org.biolegato.tables

Class TableCanvas

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Panel

java.applet.Applet

javax.swing.JApplet

org.biolegato.main.DataCanvas

org.biolegato.tables.TableCanvas

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, org.biopcd.parser.PCDIO

public class TableCanvas
extends org.biolegato.main.DataCanvas

BioLegato's table canvas.

Author:

Graham Alvare, Brian Fristensky

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	TableCanvas.SelectionMode The selection modes available for the table canvas.

Nested classes/interfaces inherited from class javax.swing.JApplet

javax.swing.JApplet.AccessibleJApplet

Nested classes/interfaces inherited from class java.applet.Applet

java.applet.Applet.AccessibleApplet

Nested classes/interfaces inherited from class java.awt.Panel

java.awt.Panel.AccessibleAWTPanel

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
javax.swing.AbstractAction	selectAllA The menu item "Select All"

Fields inherited from class org.biolegato.main.DataCanvas

ABOUT_MENUITEM, EMPTY_STRING, EXIT_MENUITEM, NAME, properties, serialVersionUID

Fields inherited from class javax.swing.JApplet

accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Modifier	Constructor and Description
	TableCanvas() Creates a new instance of a TableCanvas.
	TableCanvas(java.util.Map<? extends java.lang.Object,? extends java.lang.Object> props) Creates a new instance of TableCanvas.
	TableCanvas(java.util.Map<? extends java.lang.Object,? extends java.lang.Object> props, java.sql.ResultSet rs) Creates a new instance of TableCanvas, reading results from an SQL query into the table, by default.
	TableCanvas(java.util.Map<? extends java.lang.Object,? extends java.lang.Object> propertiesadd, java.lang.String[][] dataImport) Creates a new instance of TableCanvas.
protected	TableCanvas(java.sql.ResultSet rs) Creates a new instance of TableCanvas, reading results from an SQL query into the table, by default.

Method Summary

Modifier and Type	Method and Description
void	addColumns(java.lang.String[] columns) Adds a list of column headers to the current table model.
static java.lang.String	columnLetter(int columnCount) Converts a number into a column letter(s).
java.awt.Component	display() Displays the table canvas within a BioLegato window.
java.lang.String[][]	getData() Returns the current/selected data in the canvas as a 2D string array.
java.lang.String[][]	getData(boolean forceall) Returns the current/selected data in the canvas as a 2D string array.
java.lang.String	getPluginName() Deprecated. vestigial code from a previous BioLegato framework structure.
static void	main(java.lang.String[] args) Starts a new instance of BioLegato, using the table canvas.
void	readFile(java.lang.String format, java.io.Reader in, boolean overwrite, boolean forceall) Reads a data into the canvas.
void	setSelectionMode(TableCanvas.SelectionMode m) Changes the SelectioMode of the TableCanvas
void	writeFile(java.lang.String format, java.lang.Appendable out, boolean forceall) Writes data out from the canvas to an Appendable object.

Methods inherited from class org.biolegato.main.DataCanvas

addMenuHeading, addMenuHeading, createJFrame, error, getJFrame, getProperty, init, message, testNumber, warning

Methods inherited from class javax.swing.JApplet

addImpl, createRootPane, getAccessibleContext, getContentPane, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isRootPaneCheckingEnabled, paramString, remove, repaint, setContentPane, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.applet.Applet

destroy, getAppletContext, getAppletInfo, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, getParameterInfo, isActive, isValidateRoot, newAudioClip, play, play, resize, resize, setStub, showStatus, start, stop

Methods inherited from class java.awt.Panel

addNotify

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, revalidate, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

selectAllA

public final javax.swing.AbstractAction selectAllA

The menu item "Select All"

Constructor Detail

TableCanvas

public TableCanvas()

Creates a new instance of a TableCanvas. This is the most basic constructor available.

TableCanvas

public TableCanvas(java.util.Map<? extends java.lang.Object,? extends java.lang.Object> props)

Creates a new instance of TableCanvas. This constructor will accept a Map of values for BioLegato properties.

Parameters:

props - the BioLegato properties to initialize the canvas with. This parameter is ignored if null.

TableCanvas

protected TableCanvas(java.sql.ResultSet rs)

Creates a new instance of TableCanvas, reading results from an SQL query into the table, by default.

Parameters:

rs - the results of an SQL query; these are to be used as the initial contents of the table canvas.

TableCanvas

public TableCanvas(java.util.Map<? extends java.lang.Object,? extends java.lang.Object> props,
                   java.sql.ResultSet rs)

Creates a new instance of TableCanvas, reading results from an SQL query into the table, by default. This constructor will also accept a Map of values for BioLegato properties.

Parameters:

props - the BioLegato properties to initialize the canvas with. This parameter is ignored if null.

rs - the results of an SQL query; these are to be used as the initial contents of the table canvas.

