com.compomics.util.gui.spectrum

Class ChromatogramPanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

com.compomics.util.gui.spectrum.GraphicsPanel

com.compomics.util.gui.spectrum.ChromatogramPanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible

public class ChromatogramPanel
extends GraphicsPanel

This class provides a JPanel that can display a profileChromatogram.

Version:

$Id$

Author:

Lennart Martens, Harald Barsnes

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.compomics.util.gui.spectrum.GraphicsPanel

GraphicsPanel.DrawingStyle, GraphicsPanel.GraphicsPanelType

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

JPanel.AccessibleJPanel

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

JComponent.AccessibleJComponent

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

Container.AccessibleAWTContainer

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

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields inherited from class com.compomics.util.gui.spectrum.GraphicsPanel

alphaLevel, ANNOTATED_STATUS, annotateHighestPeak, currentGraphicsPanelType, currentPadding, dataSetCounter, dataSetCounterMirroredSpectra, deltaMassWindow, iAnnotations, iAnnotationsMirroredSpectra, iAnnotationYAxisThreshold, iAreaUnderCurveColor, iAreaUnderCurveColorMirroredSpectra, iClicked, iClickedDataSetIndex, iClickedDataSetIndexMirrored, iClickedIndex, iClickedIndexMirrored, iClickedList, iClickedListDatasetIndices, iClickedListDatasetIndicesMirrored, iClickedListMirrored, iClickedMirrored, iCurrentDrawStyle, iDataPointAndLineColor, iDataPointAndLineColorMirroredSpectra, iDotRadius, iDragged, iDragXLoc, iEndXLoc, iFilename, iFilenameColor, iFilenameMirrorredSpectrum, iHighLight, iHighLightDatasetIndex, iHighLightDatasetIndexMirrored, iHighLightIndex, iHighLightIndexMirrored, iHighLightMirrored, iKnownMassDeltas, iMinDrag, iMSLevel, INTERACTIVE_STATUS, iPointDetectionTolerance, iPointSize, iPrecursorCharge, iPrecursorChargeMirorredSpectrum, iPrecursorMZ, iPrecursorMZMirroredSpectrum, iSpecPanelListeners, iStartXLoc, iStartYLoc, iStoredSequence, iStoredSequenceDatasetIndices, iStoredSequenceDatasetIndicesMirrored, iStoredSequenceMirrored, iTopPadding, iXAxisData, iXAxisDataInPixels, iXAxisDataInPixelsMirroredSpectrum, iXAxisDataMirroredSpectrum, iXAxisLabel, iXAxisMax, iXAxisMin, iXAxisStartAtZero, iXPadding, iXScaleUnit, iXUnit, iYAxisData, iYAxisDataInPixels, iYAxisDataInPixelsMirroredSpectrum, iYAxisDataMirroredSpectrum, iYAxisLabel, iYAxisMax, iYAxisMin, iYScaleUnit, iYUnit, maxPadding, miniature, padding, showAllPeaks, showFileName, showPrecursorDetails, showResolution, xAxisZoomRangeLowerValue, xAxisZoomRangeUpperValue, xTagCount, yAxisZoomExcludesBackgroundPeaks, yDataIsPositive, yTagCount

Fields inherited from class javax.swing.JComponent

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

accessibleContext, 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

Constructor and Description
ChromatogramPanel(double[] aXAxisData, double[] aYAxisData) This constructor creates a ChromatogramPanel based on the passed parameters.
ChromatogramPanel(double[] aXAxisData, double[] aYAxisData, String aXAxisLabel, String aYAxisLabel) This constructor creates a ChromatogramPanel based on the passed parameters.
ChromatogramPanel(double[] aXAxisData, double[] aYAxisData, String aXAxisLabel, String aYAxisLabel, Integer aPointSize) This constructor creates a ChromatogramPanel based on the passed parameters.
ChromatogramPanel(double[] aXAxisData, double[] aYAxisData, String aXAxisLabel, String aYAxisLabel, Integer aPointSize, boolean profileChromatogram) This constructor creates a ChromatogramPanel based on the passed parameters.

Method Summary

Modifier and Type	Method and Description
void	addAdditionalDataset(double[] aXAxisData, double[] aYAxisData, Color dataPointAndLineColor, Color areaUnderCurveColor) Adds an additional profileChromatogram dataset to be displayed in the same Chromatogram Panel.
void	setPointSize(Integer aPointSize) This method allows the caller to set the point size for the profileChromatogram.
void	setProfileMode(boolean profileMode) Set the drawing style to profile or centroid mode.

