loci.plugins.in

Class ImporterOptions

java.lang.Object

loci.plugins.prefs.OptionsList

loci.plugins.in.ImporterOptions

public class ImporterOptions
extends OptionsList

Helper class for managing Bio-Formats Importer options. Gets default parameter values from IJ_Prefs.txt.

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.List<java.lang.Integer>	cBegin
private java.util.List<java.lang.Integer>	cEnd
private static java.lang.String	CLASS_IMAGE_5D
private static java.lang.String	CLASS_VIEW_5D
static java.lang.String	COLOR_MODE_COLORIZED
static java.lang.String	COLOR_MODE_COMPOSITE
static java.lang.String	COLOR_MODE_CUSTOM
static java.lang.String	COLOR_MODE_DEFAULT
static java.lang.String	COLOR_MODE_GRAYSCALE
private java.util.List<loci.common.Region>	cropRegion
private java.util.List<java.lang.Integer>	cStep
private java.util.List<java.util.List<DoubleOption>>	customColors
private static java.awt.Color[]	DEFAULT_COLORS Default custom colors for each channel.
private java.util.List<java.lang.String>	inputOrder
static java.lang.String	KEY_AUTOSCALE
static java.lang.String	KEY_COLOR_MODE
static java.lang.String	KEY_CONCATENATE
static java.lang.String	KEY_CROP
static java.lang.String	KEY_FIRST
static java.lang.String	KEY_FORCE_THUMBS
static java.lang.String	KEY_GROUP_FILES
static java.lang.String	KEY_ID
static java.lang.String	KEY_LOCATION
static java.lang.String	KEY_MUST_GROUP
static java.lang.String	KEY_OPEN_ALL_SERIES
static java.lang.String	KEY_QUIET
static java.lang.String	KEY_ROIS_MODE
static java.lang.String	KEY_SHOW_METADATA
static java.lang.String	KEY_SHOW_OME_XML
static java.lang.String	KEY_SHOW_ROIS
static java.lang.String	KEY_SPECIFY_RANGES
static java.lang.String	KEY_SPLIT_C
static java.lang.String	KEY_SPLIT_T
static java.lang.String	KEY_SPLIT_Z
static java.lang.String	KEY_STACK_FORMAT
static java.lang.String	KEY_STACK_ORDER
static java.lang.String	KEY_STITCH_TILES
static java.lang.String	KEY_SWAP_DIMS
static java.lang.String	KEY_UNGROUP_FILES
static java.lang.String	KEY_UPGRADE_CHECK
static java.lang.String	KEY_VIRTUAL
static java.lang.String	KEY_WINDOWLESS
static java.lang.String	LOCATION_HTTP
static java.lang.String	LOCATION_LOCAL
static java.lang.String	LOCATION_OMERO
static java.lang.String	ORDER_DEFAULT
static java.lang.String	ORDER_XYCTZ
static java.lang.String	ORDER_XYCZT
static java.lang.String	ORDER_XYTCZ
static java.lang.String	ORDER_XYTZC
static java.lang.String	ORDER_XYZCT
static java.lang.String	ORDER_XYZTC
static java.lang.String	ROIS_MODE_MANAGER
static java.lang.String	ROIS_MODE_OVERLAY
private java.util.List<java.lang.Boolean>	seriesOn
private java.util.List<java.lang.Integer>	tBegin
private java.util.List<java.lang.Integer>	tEnd
private java.util.List<java.lang.Integer>	tStep
private boolean	usePatternIds
static java.lang.String	VIEW_BROWSER
static java.lang.String	VIEW_HYPERSTACK
static java.lang.String	VIEW_IMAGE_5D
static java.lang.String	VIEW_NONE
static java.lang.String	VIEW_STANDARD
static java.lang.String	VIEW_VIEW_5D
private java.util.List<java.lang.Integer>	zBegin
private java.util.List<java.lang.Integer>	zEnd
private java.util.List<java.lang.Integer>	zStep

