ChromatogramGraphic (biojava-legacy 1.9.1 API)

java.lang.Object
- org.biojava.bio.chromatogram.graphic.ChromatogramGraphic

All Implemented Interfaces:

Cloneable
```
public class ChromatogramGraphic
extends Object
implements Cloneable
```
Encapsulates a configurable method for drawing a Chromatogram into a graphics context.

Since:

1.3

Author:

Rhett Sutphin (UI CBCB), Matthew Pocock

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`ChromatogramGraphic.Option` A typesafe enumeration of the options available for configuring the behavior of a `ChromatogramGraphic` instance.

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`callboxesValid` Flag for call boxes.
`protected Map`	`colors` The map containing the colors for drawing traces.
`protected boolean`	`drawableCallboxesValid` Flag for drawable call boxes.
`protected Map`	`fillColors` The map containing the fill colors for callboxes.
`protected Map`	`options` The map containing the `ChromatogramGraphic.Option`s and values for this instance.
`protected boolean`	`subpathsValid` Flag for subpaths.

Constructor Summary

Constructors
Constructor and Description
`ChromatogramGraphic()` Default constructor with no Chromatogram.
`ChromatogramGraphic(Chromatogram c)` Creates a new `ChromatogramGraphic`, initially displaying the given chromatogram.

Method Summary

Methods
Modifier and Type	Method and Description
`Object`	`clone()` Performs a partial deep copy and invalidates regenerable structures.
`void`	`drawTo(Graphics2D g2)` Draws the chromatogram onto the provided graphics context.
`protected void`	`generateCallboxes()` Precomputes the `Rectangle2D`s that are the in-memory representation of the callboxes.
`protected void`	`generateDrawableCallboxes(AffineTransform shapeTx)` Precomputes the callboxes in screen coordinates.
`protected void`	`generateSubpaths()` Precomputes the `GeneralPath`s used to draw the traces.
`Color`	`getBaseColor(Symbol b)` Returns the color that will be used to draw the trace for the given DNA symbol.
`Color`	`getBaseFillColor(Symbol b)` Returns the color that will be used to fill in the callboxes for calls with the given symbol.
`Rectangle2D`	`getCallboxBounds(int index)` Returns the screen-coordinate bounds of the callbox for a given call.
`Rectangle2D`	`getCallboxBounds(int index, boolean boundsOnScreen)` Returns the bounds of the callbox for a given call.
`int`	`getCallboxCount()` Returns the number of callboxes, regenerating them if necessary.
`int`	`getCallContaining(float x)` Synonym for `getCallContaining(float, boolean)` with `pointOnScreen`=true.
`int`	`getCallContaining(float x, boolean xOnScreen)` Same as `getCallContaining(Point2D, boolean)`, except that only the x-coordinate of the point is specified.
`int`	`getCallContaining(Point2D point)` Synonym for `getCallContaining(Point2D, boolean)` with `pointOnScreen`=true.
`int`	`getCallContaining(Point2D point, boolean pointOnScreen)` Returns the 0-based index of the call containing a given point.
`Chromatogram`	`getChromatogram()` Accessor for the in-use chromatogram.
`float`	`getFloatOption(ChromatogramGraphic.Option opt)` Helper method for converting a `Number`-valued option into a `float` primitive.
`int`	`getHeight()` Returns the height of the whole graphic (in pixels).
`float`	`getHorizontalScale()` Returns the in-use horizontal scale factor.
`int`	`getIntOption(ChromatogramGraphic.Option opt)` Helper method for converting a `Number`-valued option into an `int` primitive.
`AffineTransform`	`getInvTransform()` Returns a new AffineTransform describing the transformation from output space to chromatogram space.
`Object`	`getOption(ChromatogramGraphic.Option opt)` Returns the current value for the specified option.
`int`	`getRenderedWidth()` Returns the width of the graphic as it will be rendered.
`int`	`getRenderedWidth(float horizontalScale)` Returns the width of the graphic as it would be rendered with the specified horizontal scale.
`AffineTransform`	`getTransform()` Returns a new AffineTransform describing the transformation from chromatogram coordinates to output coordinates.
`void`	`getTransformAndConcat(AffineTransform target)` Concatenates the chromatogram-to-output transform to the provided given AffineTransform.
`float`	`getVerticalScale()` Returns the in use vertical scale factor.
`int`	`getWidth()` Returns the width of the whole graphic (in pixels).
`boolean`	`optionIsTrue(ChromatogramGraphic.Option opt)` Helper method for converting a `Boolean`-valued option into a `boolean` primitive.
`void`	`setBaseColor(Symbol b, Color c)` Maps a color to a DNA symbol.
`void`	`setChromatogram(Chromatogram c)` Sets the chromatogram to draw.
`void`	`setHeight(int h)` Sets the height (in pixels).
`void`	`setHorizontalScale(float hs)` Sets the horizontal scale (proportional).
`void`	`setOption(ChromatogramGraphic.Option opt, Object value)` Sets a new value for the specified option.
`void`	`setVerticalScale(float vs)` Sets the vertical scale (proportional).
`void`	`setWidth(int w)` Sets the width of the whole graphic (in pixels).

