A B C D E F G I L M N O P R S T U V W

A

aboutPopup() - Method in class org.biolegato.core.main.ProgramWindow

Displays an about popup for BioLegato.

actionPerformed(ActionEvent) - Method in class org.biolegato.core.properties.PropertiesCheckbox

Handles changes in the status of the checkbox.

addData(Sequence[]) - Method in class org.biolegato.core.main.ProgramWindow

Adds the data to the canvas.

addExtension(PropertiesExtension) - Method in class org.biolegato.core.properties.BLProperties

Adds a properties extension to the properties registry.

addFormats(JFileChooser, String) - Static method in class org.biolegato.core.plugintypes.DataFormat

This function loads all of the available file formats into a JFileChooser.

addListener(SeqDocListener) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Adds a listener object to the data container.

addListener(SequenceListener) - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Adds a listener to the wrapped sequence.

addListener(SequenceListener) - Method in class org.biolegato.core.data.sequence.Sequence

Adds a sequence listener to keep track of sequence modifications.

addMenuHeading(String) - Method in class org.biolegato.core.main.ProgramWindow

Adds a menu heading (JMenu) to our menu (BLMenu).

addMenuHeading(int, String) - Method in class org.biolegato.core.main.ProgramWindow

Adds a menu heading (JMenu) to our menu (BLMenu).

addMenuItem(String, JMenuItem) - Method in class org.biolegato.core.main.ProgramWindow

Adds a menu item (JMenuItem) to a menu heading (JMenu) within the window (ProgramWindow)

addPropertiesListener(String, PropertiesListener) - Method in class org.biolegato.core.main.ProgramWindow

Adds a properties listener to the properties object.

addPropertiesListener(String, PropertiesListener) - Method in class org.biolegato.core.properties.BLProperties

Adds a listener for property changes NOTE: this method allows filtering based on which property changed

addSequence(Sequence) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Adds a sequence to the end of the data container.

addSequence(int, Sequence) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Adds a sequence to the document.

addSequences(int, Sequence[]) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Adds an array of sequences to a data container at position "lineNumber".

addSequences(Sequence[]) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Adds an array of sequences to the end of the data container.

auto(File) - Static method in class org.biolegato.core.plugintypes.DataFormat

Used to auto-detect and parse files into BioLegato sequence objects.

auto(InputStream) - Static method in class org.biolegato.core.plugintypes.DataFormat

Used to auto-detect and parse an input stream's data into BioLegato sequence objects.

B

BLMain - Class in org.biolegato.core.main

The main program and generic function class.

BLMain() - Constructor for class org.biolegato.core.main.BLMain

BLProperties - Class in org.biolegato.core.properties

Stores the properties for BioLegato.

BLProperties() - Constructor for class org.biolegato.core.properties.BLProperties

Create a new BLProperties instance

C

clipboard - Variable in class org.biolegato.core.main.ProgramWindow

Global clipboard used for copy, cut, and paste

clone() - Method in class org.biolegato.core.data.sequence.Sequence

Clones the current sequence object.

create() - Method in class org.biolegato.core.plugins.PluginWrapper

Creates a new object the plugin class.

create(Class[], Object[]) - Method in class org.biolegato.core.plugins.PluginWrapper

Creates a new object the wrapped plugin class (returns null if unsuccessful).

CURRENT_DIR - Static variable in class org.biolegato.core.main.ProgramWindow

This constant is set to the path of where biolegato was run The value of this constant determined at runtime.

D

DataCanvas - Class in org.biolegato.core.plugintypes

All subclasses are expected to implement a displayable canvas for BioLegato.

DataCanvas(ProgramWindow, int) - Constructor for class org.biolegato.core.plugintypes.DataCanvas

Creates a new instance of BLCanvas

DataFormat - Class in org.biolegato.core.plugintypes

DataFormat() - Constructor for class org.biolegato.core.plugintypes.DataFormat

Creates a new instance of DataFormat

DEFAULT_FONT - Static variable in class org.biolegato.core.main.ProgramWindow

The default font for BioLegato

delete(int, int) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Removes text from the document.

delete(int, int, int) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Removes text from the document.

