegato.sequence.data.GenBankFile2008
-
Creates a new instance of GenBankFile2008
- getDefaultMask() - Method in class org.biolegato.sequence.canvas.SequenceCanvas
-
Load the default colour masks into BioLegato (this was the only way I was
able to get the default colour mask to load properly and efficiently).
- getDescription() - Method in class org.biolegato.sequence.data.FastAFile
-
Returns a description of the file format that can be displayed to the
user.
- getDescription() - Method in class org.biolegato.sequence.data.GDEFile
-
Returns a description of the file format that can be displayed to the
user.
- getDescription() - Method in class org.biolegato.sequence.data.GDEFlatfile
-
Returns a description of the file format that can be displayed to the
user.
- getDescription() - Method in class org.biolegato.sequence.data.GenBankFile2008
-
Returns a description of the file format that can be displayed to the
user.
- getElementAt(int) - Method in class org.biolegato.sequence.data.Dataset
-
Returns the names of sequences based on their Y-coordinate/"line number".
- getFormat(String) - Static method in class org.biolegato.sequence.data.DataFormat
-
Finds the file type that corresponds to a given GDE/PCD file format
hashname (returns the GDE flat file, by default, if not successful).
- getgroup(int) - Method in class org.biolegato.sequence.data.Dataset
-
Obtains all of the line numbers of the sequences in a particular group.
- getInfoAction - Variable in class org.biolegato.sequence.canvas.SequenceList
-
The menu item "Get info..."
- getMask(int) - Method in class org.biolegato.sequence.data.Dataset
-
Retrieves the colour mask object for a given sequence 'line' in the
Dataset sequence object container.
- getPluginName() - Method in class org.biolegato.sequence.canvas.SequenceCanvas
-
- getSequence(char[], int, int, int) - Method in class org.biolegato.sequence.data.Dataset
-
Retrieves the text contained within a sequence object in the Dataset.
- getSequenceLength(int) - Method in class org.biolegato.sequence.data.Dataset
-
Retrieves the length (in characters) of a given sequence 'line' in the
Dataset sequence object container.
- getSize() - Method in class org.biolegato.sequence.data.Dataset
-
Returns a count of the total number of sequences (lines) in the Dataset
sequence object container.
- group(int[]) - Method in class org.biolegato.sequence.data.Dataset
-
Creates a new sequence-group comprised of the sequences specified by
Y-coordinate/"line numbers" in the array parameter 'sequences'.
- groupAction - Variable in class org.biolegato.sequence.canvas.SequenceList
-
Action for grouping sequences in the canvas
- insert(int, int, char[], boolean) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Inserts a string into the textarea's underlying Dataset object.
- insert(int, int, char[], int, int, boolean) - Method in class org.biolegato.sequence.data.Dataset
-
Inserts text into the Dataset sequence object container.
- insertionMode(boolean) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
-
Thie method receives insertion mode change updates for use in the status
bar.
- insertionMode(boolean) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
This method receives insertion mode change updates.
- insertMode - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
-
If set to true, when the user types text, it will overwrite whatever
existing text is already under the cursor.
- intervalAdded(ListDataEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Called when a sequence is added to a Dataset.
- intervalRemoved(ListDataEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Called when a sequence is removed from a Dataset.
- isFormat(Scanner) - Method in class org.biolegato.sequence.data.DataFormat
-
Used as part of the DataFormat auto-detection algorithm.
- isFormat(Scanner) - Method in class org.biolegato.sequence.data.FastAFile
-
Used as part of the DataFormat auto-detection algorithm.
- isFormat(Scanner) - Method in class org.biolegato.sequence.data.GDEFile
-
Used as part of the DataFormat auto-detection algorithm.
- isFormat(Scanner) - Method in class org.biolegato.sequence.data.GDEFlatfile
-
Used as part of the DataFormat auto-detection algorithm.
- isFormat(Scanner) - Method in class org.biolegato.sequence.data.GenBankFile2008
-
Used as part of the DataFormat auto-detection algorithm.
- isProtectionsOn(Seq.Type, boolean, boolean, boolean, char[], int, int) - Static method in class org.biolegato.sequence.data.Dataset
-
Checks a string against all of a sequence's protection settings.
- isSelectionEmpty() - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Tests if the text selection shape is empty (i.e.
- itemStateChanged(ItemEvent) - Method in class org.biolegato.sequence.data.SequenceWindow
-
Handles sequence-type changes made (this includes greying out parameters
which are not applicable to the current sequence type).
- saveAsAction - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
-
The "Save ALL As..." menu item action.
- selectAllAction - Variable in class org.biolegato.sequence.canvas.SequenceList
-
The menu item "Select All"
- SELECTBG - Static variable in class org.biolegato.sequence.canvas.SequenceTextArea
-
The background colour of selected text.
- selectByNameAction - Variable in class org.biolegato.sequence.canvas.SequenceList
-
The abstract action "Select sequence by name"
- SELECTFG - Static variable in class org.biolegato.sequence.canvas.SequenceTextArea
-
The foreground colour of selected text.
- selectGroupAction - Variable in class org.biolegato.sequence.canvas.SequenceList
-
The menu item "Select group"
- selectionMade(SequenceTextArea) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
-
Manages mutual exclusion between the textareas and the list
This method listens to the sequence text area, and deselects any
sequences in the sequence list, and the other text area (if the text area
is split), whenever something is selected in one of the sequence text
areas.