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - subpathsValid
```
protected boolean subpathsValid
```
    Flag for subpaths.
  - callboxesValid
```
protected boolean callboxesValid
```
    Flag for call boxes.
  - drawableCallboxesValid
```
protected boolean drawableCallboxesValid
```
    Flag for drawable call boxes.
  - options
```
protected Map options
```
    The map containing the ChromatogramGraphic.Options and values for this instance.
  - colors
```
protected Map colors
```
    The map containing the colors for drawing traces. Keys are DNA Symbols.
  - fillColors
```
protected Map fillColors
```
    The map containing the fill colors for callboxes. Keys are DNA Symbols.
- Constructor Detail
  - ChromatogramGraphic
```
public ChromatogramGraphic()
```
    Default constructor with no Chromatogram.
  - ChromatogramGraphic
```
public ChromatogramGraphic(Chromatogram c)
```
    Creates a new ChromatogramGraphic, initially displaying the given chromatogram.
    
    Parameters:
    c - the Chromomatogram to display
- Method Detail
  - generateSubpaths
```
protected void generateSubpaths()
```
    Precomputes the GeneralPaths used to draw the traces.
  - generateCallboxes
```
protected void generateCallboxes()
```
    Precomputes the Rectangle2Ds that are the in-memory representation of the callboxes. These rectangles are used for drawing (via generateDrawableCallboxes) as well as queries (e.g., getCallContaining(java.awt.geom.Point2D, boolean)).
  - generateDrawableCallboxes
```
protected void generateDrawableCallboxes(AffineTransform shapeTx)
```
    Precomputes the callboxes in screen coordinates.
    
    Parameters:
    shapeTx - the transform to apply to the callboxes to move them into screen space.
  - getChromatogram
```
public Chromatogram getChromatogram()
```
    Accessor for the in-use chromatogram.
    
    Returns:
    the chromatogram that a call to drawTo(java.awt.Graphics2D) will draw
  - setChromatogram
```
public void setChromatogram(Chromatogram c)
```
    Sets the chromatogram to draw.
    
    Parameters:
    c - the new chromatogram
    See Also:
    ChromatogramGraphic.Option.WIDTH_IS_AUTHORITATIVE, ChromatogramGraphic.Option.HEIGHT_IS_AUTHORITATIVE
  - getWidth
```
public int getWidth()
```
    Returns the width of the whole graphic (in pixels).
    
    Returns:
    the width
  - getHeight
```
public int getHeight()
```
    Returns the height of the whole graphic (in pixels).
    
    Returns:
    the height
  - getHorizontalScale
```
public float getHorizontalScale()
```
    Returns the in-use horizontal scale factor. The "units" of this value are (trace samples) / pixel. For example, a horizontal scale of 1.0 means that there will be one pixel horizontally for each trace sample.
    
    Returns:
    the horizontal scale
  - getVerticalScale
```
public float getVerticalScale()
```
    Returns the in use vertical scale factor. The "units" of this value are (trace value bins) / pixel. For example, a vertical scale of 1.0 means that there will be one pixel vertically for each value in the range [0, getChromatogram().getMax()].
    
    Returns:
    the vertical scale
  - getRenderedWidth
```
public int getRenderedWidth()
```
    Returns the width of the graphic as it will be rendered. This means that the ChromatogramGraphic.Option.FROM_TRACE_SAMPLE and ChromatogramGraphic.Option.TO_TRACE_SAMPLE bounds are taken into account.
    
