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	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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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

Class ChromatogramGraphic.Option

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DRAW_CALL_A

DRAW_CALL_C

DRAW_CALL_G

DRAW_CALL_T

DRAW_CALL_OTHER

DRAW_TRACE_A

DRAW_TRACE_C

DRAW_TRACE_G

DRAW_TRACE_T

DRAW_CALL_SEPARATORS

SEPARATOR_COLOR

WIDTH_IS_AUTHORITATIVE

HEIGHT_IS_AUTHORITATIVE

USE_CUSTOM_STROKE

TRACE_STROKE

SEPARATOR_STROKE

USE_PER_SHAPE_TRANSFORM

SUBPATH_LENGTH

FROM_TRACE_SAMPLE

TO_TRACE_SAMPLE

HORIZONTAL_NONLINEAR_SCALER

Method Detail

toString

lookup