- selectionMouse - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
-
Used to track mouse holds and releases.
- selectionMove - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
-
Used to track whether the shift key is pressed.
- Seq - Class in org.biolegato.sequence.data
-
This class is used to contain all sequence related functions.
- Seq() - Constructor for class org.biolegato.sequence.data.Seq
-
Constructs new instances of a sequence object.
- Seq(Seq.Type, String, StringBuffer) - Constructor for class org.biolegato.sequence.data.Seq
-
Constructs new instances of a sequence object.
- Seq(Seq.Type, String, StringBuffer, String) - Constructor for class org.biolegato.sequence.data.Seq
-
Constructs new instances of a sequence object.
- Seq(Seq.Type, String, StringBuffer, Seq.Direction, Seq.Topology, Seq.Strandedness) - Constructor for class org.biolegato.sequence.data.Seq
-
Constructs new instances of a sequence object.
- Seq(Seq.Type, String, StringBuffer, Seq.Direction, Seq.Topology, Seq.Strandedness, CharSequence) - Constructor for class org.biolegato.sequence.data.Seq
-
Constructs new instances of a sequence object.
- Seq(Seq.Type, String, StringBuffer, Seq.Direction, Seq.Topology, Seq.Strandedness, int, String) - Constructor for class org.biolegato.sequence.data.Seq
-
Constructs new instances of a sequence object.
- Seq(Seq) - Constructor for class org.biolegato.sequence.data.Seq
-
Constructs new instance of a sequence object by copying data from
another, pre-existing sequence object.
- Seq.Direction - Enum in org.biolegato.sequence.data
-
Used for typing/storing sequence direction.
- Seq.Strandedness - Enum in org.biolegato.sequence.data
-
Used for typing/storing sequence strandedness.
- Seq.Topology - Enum in org.biolegato.sequence.data
-
Used for typing/storing sequence topology.
- Seq.Type - Enum in org.biolegato.sequence.data
-
This enum is used for typing/storing sequence types.
- SequenceCanvas - Class in org.biolegato.sequence.canvas
-
The BioLegato sequence-based canvas class (based on GDE).
- SequenceCanvas() - Constructor for class org.biolegato.sequence.canvas.SequenceCanvas
-
Creates a new instance of a SequenceCanvas.
- SequenceCanvas(Map<? extends Object, ? extends Object>) - Constructor for class org.biolegato.sequence.canvas.SequenceCanvas
-
Creates a new instance of a SequenceCanvas.
- SequenceCanvasObject - Interface in org.biolegato.sequence.canvas
-
An interface for abstracting the two canvas objects (SequenceTextArea and
SequenceList) within BioLegato's Sequence canvas.
- SequenceCanvasProperties - Class in org.biolegato.sequence.canvas
-
A class for setting properties for the Sequence canvas.
- SequenceCanvasProperties(JFrame, SequenceCanvas) - Constructor for class org.biolegato.sequence.canvas.SequenceCanvasProperties
-
Creates a new SequenceCanvasProperties object.
- SequenceList - Class in org.biolegato.sequence.canvas
-
The JList of sequences in the Sequence canvas (to the left of the text-area).
- SequenceList(SequenceCanvas, Dataset) - Constructor for class org.biolegato.sequence.canvas.SequenceList
-
Constructs a new SequenceList
- SequenceTextArea - Class in org.biolegato.sequence.canvas
-
A general canvas with more functionality support than JTextArea.
- SequenceTextArea(SequenceCanvas, Dataset) - Constructor for class org.biolegato.sequence.canvas.SequenceTextArea
-
Creates a new instance of a SequenceTextArea.
- SequenceWindow - Class in org.biolegato.sequence.data
-
A window for editing/viewing the properties of sequences in the canvas.
- SequenceWindow(SequenceCanvas, Dataset, JFrame, int[]) - Constructor for class org.biolegato.sequence.data.SequenceWindow
-
Creates a window for editing the properties of selected sequences.
- serialVersionUID - Static variable in class org.biolegato.sequence.canvas.SequenceTextArea
-
This constant is used for serialization purposes.
- serialVersionUID - Static variable in class org.biolegato.sequence.data.SequenceWindow
-
Used for serialization purposes.
- setFont(Font) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
-
Updates the font for the text area.
- stateChanged(ChangeEvent) - Method in class org.biolegato.sequence.canvas.SequenceCanvasProperties
-
Handles changes to the font size spinner
(updates the font on spinner value change).
- STDCOLOURS - Static variable in class org.biolegato.sequence.canvas.ColourMask
-
These are the default colours specified in GDE colour mask files.
- valueChanged(ListSelectionEvent) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
-
This method listens to the sequence list, and deselects any text in the
sequence text area(s) whenever something is selected in the sequence
list.
- valueOf(String) - Static method in enum org.biolegato.sequence.canvas.ColourMask.MaskType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biolegato.sequence.data.Seq.Direction
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biolegato.sequence.data.Seq.Strandedness
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biolegato.sequence.data.Seq.Topology
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.biolegato.sequence.data.Seq.Type
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum org.biolegato.sequence.canvas.ColourMask.MaskType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biolegato.sequence.data.Seq.Direction
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biolegato.sequence.data.Seq.Strandedness
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biolegato.sequence.data.Seq.Topology
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.biolegato.sequence.data.Seq.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.