DOUBLE_CLICK_TIME - Static variable in class org.biolegato.core.main.ProgramWindow

The amount of time between clicks to be considered a double click.

E

equals(Object) - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Tests equality of the inner sequence.

error(String) - Static method in class org.biolegato.core.main.BLMain

Sends an error message to BioLegato's standard err.

error(String, String) - Static method in class org.biolegato.core.main.BLMain

Sends an error message to BioLegato's standard err.

F

finalize() - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Removes the sequence wrapper as a sequence listener.

G

getAllData() - Method in class org.biolegato.core.main.ProgramWindow

Returns the complete contents of the data in the canvas.

getAllData() - Method in class org.biolegato.core.plugintypes.DataCanvas

Returns the complete contents of the data in the canvas.

getClipboard() - Method in class org.biolegato.core.main.ProgramWindow

Obtains the current contents of the clipboard.

getData() - Method in class org.biolegato.core.main.ProgramWindow

Returns the current/selected data in the canvas.

getData() - Method in class org.biolegato.core.plugintypes.DataCanvas

Returns the current/selected data in the canvas.

getDefault(String) - Static method in class org.biolegato.core.data.sequence.Sequence

This function obtains the default value of a field for a Sequence.

getField(String) - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Returns the content of a field within the wrapped sequence.

getField(String) - Method in class org.biolegato.core.data.sequence.Sequence

Obtains a value for a field of the sequence.

getFormat(String) - Static method in class org.biolegato.core.plugintypes.DataFormat

Finds the filetype that corresponds to the given hashname (null if not successful).

getLength() - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Returns the length of the data container's content.

getLine(int) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Retrieves a given line of text from the document.

getLineCount() - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Returns the number of lines in the document.

getLineEndOffset(int) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Retrieves the end offset of the given line.

getLineLength(int) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Retrieves the length of a line in the document.

getLineNumber(int) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Obtains the line number for a given offset.

getLineStartOffset(int) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Retrieves the start offset of a line.

getLongestLineLength() - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Returns the length of the longest line in the data container

getName() - Method in class org.biolegato.core.plugins.PluginWrapper

Returns the class's name.

getName() - Method in class org.biolegato.core.plugintypes.DataFormat

Obtains the name of the file format for File Chooser purposes

getPlugin(String) - Static method in class org.biolegato.core.plugins.PluginLoader

Retrieves a plugin by name.

getPluginHash() - Static method in class org.biolegato.core.plugins.PluginLoader

Maintains a list with all of the plugins loaded by BioLegato.

getPlugins(Class<?>) - Static method in class org.biolegato.core.plugins.PluginLoader

Returns a list with all of the plugins loaded by BioLegato that are instances of the class type indicated.

getProperty(String) - Method in class org.biolegato.core.main.ProgramWindow

Retrieves individual settings for BioLegato.

getProperty(String) - Method in class org.biolegato.core.properties.BLProperties

Obtains a property from the BLProperties object.

getSeqDoc() - Method in class org.biolegato.core.main.ProgramWindow

Returns the root sequence document for BioLegato.

getSequence(int) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Retrieves a sequence object from the SeqDoc specified by its line number.

getSequence() - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Retrieves the wrapped sequence object.

getSequences(int[]) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Calls getSequence multiple times for multiple line numbers.

getStart() - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Retrieves the start offset for the sequence wrapper object.

getTabName() - Method in class org.biolegato.core.plugintypes.DataCanvas

Returns the name of the canvas.

getText(int, int) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Retrieves a body of text from the data container.

I

insert(int, int, String) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Inserts a string into the document on a given line.

insert(int, Sequence[]) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Inserts sequences at a specific offset in the document.

isA(Class<?>) - Method in class org.biolegato.core.plugins.PluginWrapper

Used to test instanceof for the plugin class.

isFormat(Reader) - Method in class org.biolegato.core.plugintypes.DataFormat

Used to auto-detect Bio Legato formats

L

loadMenu(ProgramWindow) - Static method in class org.biolegato.core.plugintypes.MenuType

Reads a menu into the given window/menu instances.

loadPlugins(String) - Static method in class org.biolegato.core.plugins.PluginLoader

Loads an the plugins into BioLegato.

