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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
org.jfree.chart.ChartPanel
biggests.gui.PanelExpressionChart
public class PanelExpressionChart
Title: Expression Chart Panel
Description: A panel which holds an expression chart. Allows one to construct specific charts for gene expression data.
Copyright: Copyright (C) 2007 Joana Gonçalves This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JPanel |
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javax.swing.JPanel.AccessibleJPanel |
Nested classes/interfaces inherited from class javax.swing.JComponent |
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javax.swing.JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Container |
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java.awt.Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary |
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Fields inherited from class org.jfree.chart.ChartPanel |
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DEFAULT_BUFFER_USED, DEFAULT_HEIGHT, DEFAULT_MAXIMUM_DRAW_HEIGHT, DEFAULT_MAXIMUM_DRAW_WIDTH, DEFAULT_MINIMUM_DRAW_HEIGHT, DEFAULT_MINIMUM_DRAW_WIDTH, DEFAULT_WIDTH, DEFAULT_ZOOM_TRIGGER_DISTANCE, localizationResources, PRINT_COMMAND, PROPERTIES_COMMAND, SAVE_COMMAND, ZOOM_IN_BOTH_COMMAND, ZOOM_IN_DOMAIN_COMMAND, ZOOM_IN_RANGE_COMMAND, ZOOM_OUT_BOTH_COMMAND, ZOOM_OUT_DOMAIN_COMMAND, ZOOM_OUT_RANGE_COMMAND, ZOOM_RESET_BOTH_COMMAND, ZOOM_RESET_DOMAIN_COMMAND, ZOOM_RESET_RANGE_COMMAND |
Fields inherited from class javax.swing.JComponent |
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accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW |
Fields inherited from class java.awt.Component |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface java.awt.print.Printable |
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NO_SUCH_PAGE, PAGE_EXISTS |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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PanelExpressionChart(Bicluster bicluster,
boolean pattern,
int width,
int height,
java.lang.String title,
int minimumDrawWidth,
int minimumDrawHeight,
int maximumDrawWidth,
int maximumDrawHeight,
boolean useBuffer,
boolean properties,
boolean save,
boolean print,
boolean zoom,
boolean tooltips,
boolean shapesVisible,
boolean includeLegend,
boolean normalize)
Constructs a gene or pattern expression chart with the genes names, conditions names and gene expression data retrieved from the given bicluster . |
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PanelExpressionChart(char[] pattern,
char[] alphabet,
char missingValue,
java.lang.String[] conditionsNames,
int[] columnIndexes,
int width,
int height,
java.lang.String title,
int minimumDrawWidth,
int minimumDrawHeight,
int maximumDrawWidth,
int maximumDrawHeight,
boolean useBuffer,
boolean properties,
boolean save,
boolean print,
boolean zoom,
boolean tooltips,
boolean shapesVisible,
boolean includeLegend)
Constructs a pattern expression chart based on the given expression pattern (sequence of symbols) within
the given alphabet (set of symbols that can appear
in pattern ). |
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PanelExpressionChart(java.lang.String[] genesNames,
java.lang.String[] conditionsNames,
float[][] expressionValues,
float missingValue,
int width,
int height,
java.lang.String title,
int minimumDrawWidth,
int minimumDrawHeight,
int maximumDrawWidth,
int maximumDrawHeight,
boolean useBuffer,
boolean properties,
boolean save,
boolean print,
boolean zoom,
boolean tooltips,
boolean shapesVisible,
boolean includeLegend,
boolean normalize)
Constructs a gene expression chart with the given genesNames , conditionsNames and respective
expressionValues |
Method Summary | |
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static org.jfree.chart.JFreeChart |
createBiclusterChart(org.jfree.data.category.CategoryDataset dataset,
java.lang.String title,
boolean pattern,
boolean shapesVisible,
boolean includeLegend)
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static org.jfree.data.category.CategoryDataset |
createBiclusterDataset(Bicluster bicluster,
boolean pattern,
boolean normalize)