    Returns:
    the rendered width
  - getRenderedWidth
```
public int getRenderedWidth(float horizontalScale)
```
    Returns the width of the graphic as it would be rendered with the specified horizontal scale. The ChromatogramGraphic.Option.FROM_TRACE_SAMPLE and ChromatogramGraphic.Option.TO_TRACE_SAMPLE bounds are taken into account.
    
    Parameters:
    horizontalScale - the horizontal scale
    
    Returns:
    the rendered width at that scale
  - setHeight
```
public void setHeight(int h)
```
    Sets the height (in pixels). This will also change the vertical scale.
    
    Parameters:
    h - the desired height in pixels
    See Also:
    ChromatogramGraphic.Option.HEIGHT_IS_AUTHORITATIVE
  - setVerticalScale
```
public void setVerticalScale(float vs)
```
    Sets the vertical scale (proportional). This will also change the height.
    
    Parameters:
    vs - the desired vertical scale. See getVerticalScale() for semantics.
    See Also:
    ChromatogramGraphic.Option.HEIGHT_IS_AUTHORITATIVE
  - setWidth
```
public void setWidth(int w)
```
    Sets the width of the whole graphic (in pixels). This will also change the horizontal scale.
    
    Parameters:
    w - the desired width in pixels
    See Also:
    ChromatogramGraphic.Option.WIDTH_IS_AUTHORITATIVE
  - setHorizontalScale
```
public void setHorizontalScale(float hs)
```
    Sets the horizontal scale (proportional). This will also change the width.
    
    Parameters:
    hs - the desired vertical scale. See getHorizontalScale() for semantics.
    See Also:
    ChromatogramGraphic.Option.WIDTH_IS_AUTHORITATIVE
  - getBaseColor
```
public Color getBaseColor(Symbol b)
```
    Returns the color that will be used to draw the trace for the given DNA symbol.
    
    Parameters:
    b - the symbol
    
    Returns:
    the color, or null if none is set
  - getBaseFillColor
```
public Color getBaseFillColor(Symbol b)
```
    Returns the color that will be used to fill in the callboxes for calls with the given symbol.
    
    Parameters:
    b - the symbol
    
    Returns:
    the color, or null if none is set
  - setBaseColor
```
public void setBaseColor(Symbol b,
                Color c)
```
    Maps a color to a DNA symbol. The color as specified will be used for to draw the trace for the symbol (if any). The fill color for calls to the symbol will be derived from the trace color.
    
    Parameters:
    b - the symbol
    c - the color
  - getCallboxCount
```
public int getCallboxCount()
```
    Returns the number of callboxes, regenerating them if necessary. This should almost always equal getChromatogram().getSequenceLength()
    
    Returns:
    the number of callboxes
  - getCallboxBounds
```
public Rectangle2D getCallboxBounds(int index)
```
    Returns the screen-coordinate bounds of the callbox for a given call.
    
    Parameters:
    index - the callbox for which to get the bounds 0-based
    
    Returns:
    a Rectangle2D giving the bounds of the call box
  - getCallboxBounds
```
public Rectangle2D getCallboxBounds(int index,
                           boolean boundsOnScreen)
```
    Returns the bounds of the callbox for a given call.
    
    Parameters:
    index - the callbox for which to get the bounds 0-based.
    boundsOnScreen - determines the coordinate system of the returned bounds
    
    Returns:
    the bounds of the callbox in screen coordinates if boundsOnScreen is true, otherwise the bounds of the callbox in chromatogram coordinates
  - getCallContaining
```
public int getCallContaining(Point2D point,
                    boolean pointOnScreen)
```
    Returns the 0-based index of the call containing a given point. The point may be either in screen space or chromatogram space, scale-wise. If the point is in screen space, the caller must translate the point such that if it is, for instance, from a mouse click, a click on the upper-left corner of the graphic would be (0,0).
    
    Parameters:
    point - the point to search for
    pointOnScreen - if true, the point will be treated as though it is in screen space. Otherwise, it will be considered to be in chromatogram space.
    
