com.compomics.util.gui.spectrum
Class IsotopicDistributionPanel

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.IsotopicDistributionPanel
All Implemented Interfaces:
ImageObserver, MenuContainer, Serializable, Accessible

public class IsotopicDistributionPanel
extends GraphicsPanel

This class provides a JPanel that can display a peptide isotopic distribution.

Version:
$Id$
Author:
Harald Barsnes, Niklaas Colaert, Lennart Martens
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, yAxisZoomExcludesBackgroundPeaks, 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
IsotopicDistributionPanel(String peptideSequence, Integer peptideCharge, boolean profileMode, int labelDifference)
          This constructor creates an IsotopicDistributionPanel based on the passed parameters.
 
Method Summary
 void addAdditionalDataset(String peptideSequence, Integer peptideCharge, Color dataPointAndLineColor, Color areaUnderCurveColor, int labelDifference)
          Adds an additional isotopic distribution dataset to be displayed in the same panel.
 ArrayList<AASequenceImpl> getPeptideSequences()
          Get the set of peptide sequences.
 boolean isElement(String lElement)
          Method that checks if a given string is an element we can calculate an isotopic distribution for
 void rescaleWithLeftSidePadding()
          Rescales to show all peaks, adds a minimum padding on the left side to make sure the that first peak is not too close to the y-axis.
 
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, isSubscriptAnnotationNumbers, paint, processXAndYData, removeAllReferenceAreasXAxis, removeAllReferenceAreasYAxis, removeReferenceAreaXAxis, removeReferenceAreaYAxis, rescale, rescale, setAlphaLevel, setAnnotations, setAnnotationYAxisThreshold, setAreaUnderCurveColor, setDataPointAndLineColor, setDeltaMassWindow, setFilenameColor, setKnownMassDeltas, setMaxPadding, setMiniature, setPeakWaterMarkColor, setScientificXAxis, setScientificXAxis, setScientificYAxis, setScientificYAxis, setSubscriptAnnotationNumbers, setXAxisStartAtZero, setYAxisZoomExcludesBackgroundPeaks, setYDataIsPositive, 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, 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

IsotopicDistributionPanel

public IsotopicDistributionPanel(String peptideSequence,
                                 Integer peptideCharge,
                                 boolean profileMode,
                                 int labelDifference)
                          throws IOException
This constructor creates an IsotopicDistributionPanel based on the passed parameters.

Parameters:
peptideSequence - the peptide sequence to display the isotopic distribution for
peptideCharge - the charge of the peptide
profileMode - if true the peaks will be showned in a profile like mode where support peaks are added in front of and after the real peak (note that this is unlike the profile modes of the other graphics panels)
labelDifference - the number of neutrons to add due to the label
Throws:
IOException
Method Detail

addAdditionalDataset

public void addAdditionalDataset(String peptideSequence,
                                 Integer peptideCharge,
                                 Color dataPointAndLineColor,
                                 Color areaUnderCurveColor,
                                 int labelDifference)
                          throws IOException
Adds an additional isotopic distribution dataset to be displayed in the same panel. Remember to use different colors for the different datasets.

Parameters:
peptideSequence - the peptide sequence to display the isotopic distribution for
peptideCharge - the charge of the peptide
dataPointAndLineColor - the color to use for the data points and lines
areaUnderCurveColor - the color to use for the area under the curve
labelDifference - the number of neutrons to add due to the label
Throws:
IOException

rescaleWithLeftSidePadding

public void rescaleWithLeftSidePadding()
Rescales to show all peaks, adds a minimum padding on the left side to make sure the that first peak is not too close to the y-axis.


isElement

public boolean isElement(String lElement)
Method that checks if a given string is an element we can calculate an isotopic distribution for

Parameters:
lElement - String with the element to check
Returns:
boolean that indicates if we can use this element

getPeptideSequences

public ArrayList<AASequenceImpl> getPeptideSequences()
Get the set of peptide sequences.

Returns:
the peptideSequences


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