M

main(String[]) - Static method in class org.biolegato.core.main.BLMain

Starts up BioLegato.

mainSeqDoc - Variable in class org.biolegato.core.main.ProgramWindow

The main data container for BioLegato.

MenuType - Class in org.biolegato.core.plugintypes

An interface for menu reader objects.

MenuType() - Constructor for class org.biolegato.core.plugintypes.MenuType

message(String) - Static method in class org.biolegato.core.main.BLMain

Sends a message to BioLegato's standard out.

message(String, String) - Static method in class org.biolegato.core.main.BLMain

Sends a message to BioLegato's standard out.

N

NAME - Static variable in class org.biolegato.core.main.BLMain

This constant stores the program's name

O

org.biolegato.core.data.seqdoc - package org.biolegato.core.data.seqdoc

org.biolegato.core.data.seqdoc.undo - package org.biolegato.core.data.seqdoc.undo

org.biolegato.core.data.sequence - package org.biolegato.core.data.sequence

org.biolegato.core.main - package org.biolegato.core.main

org.biolegato.core.plugins - package org.biolegato.core.plugins

org.biolegato.core.plugintypes - package org.biolegato.core.plugintypes

org.biolegato.core.properties - package org.biolegato.core.properties

P

PluginLoader - Class in org.biolegato.core.plugins

This class is used to handle plugins.

PluginLoader() - Constructor for class org.biolegato.core.plugins.PluginLoader

PluginWrapper - Class in org.biolegato.core.plugins

This class is used to wrap plugins.

PluginWrapper(String, Class<?>) - Constructor for class org.biolegato.core.plugins.PluginWrapper

Creates a new instance of the plugin wrapper class.

program - Variable in class org.biolegato.core.plugintypes.DataCanvas

The program window to use to obtain program data from.

PROGRAM_DIR - Static variable in class org.biolegato.core.main.ProgramWindow

This constant is set to the path of BioLegato.jar The value of this constant determined at runtime.

ProgramWindow - Class in org.biolegato.core.main

The main program and generic function class.

ProgramWindow(String[]) - Constructor for class org.biolegato.core.main.ProgramWindow

Creates a new instance of ProgramWindow.

properties - Variable in class org.biolegato.core.main.ProgramWindow

Stores the properties for BioLegato.

PropertiesCheckbox - Class in org.biolegato.core.properties

Class used to create widgets to obtain boolean values for properties.

PropertiesCheckbox(BLProperties, String, String) - Constructor for class org.biolegato.core.properties.PropertiesCheckbox

Creates a new instance of PropertiesCheckbox

propertiesComponent(Container) - Method in interface org.biolegato.core.plugintypes.PropertiesExtension

Adds a component/container to a properties modification widget.

PropertiesExtension - Interface in org.biolegato.core.plugintypes

This plugin type is for extending BioLegato's property set.

PropertiesListener - Interface in org.biolegato.core.properties

Handler/listener interface for properties changes.

PropertiesNumber - Class in org.biolegato.core.properties

Class used to create widgets to obtain numerical values for properties.

PropertiesNumber(BLProperties, String, String, int, int) - Constructor for class org.biolegato.core.properties.PropertiesNumber

Creates a new instance of PropertiesNumber

propertiesUpdate(String, String) - Method in class org.biolegato.core.properties.PropertiesCheckbox

Handles changes in the status of the associated properties key.

propertiesUpdate(String, String) - Method in interface org.biolegato.core.properties.PropertiesListener

Receives properties update information from BioLegato

propertiesUpdate(String, String) - Method in class org.biolegato.core.properties.PropertiesNumber

Handles changes in the status of the associated properties key.