    Returns:
    the 0-based index of the callbox which contains the point
  - getCallContaining
```
public int getCallContaining(Point2D point)
```
    Synonym for getCallContaining(Point2D, boolean) with pointOnScreen=true.
    
    Parameters:
    point - the Point2D to search with
    
    Returns:
    the call containing this point
  - getCallContaining
```
public int getCallContaining(float x,
                    boolean xOnScreen)
```
    Same as getCallContaining(Point2D, boolean), except that only the x-coordinate of the point is specified.
    
    Parameters:
    x - the x-coordinate to search for
    xOnScreen - whether the coordinate in screen space or chromatogram space
    
    Returns:
    the index of the call containing the position x
  - getCallContaining
```
public int getCallContaining(float x)
```
    Synonym for getCallContaining(float, boolean) with pointOnScreen=true.
    
    Parameters:
    x - the x-coordinate to search for
    
    Returns:
    the index of the call containing the position x
  - getTransform
```
public AffineTransform getTransform()
```
    Returns a new AffineTransform describing the transformation from chromatogram coordinates to output coordinates.
  - getTransformAndConcat
```
public void getTransformAndConcat(AffineTransform target)
```
    Concatenates the chromatogram-to-output transform to the provided given AffineTransform.
  - getInvTransform
```
public AffineTransform getInvTransform()
```
    Returns a new AffineTransform describing the transformation from output space to chromatogram space. Should be much more efficient than getTransform().createInverse()
  - drawTo
```
public void drawTo(Graphics2D g2)
```
    Draws the chromatogram onto the provided graphics context.
    
    Parameters:
    g2 - the Graphics2D to draw to
  - setOption
```
public void setOption(ChromatogramGraphic.Option opt,
             Object value)
```
    Sets a new value for the specified option. Be sure that the value is appropriate per the documentation, or you'll induce a ClassCastException somewhere else.
    
    Parameters:
    opt - Option to set
    value - new value for the option
    See Also:
    ChromatogramGraphic.Option
  - getOption
```
public Object getOption(ChromatogramGraphic.Option opt)
```
    Returns the current value for the specified option.
    
    See Also:
    ChromatogramGraphic.Option
  - optionIsTrue
```
public boolean optionIsTrue(ChromatogramGraphic.Option opt)
                     throws ClassCastException
```
    Helper method for converting a Boolean-valued option into a boolean primitive.
    
    Parameters:
    opt - the ChromatogramGraphic.Option to convert
    
    Returns:
    true if the option is enabled
    
    Throws:
    
    ClassCastException - when the option isn't Boolean-valued
  - getFloatOption
```
public float getFloatOption(ChromatogramGraphic.Option opt)
                     throws ClassCastException
```
    Helper method for converting a Number-valued option into a float primitive.
    
    Parameters:
    opt - the ChromatogramGraphic.Option to convert
    
    Throws:
    
    ClassCastException - when the option isn't Number-valued
  - getIntOption
```
public int getIntOption(ChromatogramGraphic.Option opt)
                 throws ClassCastException
```
    Helper method for converting a Number-valued option into an int primitive.
    
    Parameters:
    opt - the ChromatogramGraphic.Option to convert
    
    Throws:
    
    ClassCastException - when the option isn't Number-valued
  - clone
```
public Object clone()
```
    Performs a partial deep copy and invalidates regenerable structures.
    
    Overrides:
    
    clone in class Object
    
    Returns:
    an Object that is castable to ChromatogramGraphic

Class ChromatogramGraphic

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

subpathsValid

callboxesValid

drawableCallboxesValid

options

colors

fillColors

Constructor Detail

ChromatogramGraphic

ChromatogramGraphic

Method Detail

generateSubpaths

generateCallboxes

generateDrawableCallboxes

getChromatogram

setChromatogram

getWidth

getHeight

getHorizontalScale

getVerticalScale

getRenderedWidth

getRenderedWidth

setHeight

setVerticalScale

setWidth

setHorizontalScale

getBaseColor

getBaseFillColor

setBaseColor

getCallboxCount

getCallboxBounds

getCallboxBounds

getCallContaining

getCallContaining

getCallContaining

getCallContaining

getTransform

getTransformAndConcat

getInvTransform

drawTo

setOption

getOption

optionIsTrue

getFloatOption

getIntOption

clone