Methods inherited from class com.compomics.util.gui.spectrum.GraphicsPanel

addListeners, addReferenceAreaXAxis, addReferenceAreaYAxis, addSpectrumPanelListener, annotate, annotatePeaks, drawAxes, drawDaisyChain, drawFilledPolygon, drawMeasurementLine, drawMirroredPeaks, drawPeaks, drawXAxisReferenceAreas, drawXTags, drawYAxisReferenceAreas, drawYTags, dropDottedLine, findDeltaMassMatches, getAllReferenceAreasXAxis, getAllReferenceAreasYAxis, getAlphaLevel, getAreaUnderCurveColors, getBackgroundPeakWidth, getDeltaMassWindow, getiXAxisMax, getiXAxisMin, getiYAxisMax, getiYAxisMin, getKnownMassDeltas, getMaxPadding, getMaxXAxisValue, getMinXAxisValue, getPeakWaterMarkColor, getPeakWidth, getXAxisData, getXAxisZoomRangeLowerValue, getXAxisZoomRangeUpperValue, getYAxisData, highLight, highlightClicked, highLightPeak, isAnnotateHighestPeak, isMiniature, isSubscriptAnnotationNumbers, paint, processMirroredXAndYData, processXAndYData, removeAllReferenceAreasXAxis, removeAllReferenceAreasYAxis, removeReferenceAreaXAxis, removeReferenceAreaYAxis, rescale, rescale, setAlphaLevel, setAnnotateHighestPeak, setAnnotations, setAnnotations, setAnnotationsMirrored, setAnnotationsMirrored, setAnnotationYAxisThreshold, setAreaUnderCurveColor, setBackgroundPeakWidth, setDataPointAndLineColor, setDeltaMassWindow, setFilenameColor, setiXAxisMax, setiXAxisMin, setiYAxisMax, setiYAxisMin, setKnownMassDeltas, setMaxPadding, setMiniature, setPeakWaterMarkColor, setPeakWidth, setScientificXAxis, setScientificXAxis, setScientificYAxis, setScientificYAxis, setShowPrecursorDetails, setShowResolution, setSubscriptAnnotationNumbers, setUseMassDeltaCombinations, setXAxisStartAtZero, setYAxisZoomExcludesBackgroundPeaks, setYDataIsPositive, showPrecursorDetails, showResolution, useMassDeltaCombinations, yAxisZoomOnlyExcludesBackgroundPeaks, yDataIsPositive

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paintBorder, paintChildren, paintComponent, 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

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, 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, 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, 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, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Constructor Detail

ChromatogramPanel

public ChromatogramPanel(double[] aXAxisData,
                         double[] aYAxisData)

This constructor creates a ChromatogramPanel based on the passed parameters. This constructor assumes profileChromatogram data rather than spectrum data. (For profile spectrum data use the SpectrumPanel class instead and set ProfileMode to 'true'.)

Parameters:

aXAxisData - double[] with all the X axis data.

aYAxisData - double[] with all the Y axis data.

ChromatogramPanel

public ChromatogramPanel(double[] aXAxisData,
                         double[] aYAxisData,
                         String aXAxisLabel,
                         String aYAxisLabel)

This constructor creates a ChromatogramPanel based on the passed parameters. This constructor assumes profileChromatogram data rather than spectrum data. (For profile spectrum data use the SpectrumPanel class instead and set ProfileMode to 'true'.)

Parameters:

aXAxisData - double[] with all the X axis data.

aYAxisData - double[] with all the Y axis data.

aXAxisLabel - String with the label for the x-axis (can have a unit between brackets, if available) - can be 'null' for no label

aYAxisLabel - String with the label for the y-axis (can have a unit between brackets, if available) - can be 'null' for no label

ChromatogramPanel

public ChromatogramPanel(double[] aXAxisData,
                         double[] aYAxisData,
                         String aXAxisLabel,
                         String aYAxisLabel,
                         Integer aPointSize)

This constructor creates a ChromatogramPanel based on the passed parameters. This constructor assumes profileChromatogram data rather than spectrum data. (For profile spectrum data use the SpectrumPanel class instead and set ProfileMode to 'true'.)

Parameters:

aXAxisData - double[] with all the X axis data.

aYAxisData - double[] with all the Y axis data.

aXAxisLabel - String with the label for the x-axis (can have a unit between brackets, if available) - can be 'null' for no label

aYAxisLabel - String with the label for the y-axis (can have a unit between brackets, if available) - can be 'null' for no label

aPointSize - Integer with the point size to use

ChromatogramPanel

public ChromatogramPanel(double[] aXAxisData,
                         double[] aYAxisData,
                         String aXAxisLabel,
                         String aYAxisLabel,
                         Integer aPointSize,
                         boolean profileChromatogram)

This constructor creates a ChromatogramPanel based on the passed parameters. This constructor assumes profileChromatogram data rather than spectrum data. (For profile spectrum data use the SpectrumPanel class instead and set ProfileMode to 'true'.)

Parameters:

aXAxisData - double[] with all the X axis data.

aYAxisData - double[] with all the Y axis data.

aXAxisLabel - String with the label for the x-axis (can have a unit between brackets, if available) - can be 'null' for no label

aYAxisLabel - String with the label for the y-axis (can have a unit between brackets, if available) - can be 'null' for no label

aPointSize - Integer with the point size to use

profileChromatogram - If true, the profileChromatogram will be drawn with connected peaks, if false, only the peaks themselves are drawn. Note that profile mode is not recommended when the peak count is high as the drawing will be slow.

Method Detail

addAdditionalDataset

public void addAdditionalDataset(double[] aXAxisData,
                                 double[] aYAxisData,
                                 Color dataPointAndLineColor,
                                 Color areaUnderCurveColor)

Adds an additional profileChromatogram dataset to be displayed in the same Chromatogram Panel. Remember to use different colors for the different datasets.

Parameters:

aXAxisData - double[] with all the x-axis values.

aYAxisData - double[] with all the y-axis values

dataPointAndLineColor - the color to use for the data points and lines

areaUnderCurveColor - the color to use for the area under the curve

setPointSize

public void setPointSize(Integer aPointSize)

This method allows the caller to set the point size for the profileChromatogram. Note that this number needs to be even, so any uneven number will be replaced by the closest, lower, even integer (e.g., 5 becomes 4, 13 becomes 12).

Parameters:

aPointSize - int with the point size, that will be reduced to the closest, lower even integer (e.g., 5 becomes 4, 13 becomes 12).

setProfileMode

public void setProfileMode(boolean profileMode)

Set the drawing style to profile or centroid mode. Profile mode draws lines between the peaks while centroid mode only draws the peaks. Profile mode is only recommended for datasets with low number of peaks, as it can be slow on bigger datasets.

Parameters:

profileMode - use profile mode?