Creates an expression/pattern category dataset based on genes names, conditions names and expression values or pattern retrieved from the bicluster object. |
static PanelExpressionChart |
createExpressionAllTimePointsChart(Bicluster bicluster,
int width,
int height,
java.lang.String title,
boolean normalize)
Creates a new panel holding an all time points expression chart, with expression data retrieved from bicluster and
biclustering objects. |
static PanelExpressionChart |
createExpressionAllTimePointsChart(Bicluster bicluster,
java.lang.String title,
int width,
int height,
boolean normalize)
Creates a new panel holding an all time points expression chart, with expression data retrieved from bicluster and
biclustering objects. |
static PanelExpressionChart |
createExpressionBiclusterPatternChart(CCC_Bicluster bicluster,
int width,
int height,
java.lang.String title,
boolean miniature)
Creates a new bicluster expression pattern chart panel for a given bicluster . |
static PanelExpressionChart |
createExpressionBiclusterTimePointsChart(Bicluster bicluster,
int width,
int height,
boolean normalize,
boolean miniature)
Creates a new time points expression chart panel for a given bicluster . |
static PanelExpressionChart |
createExpressionBiclusterTimePointsChart(Bicluster bicluster,
int width,
int height,
java.lang.String title,
boolean normalize,
boolean miniature)
Creates a new time points expression chart panel for a given bicluster . |
static org.jfree.chart.JFreeChart |
createExpressionChart(org.jfree.data.category.CategoryDataset expressionDataset,
java.lang.String chartTitle,
java.lang.String conditionsAxisName,
java.lang.String expressionAxisName,
boolean shapesVisible,
boolean includeLegend)
Creates a general expression chart from the given expressionDataset and with the given
chartTitle , conditionsAxisName ,
expressionAxisName . |
static org.jfree.data.category.CategoryDataset |
createExpressionDataset(Bicluster bicluster,
boolean normalize)
Creates an expression dataset for a bicluster. |
static org.jfree.data.category.CategoryDataset |
createExpressionDataset(java.lang.String[] genesNames,
java.lang.String[] conditionsNames,
float[][] expressionValues,
float missingValue,
boolean normalize)
Creates a new expression category dataset with the given genesNames , conditionsNames and
expressionValues . |
static org.jfree.chart.JFreeChart |
createExpressionPatternChart(org.jfree.data.category.CategoryDataset patternDataset,
java.lang.String title,
boolean shapesVisible,
boolean includeLegend)
Creates a new pattern expression chart from a given expression patternDataset . |
static org.jfree.chart.JFreeChart |
createGeneExpressionChart(org.jfree.data.category.CategoryDataset expressionDataset,
java.lang.String title,
boolean shapesVisible,
boolean includeLegend)
Creates a new gene expression chart from a given expressionDataset . |
static org.jfree.data.category.CategoryDataset |
createPatternExpressionDataset(CCC_Bicluster bicluster)
Creates a pattern expression dataset for the given bicluster . |
static org.jfree.data.category.CategoryDataset |
createPatternExpressionDataset(char[] pattern,
char[] alphabet,
char missingValue,
java.lang.String[] conditionsNames,
int[] columnIndexes)
Creates an expression pattern dataset based on the given expression pattern (sequence of symbols) within
the given alphabet (set of symbols that can appear
in pattern ). |
void |
doSaveAs()
|
java.lang.String[] |
getConditionsNames()
Returns the names of the conditions in the expression chart. |
float[][] |
getExpressionValues()
Returns the expression values in the expression chart. |
java.lang.String[] |
getGenesNames()
Returns the names of the genes in the expression chart. |
PanelExpressionChart |
repaintTimePointsChart(int width,
int height,
boolean normalize)
Returns a new time points (bicluster or all time points) chart panel, repainted from the the current one. |
Methods inherited from class org.jfree.chart.ChartPanel |