TableCanvas

public TableCanvas(java.util.Map<? extends java.lang.Object,? extends java.lang.Object> propertiesadd,
                   java.lang.String[][] dataImport)

Creates a new instance of TableCanvas. This constructor will accept a Map of values for BioLegato properties, and a 2D string array containing the initial data for the TableCanvas. The first index corresponds to the row number, and the second index corresponds to the column number. For example, the index dataImport[1][4] corresponds to the 2nd row, 5th column. The first row contains the column names/headers for the table.

Parameters:

props - the BioLegato properties to initialize the canvas with. This parameter is ignored if null.

dataImport - a 2D string array to initialize the canvas with.

Method Detail

main

public static void main(java.lang.String[] args)

Starts a new instance of BioLegato, using the table canvas.

Parameters:

args - the command line arguments for BioLegato.

getData

public java.lang.String[][] getData()

Returns the current/selected data in the canvas as a 2D string array. The first index corresponds to the row number, and the second index corresponds to the column number. For example, the index dataImport[1][4] corresponds to the 2nd row, 5th column. The first row contains the column names/headers for the table. This method is an alias for: getData(false).

Returns:

the current data stored in the table canvas (as a 2D string array).

getData

public java.lang.String[][] getData(boolean forceall)

Returns the current/selected data in the canvas as a 2D string array. The first index corresponds to the row number, and the second index corresponds to the column number. For example, the index dataImport[1][4] corresponds to the 2nd row, 5th column. The first row contains the column names/headers for the table.

Parameters:

forceall - use the entire canvas instead of just only exporting whichever sequences are selected.

Returns:

the current data stored in the table canvas (as a 2D string array).

columnLetter

public static java.lang.String columnLetter(int columnCount)

Converts a number into a column letter(s). This is used if the first line of a file being imported does not contain column headers -- i.e. namedHeaders is set to false. The column letter(s) are a base-26 representation of the number 'columnCount' using alphabet letters.

The only exception is that the value zero cannot be represented, thus the letter "A" represents the value zero in the right-most digit, but the letter "A" represents the value one for every other digit. This is okay, because we are only displaying column letters, and not creating a true base-10 to base-26 converter.

For example, the value 27 is equal to "AA" (26 + 1)
Likewise, the value 3 is equal to "C", and the value 56 is "BC"

Parameters:

columnCount - the number of the column to convert into a letter

Returns:

the letter that corresponds to column #columnCount

addColumns

public void addColumns(java.lang.String[] columns)

Adds a list of column headers to the current table model. These column headers are added as new columns.

Parameters:

columns - the array of column names to use for adding columns.

getPluginName

public java.lang.String getPluginName()

Deprecated. vestigial code from a previous BioLegato framework structure.

Possible vestigial code! This code is used to provide a plugin name for the canvas. The purpose of the plugin name system was to allow multiple canvases to be loaded (via. BioLegato's plugin system), and then have the properties select which canvas to use based on the plugin names. This architecture has since been replaced, and so this code may no longer be used.

Specified by:

getPluginName in class org.biolegato.main.DataCanvas

Returns:

the name to display for the canvas in all program text referring to it.

readFile

public void readFile(java.lang.String format,
                     java.io.Reader in,
                     boolean overwrite,
                     boolean forceall)
              throws java.io.IOException

Reads a data into the canvas. This method only handles CSV (comma- separated-values) and TSV (tab-separated-values) spreadsheet table formats. If any other formats are passed to this method, this method will default to the TSV format. For more information about the exact parsing specification of BioLegato's TSV and CSV formats, please see the CSVFile and TSVFile JavaCC code and classes.

Parameters:

format - the file format to use for parsing the file. If the string "" is passed, the PCDIO object should auto- detect the format of the data.

in - the "file" (or stream) to read in from.

overwrite - whether to overwrite the currently selected data in the current canvas with the data being imported by this function/method.

forceall - force selection of the entire canvas.

Throws:

java.io.IOException - if an error occurs while reading

See Also:

CSVFile, TSVFile

writeFile

public void writeFile(java.lang.String format,
                      java.lang.Appendable out,
                      boolean forceall)
               throws java.io.IOException

Writes data out from the canvas to an Appendable object. This method only handles CSV (comma-separated-values) and TSV (tab-separated-values) spreadsheet table formats. If any other formats are passed to this method, this method won't write any data to the Appendable object. For more information about the exact parsing specification of BioLegato's TSV and CSV formats, please see the CSVFile and TSVFile JavaCC code and classes.

Parameters:

format - the file format to use for writing the file.

out - the "file" (or stream) to write out to.

forceall - write the entire contents of the canvas instead of just the currently selected sequences in the canvas.

Throws:

java.io.IOException - if an error occurs while writing

See Also:

CSVFile, TSVFile

setSelectionMode

public void setSelectionMode(TableCanvas.SelectionMode m)

Changes the SelectioMode of the TableCanvas

Parameters:

m - Selection mode from TableCanvas.SelectionMode

See Also:

CSVFile, TSVFile

display

public java.awt.Component display()

Displays the table canvas within a BioLegato window.

Specified by:

display in class org.biolegato.main.DataCanvas

Returns:

the Component object containing the canvas display data.