org.biojava.bio.chromatogram.graphic

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 Summary

Fields

Modifier and Type	Field and Description
static ChromatogramGraphic.Option	DRAW_CALL_A Option indicating whether to fill in the callboxes for calls of nucleotide A.
static ChromatogramGraphic.Option	DRAW_CALL_C Option indicating whether to fill in the callboxes for calls of nucleotide C.
static ChromatogramGraphic.Option	DRAW_CALL_G Option indicating whether to fill in the callboxes for calls of nucleotide G.
static ChromatogramGraphic.Option	DRAW_CALL_OTHER Option indicating whether to fill in the callboxes for non-base calls (gaps, ambiguities).
static ChromatogramGraphic.Option	DRAW_CALL_SEPARATORS Option indicating whether to draw vertical lines separating the calls.
static ChromatogramGraphic.Option	DRAW_CALL_T Option indicating whether to fill in the callboxes for calls of nucleotide T.
static ChromatogramGraphic.Option	DRAW_TRACE_A Option indicating whether to draw the chromatogram trace for nucleotide A.
static ChromatogramGraphic.Option	DRAW_TRACE_C Option indicating whether to draw the chromatogram trace for nucleotide C.
static ChromatogramGraphic.Option	DRAW_TRACE_G Option indicating whether to draw the chromatogram trace for nucleotide G.
static ChromatogramGraphic.Option	DRAW_TRACE_T Option indicating whether to draw the chromatogram trace for nucleotide T.
static ChromatogramGraphic.Option	FROM_TRACE_SAMPLE Option indicating the lowest (leftmost) trace sample that should be drawn.
static ChromatogramGraphic.Option	HEIGHT_IS_AUTHORITATIVE Option indicating whether height or vertical scale is the authoritative measure.
static ChromatogramGraphic.Option	HORIZONTAL_NONLINEAR_SCALER Option specifying the non-linear scaling function to apply, as embodied in a ChromatogramNonlinearScaler object.
static ChromatogramGraphic.Option	SEPARATOR_COLOR Option indicating the color that the call separators should be.
static ChromatogramGraphic.Option	SEPARATOR_STROKE Option providing the the stroke to use for drawing call separators.
static ChromatogramGraphic.Option	SUBPATH_LENGTH To improve performance, the drawing objects for the chromatogram traces are precomputed.
static ChromatogramGraphic.Option	TO_TRACE_SAMPLE Option indicating the highest (rightmost) trace sample that should be drawn.
static ChromatogramGraphic.Option	TRACE_STROKE Option providing the the stroke to use for drawing the chromatogram traces.
static ChromatogramGraphic.Option	USE_CUSTOM_STROKE Option indicating whether to use custom strokes when drawing traces and separators.
static 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.
static ChromatogramGraphic.Option	WIDTH_IS_AUTHORITATIVE Option indicating whether width or horizontal scale is the authoritative measure.

Method Summary

Methods

Modifier and Type	Method and Description
static ChromatogramGraphic.Option	lookup(String desc) Looks up an Option instance based on its string description.
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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.

DRAW_CALL_SEPARATORS

public static final ChromatogramGraphic.Option DRAW_CALL_SEPARATORS

Option indicating whether to draw vertical lines separating the calls.

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

SEPARATOR_COLOR

public static final ChromatogramGraphic.Option SEPARATOR_COLOR

Option indicating the color that the call separators should be.

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

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.

FROM_TRACE_SAMPLE

public static final ChromatogramGraphic.Option 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

public static final ChromatogramGraphic.Option 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

public static final ChromatogramGraphic.Option 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 Detail

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