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actionPerformed, addChartMouseListener, chartChanged, chartProgress, createChartPrintJob, createPopupMenu, displayPopupMenu, doEditChartProperties, getAnchor, getChart, getChartRenderingInfo, getDismissDelay, getEntityForPoint, getFillZoomRectangle, getHorizontalAxisTrace, getHorizontalTraceLine, getInitialDelay, getListeners, getMaximumDrawHeight, getMaximumDrawWidth, getMinimumDrawHeight, getMinimumDrawWidth, getPopupMenu, getRefreshBuffer, getReshowDelay, getScaleX, getScaleY, getScreenDataArea, getScreenDataArea, getToolTipText, getVerticalAxisTrace, getVerticalTraceLine, getZoomInFactor, getZoomOutFactor, getZoomTriggerDistance, isDomainZoomable, isEnforceFileExtensions, isRangeZoomable, mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mousePressed, mouseReleased, paintComponent, print, removeChartMouseListener, restoreAutoBounds, restoreAutoDomainBounds, restoreAutoRangeBounds, scale, setAnchor, setChart, setDismissDelay, setDisplayToolTips, setDomainZoomable, setEnforceFileExtensions, setFillZoomRectangle, setHorizontalAxisTrace, setHorizontalTraceLine, setInitialDelay, setMaximumDrawHeight, setMaximumDrawWidth, setMinimumDrawHeight, setMinimumDrawWidth, setMouseZoomable, setMouseZoomable, setPopupMenu, setRangeZoomable, setRefreshBuffer, setReshowDelay, setVerticalAxisTrace, setVerticalTraceLine, setZoomInFactor, setZoomOutFactor, setZoomTriggerDistance, translateJava2DToScreen, translateScreenToJava2D, zoom, zoomInBoth, zoomInDomain, zoomInRange, zoomOutBoth, zoomOutDomain, zoomOutRange |
Methods inherited from class javax.swing.JPanel |
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getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI |
Methods inherited from class javax.swing.JComponent |
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addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update |
Methods inherited from class java.awt.Container |
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add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate, validateTree |
Methods inherited from class java.awt.Component |
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action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public PanelExpressionChart(Bicluster bicluster, boolean pattern, int width, int height, java.lang.String title, int minimumDrawWidth, int minimumDrawHeight, int maximumDrawWidth, int maximumDrawHeight, boolean useBuffer, boolean properties, boolean save, boolean print, boolean zoom, boolean tooltips, boolean shapesVisible, boolean includeLegend, boolean normalize) throws InvalidNodeObjectTypeException
bicluster
.
bicluster
- the Bicluster
which contains the matrix
object with the data to represent on the expression
chartpattern
- the boolean
value that indicates if this
chart is meant to be a pattern expression chart (
true
)or a gene expression chart (
false
)width
- the int
width of the expression chartheight
- the int
height of the expression chartminimumDrawWidth
- the int
minimum draw width
of the expression chartminimumDrawHeight
- the int
minimum draw height
of the expression chartmaximumDrawWidth
- the int
maximum draw width
of the expression chartmaximumDrawHeight
- the int
maximum draw height
of the expression chartuseBuffer
- boolean
true
if a
buffer should be used; false
if notproperties
- boolean
true
if properties
should be accessible via context menu;
false
if otherwisesave
- boolean
true
if save option
should be available via context menu; false
if otherwiseprint
- boolean
true
if print option
should be available via context menu; false
if otherwisezoom
- boolean
true
if zoom option
should be available via context menu; false
if otherwisetooltips
- boolean
true
if tooltips
should be displayed; false
otherwiseshapesVisible
- boolean
true
if the
shapes of the expression points should be
displayed in the chartincludeLegend
- boolean
true
if a legend
with the genes names should be displayed;
false
othwerwisenormalize
- boolean
true
if expression
values should be normalized before creating the
expression chart; false
otherwise
InvalidNodeObjectTypeException
- if nodeInfo
does
not contain a valid node objectpublic PanelExpressionChart(java.lang.String[] genesNames, java.lang.String[] conditionsNames, float[][] expressionValues, float missingValue, int width, int height, java.lang.String title, int minimumDrawWidth, int minimumDrawHeight, int maximumDrawWidth, int maximumDrawHeight, boolean useBuffer, boolean properties, boolean save, boolean print, boolean zoom, boolean tooltips, boolean shapesVisible, boolean includeLegend, boolean normalize) throws InvalidNodeObjectTypeException