R

readFile(File) - Method in class org.biolegato.core.plugintypes.DataFormat

Reads a file's contained sequences using the file filter's translation.

readStream(BufferedReader) - Static method in class org.biolegato.core.main.BLMain

Reads the complete contents of a BufferedReader into a string.

redo() - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Performs an redo operation to the data container.

redoStack - Variable in class org.biolegato.core.data.seqdoc.SeqDoc

The stack of redoable events

removeListener(SequenceListener) - Method in class org.biolegato.core.data.sequence.Sequence

Removes a sequence listener from keeping track of sequence modifications.

removeSequence(int) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Removes a sequences from the data container.

removeSequences(int[]) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Removes an array of sequences from the data container.

S

safeExecute(String) - Method in class org.biolegato.core.main.ProgramWindow

Ensures that the command will be executed properly as a shell command

SeqDoc - Class in org.biolegato.core.data.seqdoc

The internal document format for BioLegato.

SeqDoc() - Constructor for class org.biolegato.core.data.seqdoc.SeqDoc

Creates a new instance of SeqDoc

SeqDocListener - Interface in org.biolegato.core.data.seqdoc

The listener class for sequence document objects.

Sequence - Class in org.biolegato.core.data.sequence

This class is used to contain all sequence related functions and data.

Sequence() - Constructor for class org.biolegato.core.data.sequence.Sequence

Constructs new instances of Sequence objects.

Sequence(String) - Constructor for class org.biolegato.core.data.sequence.Sequence

Constructs new instances of Sequence objects.

Sequence(Map<String, Object>) - Constructor for class org.biolegato.core.data.sequence.Sequence

Constructs new instances of sequence.

Sequence.Direction - Enum in org.biolegato.core.data.sequence

Used for typing/storing sequence direction.

Sequence.Strandedness - Enum in org.biolegato.core.data.sequence

Used for typing/storing sequence strandedness.

Sequence.Topology - Enum in org.biolegato.core.data.sequence

Used for typing/storing sequence topology.

Sequence.Type - Enum in org.biolegato.core.data.sequence

This enum is used for typing/storing sequence types.

sequenceAdded(SeqDoc, int, Sequence) - Method in interface org.biolegato.core.data.seqdoc.SeqDocListener

This method is called when a sequence is added to a SeqDoc.

sequenceChanged(Sequence, String) - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Called when a field in a sequence is modified.

sequenceChanged(SeqDoc, int, Sequence, String) - Method in interface org.biolegato.core.data.seqdoc.SeqDocListener

This method is called when a field in a sequence is modified.

sequenceChanged(Sequence, String) - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Handles changes to the inner sequence.

sequenceChanged(Sequence, String) - Method in interface org.biolegato.core.data.sequence.SequenceListener

This method is called when a field in a sequence is modified.

SequenceListener - Interface in org.biolegato.core.data.sequence

This listener received change events from sequences.

sequenceRemoved(SeqDoc, int, Sequence) - Method in interface org.biolegato.core.data.seqdoc.SeqDocListener

This method is called when a sequence is removed from the SeqDoc class.

SeqWrap - Class in org.biolegato.core.data.seqdoc

Used to wrap sequences; this object is used to give sequences start offsets, so they may be ordered within a SeqDoc structure.

SeqWrap(int, Sequence) - Constructor for class org.biolegato.core.data.seqdoc.SeqWrap

Creates a new instance of SeqWrap.

serialVersionUID - Static variable in class org.biolegato.core.main.ProgramWindow

This constant is used for Serialization

setClipboard(Sequence[]) - Method in class org.biolegato.core.main.ProgramWindow

Changes the current contents of the clipboard.

setField(String, Object) - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Alters the content of a field within the wrapped sequence.

setField(String, Object) - Method in class org.biolegato.core.data.sequence.Sequence

Changes a value of a field in the sequence.

setProperty(String, String) - Method in class org.biolegato.core.main.ProgramWindow

Changes properties for BioLegato.

setProperty(String, String) - Method in class org.biolegato.core.properties.BLProperties

Changes a property within the BLProperties object

setStart(int) - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Changes the start offset of the sequence.

shellCommand(String, String) - Method in class org.biolegato.core.main.ProgramWindow

Runs simple shell commands.

