Package ubic.basecode.graphics

Class MatrixDisplay<R,C>

java.lang.Object
java.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
ubic.basecode.graphics.MatrixDisplay<R,C>
All Implemented Interfaces:
ImageObserver, MenuContainer, Serializable, Accessible
public class MatrixDisplay<R,C> extends JPanel
A visual component for displaying a color matrix
Author:
Will Braynen
See Also:

  • Field Details

    • m_cellSize

      protected Dimension m_cellSize

    • m_columnLabelHeight

      protected int m_columnLabelHeight

    • m_defaultResolution

      protected final int m_defaultResolution
      See Also:

    • m_fontGutter

      protected int m_fontGutter

    • m_fontSize

      protected int m_fontSize

    • m_isShowLabels

      protected boolean m_isShowLabels

    • m_isShowScale

      protected boolean m_isShowScale

    • m_labelFont

      protected Font m_labelFont

    • m_labelGutter

      protected int m_labelGutter

    • m_maxColumnLength

      protected int m_maxColumnLength

    • m_maxFontSize

      protected final int m_maxFontSize
      See Also:

    • m_ratioWidth

      protected int m_ratioWidth

    • m_resolution

      protected int m_resolution

    • m_rowLabelWidth

      protected int m_rowLabelWidth

    • m_textSize

      protected int m_textSize

  • Constructor Details

  • Method Details

    • newInstance

      public static <R, C> MatrixDisplay<R,C> newInstance(ColorMatrix<R,C> matrix)

    • getColor

      public Color getColor(int row, int column)

    • getColorMap

      public Color[] getColorMap()
      Returns:
      the current color map

    • getColorMatrix

      public ColorMatrix<R,C> getColorMatrix()

    • getColumnCount

      public int getColumnCount()

    • getColumnName

      public Object getColumnName(int column)

    • getColumnNames

      public String[] getColumnNames()

    • getDisplayMax

      public double getDisplayMax()

    • getDisplayMin

      public double getDisplayMin()

    • getDisplayRange

      public double getDisplayRange()

    • getMatrix

      public DoubleMatrix<R,C> getMatrix()

    • getMax

      public double getMax()
      Returns:
      the largest value in the matrix

    • getMaxColumnLength

      public int getMaxColumnLength()
      Returns:
      the m_maxColumnLength

    • getMin

      public double getMin()
      Returns:
      the smallest value in the matrix

    • getMissingColor

      public Color getMissingColor()
      Returns:
      the color used for missing values

    • getRawValue

      public double getRawValue(int row, int column)

    • getRow

      public double[] getRow(int row)

    • getRowByName

      public double[] getRowByName(R rowName)

    • getRowCount

      public int getRowCount()

    • getRowHeight

      public int getRowHeight()

    • getRowIndexByName

      public int getRowIndexByName(R rowName)

    • getRowName

      public Object getRowName(int row)

    • getRowNames

      public String[] getRowNames()

    • getStandardizedEnabled

      public boolean getStandardizedEnabled()

    • getValue

      public double getValue(int row, int column)

    • init

      public void init(ColorMatrix<R,C> matrix)

    • resetRowKeys

      public void resetRowKeys()

    • saveImage

      public void saveImage(ColorMatrix<R,C> matrix, String outPngFilename, boolean showLabels, boolean showScalebar, boolean standardize) throws IOException
      Parameters:
      outPngFilename - String
      showLabels - boolean
      standardize - normalize to deviation 1, mean 0. FIXME this is not used?
      Throws:
      IOException

    • saveImage

      public void saveImage(String outPngFilename) throws IOException
      Saves the image to a png file.
      Parameters:
      outPngFilename - String
      Throws:
      IOException

    • saveImage

      public void saveImage(String outPngFilename, boolean showLabels, boolean showScale) throws IOException
      Parameters:
      outPngFilename -
      showLabels -
      Throws:
      IOException

    • saveImageToPng

      public void saveImageToPng(ColorMatrix<R,C> matrix, OutputStream stream, boolean showLabels, boolean showScalebar, boolean standardize) throws IOException
      Parameters:
      stream -
      showLabels -
      standardize -
      Throws:
      IOException

    • setCellSize

      public void setCellSize(Dimension d)

    • setColorMap

      public void setColorMap(Color[] colorMap)
      Parameters:
      colorMap - an array of colors which define the midpoints in the color map; this can be one of the constants defined in the ColorMap class, like ColorMap.REDGREEN_COLORMAP and ColorMap.BLACKBODY_COLORMAP

    • setDisplayRange

      public void setDisplayRange(double min, double max)
      Parameters:
      min -
      max -

    • setLabelsVisible

      public void setLabelsVisible(boolean isShowLabels)
      If this display component has already been added to the GUI, it will be resized to fit or exclude the row names
      Parameters:
      isShowLabels - boolean

    • setMatrix

      public void setMatrix(ColorMatrix<R,C> matrix)
      Parameters:
      matrix - the new matrix to use; will resize this display component as necessary

    • setMaxColumnLength

      public void setMaxColumnLength(int columnLength)
      Parameters:
      columnLength - the m_maxColumnLength to set

    • setRowHeight

      public void setRowHeight(int height)

    • setRowKeys

      public void setRowKeys(int[] rowKeys)

    • setScaleBarVisible

      public void setScaleBarVisible(boolean isShowScale)

    • setStandardizedEnabled

      public void setStandardizedEnabled(boolean showStandardizedMatrix)

    • writeToPng

      public void writeToPng(ColorMatrix<R,C> matrix, OutputStream stream, boolean showLabels, boolean showScalebar) throws IOException
      Parameters:
      matrix -
      stream -
      showLabels -
      showScalebar -
      Throws:
      IOException

    • computeSize

      protected Dimension computeSize(boolean showLabels, boolean showScalebar)
      compute the size of the matrix in pixels.
      Parameters:
      withLabels -
      Returns:

    • drawColumnNames

      protected void drawColumnNames(Graphics g, boolean leaveRoomForScalebar)
      Draws column names vertically (turned 90 degrees counter-clockwise)
      Parameters:
      g - Graphics

    • drawMatrix

      protected void drawMatrix(ColorMatrix<R,C> matrix, Graphics g, boolean leaveRoomForLabels, boolean leaveRoomForScalebar)
      Gets called from #paintComponent and #saveImage. Does not draw the labels.
      Parameters:
      g - Graphics
      leaveRoomForLabels - boolean

    • drawRowNames

      protected void drawRowNames(Graphics g, boolean showScalebar)
      Draws row names (horizontally)
      Parameters:
      g - Graphics
      showScalebar -

    • drawScaleBar

      protected void drawScaleBar(Graphics g, Dimension d, double displayMin, double displayMax)
      Parameters:
      g -
      d -

    • initSize

      protected void initSize()
      Sets the display size

    • paintComponent

      protected void paintComponent(Graphics g)
      Overrides:
      paintComponent in class JComponent