Class ChromatogramGraphic.Option

    • Field Detail

      • DRAW_CALL_A

        public static final ChromatogramGraphic.Option 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

        public static final ChromatogramGraphic.Option 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

        public static final ChromatogramGraphic.Option 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

        public static final ChromatogramGraphic.Option 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

        public static final ChromatogramGraphic.Option 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

        public static final ChromatogramGraphic.Option DRAW_TRACE_A
        Option indicating whether to draw the chromatogram trace for nucleotide A.

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

      • DRAW_TRACE_C

        public static final ChromatogramGraphic.Option DRAW_TRACE_C
        Option indicating whether to draw the chromatogram trace for nucleotide C.

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

      • DRAW_TRACE_G

        public static final ChromatogramGraphic.Option DRAW_TRACE_G
        Option indicating whether to draw the chromatogram trace for nucleotide G.

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

      • DRAW_TRACE_T

        public static final ChromatogramGraphic.Option DRAW_TRACE_T
        Option indicating whether to draw the chromatogram trace for nucleotide T.

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

      • WIDTH_IS_AUTHORITATIVE

        public static final ChromatogramGraphic.Option 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

        public static final ChromatogramGraphic.Option 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

        public static final ChromatogramGraphic.Option USE_CUSTOM_STROKE
        Option indicating whether to use custom strokes when drawing traces and separators.

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

      • TRACE_STROKE

        public static final ChromatogramGraphic.Option 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

        public static final ChromatogramGraphic.Option 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 & join.

      • USE_PER_SHAPE_TRANSFORM

        public static final ChromatogramGraphic.Option 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

        public static final ChromatogramGraphic.Option 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.

    • Method Detail

      • toString

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

        public static final ChromatogramGraphic.Option lookup​(java.lang.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