Fields inherited from class loci.plugins.prefs.OptionsList

INI_TYPE, options, TYPE_BOOLEAN, TYPE_STRING

Constructor Summary

Constructors

Constructor and Description
ImporterOptions()

Method Summary

Modifier and Type	Method and Description
protected boolean	checkKey(java.lang.String options, java.lang.String key) Tests whether the given boolean key is set in the specified options.
void	checkObsoleteOptions() Handles obsolete macro keys, for backward compatibility.
void	clearSeries()
boolean	doCrop()
boolean	doMustGroup()
boolean	doStitchTiles()
boolean	doUpgradeCheck()
private <T> T	get(java.util.List<T> list, int index, T defaultValue)
java.lang.String	getAutoscaleInfo()
int	getCBegin(int s)
int	getCEnd(int s)
java.lang.String	getColorMode()
java.lang.String	getColorModeInfo()
java.lang.String[]	getColorModes()
java.lang.String	getConcatenateInfo()
java.lang.String	getCropInfo()
loci.common.Region	getCropRegion(int s)
int	getCStep(int s)
java.awt.Color	getCustomColor(int s, int c)
java.lang.String	getCustomColorKey(int s, int c)
java.awt.Color	getDefaultCustomColor(int c)
java.lang.String	getFirstTimeInfo()
java.lang.String	getForceThumbnailsInfo()
java.lang.String	getGroupFilesInfo()
java.lang.String	getId()
java.lang.String	getIdInfo()
java.lang.String	getInputOrder(int s)
java.lang.String	getLocation()
java.lang.String	getLocationInfo()
java.lang.String[]	getLocations()
java.lang.String	getMustGroupInfo()
java.lang.String	getOpenAllSeriesInfo()
java.lang.String	getQuietInfo()
java.lang.String	getROIsMode()
java.lang.String	getROIsModeInfo()
java.lang.String[]	getROIsModes()
java.lang.String	getShowMetadataInfo()
java.lang.String	getShowOMEXMLInfo()
java.lang.String	getShowROIsInfo()
java.lang.String	getSpecifyRangesInfo()
java.lang.String	getSplitChannelsInfo()
java.lang.String	getSplitFocalPlanesInfo()
java.lang.String	getSplitTimepointsInfo()
java.lang.String	getStackFormat()
java.lang.String	getStackFormatInfo()
java.lang.String[]	getStackFormats()
java.lang.String	getStackOrder()
java.lang.String	getStackOrderInfo()
java.lang.String[]	getStackOrders()
java.lang.String	getStitchTilesInfo()
java.lang.String	getSwapDimensionsInfo()
int	getTBegin(int s)
int	getTEnd(int s)
int	getTStep(int s)
java.lang.String	getUngroupFilesInfo()
java.lang.String	getUpgradeCheckInfo()
java.lang.String	getVirtualInfo()
java.lang.String	getWindowlessInfo()
int	getZBegin(int s)
int	getZEnd(int s)
int	getZStep(int s)
boolean	isAutoscale()
boolean	isColorModeColorized()
boolean	isColorModeComposite()
boolean	isColorModeCustom()
boolean	isColorModeDefault()
boolean	isColorModeGrayscale()
boolean	isConcatenate()
boolean	isFirstTime()
boolean	isForceThumbnails()
boolean	isGroupFiles()
boolean	isHTTP()
boolean	isLocal()
boolean	isOMERO()
boolean	isQuiet()
boolean	isSeriesOn(int s)
boolean	isShowMetadata()
boolean	isShowOMEXML()
boolean	isSpecifyRanges()
boolean	isSplitChannels()
boolean	isSplitFocalPlanes()
boolean	isSplitTimepoints()
boolean	isSwapDimensions()
boolean	isUngroupFiles()
boolean	isUsingPatternIds()
boolean	isViewBrowser()
boolean	isViewHyperstack()
boolean	isViewImage5D()
boolean	isViewNone()
boolean	isViewStandard()
boolean	isViewView5D()
boolean	isVirtual()
boolean	isWindowless()
boolean	openAllSeries()
void	parseArg(java.lang.String arg) Parses the plugin argument for parameter values.
private <T> void	set(java.util.List<T> list, int index, T value, T fillValue)
void	setAutoscale(boolean b)
void	setCBegin(int s, int value)
void	setCEnd(int s, int value)
void	setColorMode(java.lang.String s)
void	setConcatenate(boolean b)
void	setCrop(boolean b)
void	setCropRegion(int s, loci.common.Region r)
void	setCStep(int s, int value)
void	setCustomColor(int s, int c, java.awt.Color color)
void	setFirstTime(boolean b)
void	setForceThumbnails(boolean b)
void	setGroupFiles(boolean b)
void	setId(java.lang.String s)
void	setInputOrder(int s, java.lang.String value)
void	setLocation(java.lang.String s)
void	setMustGroup(boolean b)
void	setOpenAllSeries(boolean b)
void	setQuiet(boolean b)
void	setROIsMode(java.lang.String s)
void	setSeriesOn(int s, boolean value)
void	setShowMetadata(boolean b)
void	setShowOMEXML(boolean b)
void	setShowROIs(boolean b)
void	setSpecifyRanges(boolean b)
void	setSplitChannels(boolean b)
void	setSplitFocalPlanes(boolean b)
void	setSplitTimepoints(boolean b)
void	setStackFormat(java.lang.String s)
void	setStackOrder(java.lang.String s)
void	setStitchTiles(boolean b)
void	setSwapDimensions(boolean b)
void	setTBegin(int s, int value)
void	setTEnd(int s, int value)
void	setTStep(int s, int value)
void	setUngroupFiles(boolean b)
void	setUpgradeCheck(boolean b)
void	setUsingPatternIds(boolean b)
void	setVirtual(boolean b)
void	setWindowless(boolean b)
void	setZBegin(int s, int value)
void	setZEnd(int s, int value)
void	setZStep(int s, int value)
boolean	showROIs()