showPropertiesWindow(ProgramWindow) - Method in class org.biolegato.core.properties.BLProperties

Displays the properties window for this instance of BioLegato

smethod(String) - Method in class org.biolegato.core.plugins.PluginWrapper

Invokes a static method from the plugin.

smethod(String, Class[], Object[]) - Method in class org.biolegato.core.plugins.PluginWrapper

Invokes a static method from the plugin (returns null if not successful).

stateChanged(ChangeEvent) - Method in class org.biolegato.core.plugintypes.DataCanvas

Refreshes the canvas on tab changes.

stateChanged(ChangeEvent) - Method in class org.biolegato.core.properties.PropertiesNumber

Handles changes in the status of the spinner.

subseq(int) - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Extracts a portion of the wrapper's sequence.

subseq(int, int) - Method in class org.biolegato.core.data.seqdoc.SeqWrap

Extracts a portion of the wrapper's sequence.

subseq(int) - Method in class org.biolegato.core.data.sequence.Sequence

Extracts a portion of the current sequence.

subseq(int, int) - Method in class org.biolegato.core.data.sequence.Sequence

Extracts a portion of the current sequence.

T

toString() - Method in class org.biolegato.core.data.sequence.Sequence

Creates a string representation of the Sequence and its fields

translateFrom(BufferedReader) - Method in class org.biolegato.core.plugintypes.DataFormat

Translates a string from the given file format into the BioLegato internal format.

translateTo(Sequence) - Method in class org.biolegato.core.plugintypes.DataFormat

Translates a string from the BioLegato internal format to the given file format.

U

undo() - Method in class org.biolegato.core.data.seqdoc.SeqDoc

Performs an undo operation to the data container.

undo() - Method in interface org.biolegato.core.data.seqdoc.undo.Undoable

Undoes an action represented by the undoable object.

undo() - Method in class org.biolegato.core.data.seqdoc.undo.UndoDelete

Undoes the text deletion.

undo() - Method in class org.biolegato.core.data.seqdoc.undo.UndoInsert

Undoes the text insertion.

Undoable - Interface in org.biolegato.core.data.seqdoc.undo

This interface is used for generalizing all objects which perform undo-related actions.

UndoDelete - Class in org.biolegato.core.data.seqdoc.undo

This object is used to undo a deletion of text to a SeqDoc object.

UndoDelete(SeqDoc, int, int, String) - Constructor for class org.biolegato.core.data.seqdoc.undo.UndoDelete

Creates a new UndoDelete object for undoing text deletions.

UndoInsert - Class in org.biolegato.core.data.seqdoc.undo

This object is used to undo an insertion of text to a SeqDoc object.

UndoInsert(SeqDoc, int, int) - Constructor for class org.biolegato.core.data.seqdoc.undo.UndoInsert

Creates a new UndoInsert object for undoing text insertions.

undoStack - Variable in class org.biolegato.core.data.seqdoc.SeqDoc

The stack of undoable events.

V

valueOf(String) - Static method in enum org.biolegato.core.data.sequence.Sequence.Direction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biolegato.core.data.sequence.Sequence.Strandedness

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biolegato.core.data.sequence.Sequence.Topology

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biolegato.core.data.sequence.Sequence.Type

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biolegato.core.data.sequence.Sequence.Direction

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum org.biolegato.core.data.sequence.Sequence.Strandedness

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum org.biolegato.core.data.sequence.Sequence.Topology

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum org.biolegato.core.data.sequence.Sequence.Type

Returns an array containing the constants of this enum type, in the order they're declared.

VERSION - Static variable in class org.biolegato.core.main.ProgramWindow

This constant is used to keep track of version changes.

W

warning(String) - Static method in class org.biolegato.core.main.BLMain

Sends an warning message to BioLegato's standard err.

warning(String, String) - Static method in class org.biolegato.core.main.BLMain

Sends an warning message to BioLegato's standard err.

writeFile(File, Sequence[]) - Method in class org.biolegato.core.plugintypes.DataFormat

Writes a list of sequences to a file.

A B C D E F G I L M N O P R S T U V W