com.compomics.util.gui.spectrum
Class ChromatogramPanel

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JPanel
                  extended by com.compomics.util.gui.spectrum.GraphicsPanel
                      extended by 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 chromatogram.

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.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, currentGraphicsPanelType, currentPadding, dataSetCounter, deltaMassWindow, DOTS, iAnnotations, iAnnotationYAxisThreshold, iAreaUnderCurveColor, iClicked, iClickedDataSetIndex, iClickedIndex, iClickedList, iClickedListDatasetIndices, iDataPointAndLineColor, iDotRadius, iDragged, iDragXLoc, iDrawStyle, iEndXLoc, iFilename, iFilenameColor, iHighLight, iHighLightDatasetIndex, iHighLightIndex, iKnownMassDeltas, iMinDrag, iMSLevel, INTERACTIVE_STATUS, iPointDetectionTolerance, iPointSize, iPrecursorCharge, iPrecursorMZ, iSpecPanelListeners, iStartXLoc, iStartYLoc, iStoredSequence, iStoredSequenceDatasetIndices, iTopPadding, iXAxisData, iXAxisDataInPixels, iXAxisLabel, iXAxisMax, iXAxisMin, iXAxisStartAtZero, iXPadding, iXScaleUnit, iXUnit, iYAxisData, iYAxisDataInPixels, iYAxisLabel, iYAxisMax, iYAxisMin, iYScaleUnit, iYUnit, LINES, maxPadding, miniature, padding, showAllPeaks, showFileName, showPrecursorDetails, showResolution, xAxisZoomRangeLowerValue, xAxisZoomRangeUpperValue, xTagCount, yDataIsPositive, yTagCount
 
Fields inherited from class javax.swing.JComponent
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
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
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.
 
Method Summary
 void addAdditionalDataset(double[] aXAxisData, double[] aYAxisData, Color dataPointAndLineColor, Color areaUnderCurveColor)
          Adds an additional chromatogram 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 chromatogram. b>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).
 
Methods inherited from class com.compomics.util.gui.spectrum.GraphicsPanel
addListeners, addReferenceAreaXAxis, addReferenceAreaYAxis, addSpectrumPanelListener, annotate, drawAxes, drawFilledPolygon, drawMeasurementLine, drawPeaks, drawXAxisReferenceAreas, drawXTags, drawYAxisReferenceAreas, drawYTags, dropDottedLine, findDeltaMassMatches, getAllReferenceAreasXAxis, getAllReferenceAreasYAxis, getAlphaLevel, getAreaUnderCurveColors, getDeltaMassWindow, getKnownMassDeltas, getMaxPadding, getMaxXAxisValue, getMinXAxisValue, getPeakWaterMarkColor, getXAxisData, getXAxisZoomRangeLowerValue, getXAxisZoomRangeUpperValue, getYAxisData, highLight, highlightClicked, highLightPeak, isMiniature, paint, processXAndYData, removeAllReferenceAreasXAxis, removeAllReferenceAreasYAxis, removeReferenceAreaXAxis, removeReferenceAreaYAxis, rescale, rescale, setAlphaLevel, setAnnotations, setAnnotationYAxisThreshold, setAreaUnderCurveColor, setDataPointAndLineColor, setDeltaMassWindow, setFilenameColor, setKnownMassDeltas, setMaxPadding, setMiniature, setPeakWaterMarkColor, setScientificXAxis, setScientificXAxis, setScientificYAxis, setScientificYAxis, setXAxisStartAtZero, setYDataIsPositive, 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, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, 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, transferFocusBackward, 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, 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
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 chromatogram data rather than profile 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 chromatogram data rather than profile 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 chromatogram data rather than profile 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
Method Detail

addAdditionalDataset

public void addAdditionalDataset(double[] aXAxisData,
                                 double[] aYAxisData,
                                 Color dataPointAndLineColor,
                                 Color areaUnderCurveColor)
Adds an additional chromatogram 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 chromatogram. b>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).


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