Methods inherited from class loci.plugins.prefs.OptionsList

equals, getBooleanOption, getDefaultValue, getInfo, getLabel, getOption, getPossible, getStringOption, getValue, hashCode, isPossible, isSaved, isSet, isSetByDefault, loadOptions, parseOptions, saveOptions, setValue, setValue

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Detail

KEY_AUTOSCALE

public static final java.lang.String KEY_AUTOSCALE

See Also:

Constant Field Values

KEY_COLOR_MODE

public static final java.lang.String KEY_COLOR_MODE

See Also:

Constant Field Values

KEY_CONCATENATE

public static final java.lang.String KEY_CONCATENATE

See Also:

Constant Field Values

KEY_CROP

public static final java.lang.String KEY_CROP

See Also:

Constant Field Values

KEY_FIRST

public static final java.lang.String KEY_FIRST

See Also:

Constant Field Values

KEY_FORCE_THUMBS

public static final java.lang.String KEY_FORCE_THUMBS

See Also:

Constant Field Values

KEY_GROUP_FILES

public static final java.lang.String KEY_GROUP_FILES

See Also:

Constant Field Values

KEY_UNGROUP_FILES

public static final java.lang.String KEY_UNGROUP_FILES

See Also:

Constant Field Values

KEY_ID

public static final java.lang.String KEY_ID

See Also:

Constant Field Values

KEY_LOCATION

public static final java.lang.String KEY_LOCATION

See Also:

Constant Field Values

KEY_OPEN_ALL_SERIES

public static final java.lang.String KEY_OPEN_ALL_SERIES

See Also:

Constant Field Values

KEY_QUIET

public static final java.lang.String KEY_QUIET

See Also:

Constant Field Values

KEY_SHOW_METADATA

public static final java.lang.String KEY_SHOW_METADATA

See Also:

Constant Field Values

KEY_SHOW_OME_XML

public static final java.lang.String KEY_SHOW_OME_XML

See Also:

