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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
com.compomics.util.gui.spectrum.MassErrorBubblePlot
public class MassErrorBubblePlot
Creates a MassErrorBubblePlot displaying the mz values vs the mass error with the intensity as the size of the bubbles.
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JPanel |
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JPanel.AccessibleJPanel |
Nested classes/interfaces inherited from class javax.swing.JComponent |
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JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Container |
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Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy |
Field Summary | |
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static float |
DEFAULT_NON_VISIBLE_MARKER_ALPHA
The default non-visible alpha level. |
static float |
DEFAULT_VISIBLE_MARKER_ALPHA
The default visible alpha level. |
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.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers)
Creates a new MassErrorBubblePlot. |
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MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot. |
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MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<ArrayList<IonMatch>> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
double bubbleScale,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot. |
Method Summary | |
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static void |
addFragmentIonTypeMarkers(HashMap<String,ArrayList<XYZDataPoint>> data,
org.jfree.chart.JFreeChart chart,
boolean showMarkers)
Adds interval markers for all the fragment ion types. |
static org.jfree.data.xy.DefaultXYZDataset |
addXYZDataSeries(HashMap<String,ArrayList<XYZDataPoint>> data)
Adds the provided data series to an XYZ data set. |
org.jfree.chart.ChartPanel |
getChartPanel()
Returns the chart panel. |
int |
getNumberOfDataPointsInPlot()
Returns the current number of data points in the mass error plot. |
Methods inherited from class javax.swing.JPanel |
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getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final float DEFAULT_VISIBLE_MARKER_ALPHA
public static final float DEFAULT_NON_VISIBLE_MARKER_ALPHA
Constructor Detail |
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public MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<ArrayList<IonMatch>> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, ArrayList<MSnSpectrum> currentSpectra, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers)
dataIndexes
- the data set indexes/labelsannotations
- the full list of spectrum annotationscurrentFragmentIons
- the currently selected fragment ion typescurrentSpectra
- the current spectramassTolerance
- the mass error toleranceincludeSinglyCharge
- if singly charged fragment ions are to be includedincludeDoublyCharge
- if doubly charged fragment ions are to be includedincludeMoreThanTwoCharges
- if fragment ions with more than two charges are to be includedfragmentIonLabels
- if true, the fragment ion type is used as the data series key,
otherwise the psm index is usedaddMarkers
- if true interval markers for the fragment ions will be shownpublic MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<ArrayList<IonMatch>> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, ArrayList<MSnSpectrum> currentSpectra, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers, boolean useRelativeError)
dataIndexes
- the data set indexes/labelsannotations
- the full list of spectrum annotationscurrentFragmentIons
- the currently selected fragment ion typescurrentSpectra
- the current spectramassTolerance
- the mass error toleranceincludeSinglyCharge
- if singly charged fragment ions are to be includedincludeDoublyCharge
- if doubly charged fragment ions are to be includedincludeMoreThanTwoCharges
- if fragment ions with more than two charges are to be includedfragmentIonLabels
- if true, the fragment ion type is used as the data series key,
otherwise the psm index is usedaddMarkers
- if true interval markers for the fragment ions will be shownuseRelativeError
- if true the relative error (ppm) is used instead of the absolute error (Da)public MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<ArrayList<IonMatch>> annotations, ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, ArrayList<MSnSpectrum> currentSpectra, double massTolerance, double bubbleScale, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers, boolean useRelativeError)
dataIndexes
- the data set indexes/labelsannotations
- the full list of spectrum annotationscurrentFragmentIons
- the currently selected fragment ion typescurrentSpectra
- the current spectramassTolerance
- the mass error tolerancebubbleScale
- the bubble scale valueincludeSinglyCharge
- if singly charged fragment ions are to be includedincludeDoublyCharge
- if doubly charged fragment ions are to be includedincludeMoreThanTwoCharges
- if fragment ions with more than two charges are to be includedfragmentIonLabels
- if true, the fragment ion type is used as the data series key,
otherwise the psm index is usedaddMarkers
- if true interval markers for the fragment ions will be shownuseRelativeError
- if true the relative error (ppm) is used instead of the absolute error (Da)Method Detail |
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public static void addFragmentIonTypeMarkers(HashMap<String,ArrayList<XYZDataPoint>> data, org.jfree.chart.JFreeChart chart, boolean showMarkers)
data
- the data to get the interval markers fromchart
- the chart to add the markers toshowMarkers
- if true interval markers for the fragment ions will be addedpublic int getNumberOfDataPointsInPlot()
public static org.jfree.data.xy.DefaultXYZDataset addXYZDataSeries(HashMap<String,ArrayList<XYZDataPoint>> data)
data
- the data to add
public org.jfree.chart.ChartPanel getChartPanel()
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