Class ChromatogramGraphic.Option

java.lang.Object
org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
Enclosing class:
ChromatogramGraphic

public static class ChromatogramGraphic.Option extends Object
A typesafe enumeration of the options available for configuring the behavior of a ChromatogramGraphic instance. The semantics and expected values are described with the enumerated options.
Since:
1.3
Author:
Rhett Sutphin (UI CBCB)
  • Field Details

    • DRAW_CALL_A

      Option indicating whether to fill in the callboxes for calls of nucleotide A.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • DRAW_CALL_C

      Option indicating whether to fill in the callboxes for calls of nucleotide C.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • DRAW_CALL_G

      Option indicating whether to fill in the callboxes for calls of nucleotide G.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • DRAW_CALL_T

      Option indicating whether to fill in the callboxes for calls of nucleotide T.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • DRAW_CALL_OTHER

      Option indicating whether to fill in the callboxes for non-base calls (gaps, ambiguities).

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • DRAW_TRACE_A

      Option indicating whether to draw the chromatogram trace for nucleotide A.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • DRAW_TRACE_C

      Option indicating whether to draw the chromatogram trace for nucleotide C.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • DRAW_TRACE_G

      Option indicating whether to draw the chromatogram trace for nucleotide G.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • DRAW_TRACE_T

      Option indicating whether to draw the chromatogram trace for nucleotide T.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • DRAW_CALL_SEPARATORS

      Option indicating whether to draw vertical lines separating the calls.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • SEPARATOR_COLOR

      Option indicating the color that the call separators should be.

      Value type: Color.
      Default value: Color.lightGray.

    • WIDTH_IS_AUTHORITATIVE

      Option indicating whether width or horizontal scale is the authoritative measure. If the value is true, then when the Chromatogram displayed by the graphic is changed, the horizontal scale may be changed but the width will stay the same. If the value is false, the width may change but the horizontal scale will stay the same.

      Value type: Boolean.
      Default value: Boolean.FALSE.

    • HEIGHT_IS_AUTHORITATIVE

      Option indicating whether height or vertical scale is the authoritative measure. If the value is true, then when the Chromatogram displayed by the graphic is changed, the vertical scale may be changed but the height will stay the same. If the value is false, the height may change but the vertical scale will stay the same.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • USE_CUSTOM_STROKE

      Option indicating whether to use custom strokes when drawing traces and separators.

      Value type: Boolean.
      Default value: Boolean.TRUE.

    • TRACE_STROKE

      Option providing the the stroke to use for drawing the chromatogram traces.

      Value type: Stroke.
      Default value: BasicStroke with width 1.0, cap CAP_ROUND, join JOIN_ROUND.

    • SEPARATOR_STROKE

      Option providing the the stroke to use for drawing call separators.

      Value type: Stroke.
      Default value: BasicStroke with width 1.0, default cap invalid input: '&' join.

    • USE_PER_SHAPE_TRANSFORM

      Option indicating whether to apply scaling and translation transforms to each shape individually or to apply a single transform to the graphics context. For putative performance reasons, the latter is the default. However, setting this property to true may result in more attractive output, particularly when the horizontal and vertical scales are very different. This value must also be set to true if using a custom stroke while drawing into a Swing graphics context on JDK 1.3.1 on Mac OS X, due to a nasty rendering bug on that platform.

      Value type: Boolean.
      Default value: Boolean.FALSE.

    • SUBPATH_LENGTH

      To improve performance, the drawing objects for the chromatogram traces are precomputed. Specifically, the traces are stored as a set of GeneralPaths. This option indicates how long (in trace samples) each one of these should be. Ideally, this value would be slightly more than the average number of trace samples visible at once in the application using the graphic. However, constantly changing this value is counterproductive as it forces the recalculation of the subpaths. In general, having a value that is too small should be preferred to one that is too large.

      Value type: Integer.
      Default value: 250.

    • FROM_TRACE_SAMPLE

      Option indicating the lowest (leftmost) trace sample that should be drawn. The sample at this (0-based) index will be drawn at x=0 in the output chromatogram. Note that this option is reset to zero every time ChromatogramGraphic.setChromatogram(org.biojava.bio.chromatogram.Chromatogram) is called.

      Value type: Integer.
      Default value: 0.

    • TO_TRACE_SAMPLE

      Option indicating the highest (rightmost) trace sample that should be drawn. The sample at this (0-based) index will be the last drawn in the output chromatogram. Note that this option is reset to the length of the new chromatogram every time ChromatogramGraphic.setChromatogram(org.biojava.bio.chromatogram.Chromatogram) is called.

      Value type: Integer.
      Default value: Integer.MAX_VALUE.

    • HORIZONTAL_NONLINEAR_SCALER

      Option specifying the non-linear scaling function to apply, as embodied in a ChromatogramNonlinearScaler object.

      Value type: ChromatogramNonlinearScaler.
      Default value: an instance of ChromatogramNonlinearScaler.Identity.

  • Method Details

    • toString

      public String toString()
      Overrides:
      toString in class Object
    • lookup

      public static final ChromatogramGraphic.Option lookup(String desc)
      Looks up an Option instance based on its string description.
      Parameters:
      desc - the description of the desired Option
      Returns:
      the Option with the specified description or null if there isn't one