genesNames
, conditionsNames
and respective
expressionValues
genesNames
- the String[]
set of genes namesconditionsNames
- the String[]
set of conditions namesexpressionValues
- the float[][]
set of expression valuesmissingValue
- the value which marks missingswidth
- the int
width of the expression chartheight
- the int
height of the expression chartminimumDrawWidth
- the int
minimum draw width
of the expression chartminimumDrawHeight
- the int
minimum draw height
of the expression chartmaximumDrawWidth
- the int
maximum draw width
of the expression chartmaximumDrawHeight
- the int
maximum draw height
of the expression chartuseBuffer
- boolean
true
if a
buffer should be used; false
if notproperties
- boolean
true
if properties
should be accessible via context menu;
false
if otherwisesave
- boolean
true
if save option
should be available via context menu; false
if otherwiseprint
- boolean
true
if print option
should be available via context menu; false
if otherwisezoom
- boolean
true
if zoom option
should be available via context menu; false
if otherwisetooltips
- boolean
true
if tooltips
should be displayed; false
otherwiseshapesVisible
- boolean
true
if the
shapes of the expression points should be
displayed in the chartincludeLegend
- boolean
true
if a legend
with the genes names should be displayed;
false
othwerwisenormalize
- boolean
true
if expression
values should be normalized before creating the
expression chart; false
otherwise
InvalidNodeObjectTypeException
- if nodeInfo
does
not contain a valid node objectpublic PanelExpressionChart(char[] pattern, char[] alphabet, char missingValue, java.lang.String[] conditionsNames, int[] columnIndexes, int width, int height, java.lang.String title, int minimumDrawWidth, int minimumDrawHeight, int maximumDrawWidth, int maximumDrawHeight, boolean useBuffer, boolean properties, boolean save, boolean print, boolean zoom, boolean tooltips, boolean shapesVisible, boolean includeLegend) throws java.lang.Exception
pattern
(sequence of symbols) within
the given alphabet
(set of symbols that can appear
in pattern
).
pattern
- the char[]
expression patternalphabet
- the char[]
expression alphabetmissingValue
- the value which marks missingsconditionsNames
- the String[]
names of the conditionscolumnIndexes
- the int[]
indexes of the columns
from which the conditions were taken (exclusively
for charts of expression patterns originated from
matrices discretized by variations between
time points techniqueswidth
- the int
width of the expression chartheight
- the int
height of the expression chartminimumDrawWidth
- the int
minimum draw width
of the expression chartminimumDrawHeight
- the int
minimum draw height
of the expression chartmaximumDrawWidth
- the int
maximum draw width
of the expression chartmaximumDrawHeight
- the int
maximum draw height
of the expression chartuseBuffer
- boolean
true
if a
buffer should be used; false
if notproperties
- boolean
true
if properties
should be accessible via context menu;
false
if otherwisesave
- boolean
true
if save option
should be available via context menu; false
if otherwiseprint
- boolean
true
if print option
should be available via context menu; false
if otherwisezoom
- boolean
true
if zoom option
should be available via context menu; false
if otherwisetooltips
- boolean
true
if tooltips
should be displayed; false
otherwiseshapesVisible
- boolean
true
if the
shapes of the expression points should be
displayed in the chartincludeLegend
- boolean
true
if a legend
with the genes names should be displayed;
false
othwerwise
java.lang.Exception
Method Detail |
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public static org.jfree.data.category.CategoryDataset createPatternExpressionDataset(char[] pattern, char[] alphabet, char missingValue, java.lang.String[] conditionsNames, int[] columnIndexes) throws java.lang.Exception
pattern
(sequence of symbols) within
the given alphabet
(set of symbols that can appear
in pattern
).
pattern
- the char[]
expression patternalphabet
- the char[]
expression alphabetmissingValue
- the value which marks missingsconditionsNames
- the String[]
names of the conditionscolumnIndexes
- the int[]
indexes of the columns
from which the conditions were taken (exclusively
for charts of expression patterns originated from
matrices discretized by variations between
time points techniques
CategoryDataset
representing the given
expression pattern
java.lang.Exception
public static org.jfree.data.category.CategoryDataset createPatternExpressionDataset(CCC_Bicluster bicluster)
bicluster
. Handles all kinds of biclusters
obtained from discrete data and also biclusters from VBTP
matrices (discretized with variations between
time points technique), as well as biclusters with gene
shifts and/or restricted errors, sign changes and/or time lags.
bicluster
- the CCC_Bicluster
or one of its subclasses
object with data to create the pattern expression dataset
public static org.jfree.data.category.CategoryDataset createBiclusterDataset(Bicluster bicluster, boolean pattern, boolean normalize) throws InvalidNodeObjectTypeException
bicluster
object.
bicluster
- the Bicluster
from which the
expression data will be retrievedpattern
- the boolean
value that indicates if this
chart is meant to be a pattern expression chart (
true
)or a gene expression chart (
false
)normalize
- the boolean
true
if the
original expression values should be normalized before
creating the expression chart; false
otherwise
CategoryDataset
containing the necessary
data to construct an expression chart
InvalidNodeObjectTypeException
public static org.jfree.data.category.CategoryDataset createExpressionDataset(Bicluster bicluster, boolean normalize)
bicluster
- the Bicluster
from which the
expression dataset will be constructed.normalize
- boolean
true
if
expression data in the dataset should be
normalized by gene
public static org.jfree.data.category.CategoryDataset createExpressionDataset(java.lang.String[] genesNames, java.lang.String[] conditionsNames, float[][] expressionValues, float missingValue, boolean normalize)
given genesNames
, conditionsNames
and
expressionValues
.
genesNames
- the String[]
set of genes namesconditionsNames
- the String[]
set of conditions namesexpressionValues
- the float[][]
set of expression valuesmissingValue
- the value which marks missingsnormalize
- the boolean
true
if the
original expression values should be normalized before
creating the expression chart; false
otherwise
CategoryDataset
containing the necessary
data to construct an expression chartpublic static org.jfree.chart.JFreeChart createGeneExpressionChart(org.jfree.data.category.CategoryDataset expressionDataset, java.lang.String title, boolean shapesVisible, boolean includeLegend)
expressionDataset
.
expressionDataset
- the expression CategoryDataset
shapesVisible
- the boolean
true
if the shapes in the charts time points should
be displayed; false
if otherwiseincludeLegend
- the boolean
true
if
a legend of the chart should be included;
false
otherwise
JFreeChart
public static org.jfree.chart.JFreeChart createExpressionPatternChart(org.jfree.data.category.CategoryDataset patternDataset, java.lang.String title, boolean shapesVisible, boolean includeLegend)
patternDataset
.
patternDataset
- the expression pattern CategoryDataset
shapesVisible
- the boolean
true
if the shapes in the charts time points should
be displayed; false
if otherwiseincludeLegend
- the boolean
true
if
a legend of the chart should be included;
false
otherwise
JFreeChart
public static org.jfree.chart.JFreeChart createBiclusterChart(org.jfree.data.category.CategoryDataset dataset, java.lang.String title, boolean pattern, boolean shapesVisible, boolean includeLegend)
public static org.jfree.chart.JFreeChart createExpressionChart(org.jfree.data.category.CategoryDataset expressionDataset, java.lang.String chartTitle, java.lang.String conditionsAxisName, java.lang.String expressionAxisName, boolean shapesVisible, boolean includeLegend)
expressionDataset
and with the given
chartTitle
, conditionsAxisName
,
expressionAxisName
.
expressionDataset
- the expression CategoryDataset
chartTitle
- the chart title String
conditionsAxisName
- the name of the conditions axis String
expressionAxisName
- the name of the expression values axis String
shapesVisible
- the boolean
true
if the shapes in the charts time points should
be displayed; false
if otherwiseincludeLegend
- the boolean
true
if
a legend of the chart should be included;
false
otherwise
JFreeChart
public static PanelExpressionChart createExpressionBiclusterTimePointsChart(Bicluster bicluster, int width, int height, java.lang.String title, boolean normalize, boolean miniature) throws InvalidNodeObjectTypeException
bicluster
.
bicluster
- a Bicluster
from which the
expression data will be retrievedwidth
- the int
fixed draw width of the expression chartheight
- the int
fixed draw height of the expression charttitle
- the String
title for the chart panelnormalize
- the boolean
true
if the
original expression values should be normalized before
creating the expression chart; false
otherwiseminiature
- the boolean
true
if the
chart to create is a miniature (it will then contain
no legend, no normalized data and other specific
characteristics)
PanelExpressionChart
InvalidNodeObjectTypeException
public static PanelExpressionChart createExpressionBiclusterTimePointsChart(Bicluster bicluster, int width, int height, boolean normalize, boolean miniature) throws InvalidNodeObjectTypeException
bicluster
.
bicluster
- a Bicluster
from which the
expression data will be retrievedwidth
- the int
fixed draw width of the expression chartheight
- the int
fixed draw height of the expression chartnormalize
- the boolean
true
if the
original expression values should be normalized before
creating the expression chart; false
otherwiseminiature
- the boolean
true
if the
chart to create is a miniature (it will then contain
no legend, no normalized data and other specific
characteristics)
PanelExpressionChart
InvalidNodeObjectTypeException
#createExpressionBiclusterTimePointsChart(CCC_Bicluster bicluster, int width, int height, String title, boolean normalize, boolean miniature)
public static PanelExpressionChart createExpressionBiclusterPatternChart(CCC_Bicluster bicluster, int width, int height, java.lang.String title, boolean miniature) throws java.lang.Exception
bicluster
.
bicluster
- a CCC_Bicluster
from which the
expression data will be retrievedwidth
- the int
fixed draw width of the expression chartheight
- the int
fixed draw height of the expression charttitle
- the String
title for the chart panelminiature
- the boolean
true
if the
chart to create is a miniature (it will then contain
no legend, no normalized data and other specific
characteristics)
PanelExpressionChart
java.lang.Exception
public static PanelExpressionChart createExpressionAllTimePointsChart(Bicluster bicluster, int width, int height, java.lang.String title, boolean normalize) throws InvalidNodeObjectTypeException
bicluster
and
biclustering
objects.
bicluster
- a Bicluster
from which the
names of the genes will be retrievedwidth
- the int
fixed draw width of the expression chartheight
- the int
fixed draw height of the expression chartnormalize
- the boolean
true
if the
original expression values should be normalized before
creating the expression chart; false
otherwise
PanelExpressionChart
InvalidNodeObjectTypeException
public static PanelExpressionChart createExpressionAllTimePointsChart(Bicluster bicluster, java.lang.String title, int width, int height, boolean normalize) throws InvalidNodeObjectTypeException
bicluster
and
biclustering
objects.
bicluster
- a Bicluster
from which the
names of the genes will be retrievedwidth
- the int
fixed draw width of the expression chartheight
- the int
fixed draw height of the expression chartnormalize
- the boolean
true
if the
original expression values should be normalized before
creating the expression chart; false
otherwise
PanelExpressionChart
InvalidNodeObjectTypeException
public PanelExpressionChart repaintTimePointsChart(int width, int height, boolean normalize) throws InvalidNodeObjectTypeException, java.lang.Exception
width
- the int
fixed draw width of the expression chartheight
- the int
fixed draw height of the expression chartnormalize
- the boolean
true
if the
original expression values should be normalized before
creating the expression chart; false
otherwise
PanelExpressionChart
InvalidNodeObjectTypeException
java.lang.Exception
public java.lang.String[] getGenesNames()
String[]
set of genes namespublic java.lang.String[] getConditionsNames()
String[]
set of conditions namespublic float[][] getExpressionValues()
float[][]
set of expression valuespublic void doSaveAs() throws java.io.IOException
doSaveAs
in class org.jfree.chart.ChartPanel
java.io.IOException
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