Constant Field Values

KEY_SHOW_ROIS

public static final java.lang.String KEY_SHOW_ROIS

See Also:

Constant Field Values

KEY_ROIS_MODE

public static final java.lang.String KEY_ROIS_MODE

See Also:

Constant Field Values

KEY_SPECIFY_RANGES

public static final java.lang.String KEY_SPECIFY_RANGES

See Also:

Constant Field Values

KEY_SPLIT_Z

public static final java.lang.String KEY_SPLIT_Z

See Also:

Constant Field Values

KEY_SPLIT_T

public static final java.lang.String KEY_SPLIT_T

See Also:

Constant Field Values

KEY_SPLIT_C

public static final java.lang.String KEY_SPLIT_C

See Also:

Constant Field Values

KEY_STACK_FORMAT

public static final java.lang.String KEY_STACK_FORMAT

See Also:

Constant Field Values

KEY_STACK_ORDER

public static final java.lang.String KEY_STACK_ORDER

See Also:

Constant Field Values

KEY_SWAP_DIMS

public static final java.lang.String KEY_SWAP_DIMS

See Also:

Constant Field Values

KEY_UPGRADE_CHECK

public static final java.lang.String KEY_UPGRADE_CHECK

See Also:

Constant Field Values

KEY_VIRTUAL

public static final java.lang.String KEY_VIRTUAL

See Also:

Constant Field Values

KEY_WINDOWLESS

public static final java.lang.String KEY_WINDOWLESS

See Also:

Constant Field Values

KEY_STITCH_TILES

public static final java.lang.String KEY_STITCH_TILES

See Also:

Constant Field Values

KEY_MUST_GROUP

public static final java.lang.String KEY_MUST_GROUP

See Also:

Constant Field Values

COLOR_MODE_DEFAULT

public static final java.lang.String COLOR_MODE_DEFAULT

See Also:

Constant Field Values

COLOR_MODE_COMPOSITE

public static final java.lang.String COLOR_MODE_COMPOSITE

See Also:

Constant Field Values

COLOR_MODE_COLORIZED

public static final java.lang.String COLOR_MODE_COLORIZED

See Also:

Constant Field Values

COLOR_MODE_GRAYSCALE

public static final java.lang.String COLOR_MODE_GRAYSCALE

See Also:

Constant Field Values

COLOR_MODE_CUSTOM

public static final java.lang.String COLOR_MODE_CUSTOM

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Constant Field Values

LOCATION_LOCAL

public static final java.lang.String LOCATION_LOCAL

See Also:

Constant Field Values

LOCATION_HTTP

public static final java.lang.String LOCATION_HTTP

See Also:

Constant Field Values

LOCATION_OMERO

public static final java.lang.String LOCATION_OMERO

See Also:

Constant Field Values

ROIS_MODE_MANAGER

public static final java.lang.String ROIS_MODE_MANAGER

See Also:

Constant Field Values

ROIS_MODE_OVERLAY

public static final java.lang.String ROIS_MODE_OVERLAY

See Also:

Constant Field Values

VIEW_NONE

public static final java.lang.String VIEW_NONE

See Also:

Constant Field Values

VIEW_STANDARD

public static final java.lang.String VIEW_STANDARD

See Also:

Constant Field Values

VIEW_HYPERSTACK

public static final java.lang.String VIEW_HYPERSTACK

See Also:

Constant Field Values

VIEW_BROWSER

public static final java.lang.String VIEW_BROWSER

See Also:

Constant Field Values

VIEW_IMAGE_5D

public static final java.lang.String VIEW_IMAGE_5D

See Also:

Constant Field Values

VIEW_VIEW_5D

public static final java.lang.String VIEW_VIEW_5D

See Also:

Constant Field Values

CLASS_IMAGE_5D

private static final java.lang.String CLASS_IMAGE_5D

See Also:

Constant Field Values

CLASS_VIEW_5D

private static final java.lang.String CLASS_VIEW_5D

See Also:

Constant Field Values

ORDER_DEFAULT

public static final java.lang.String ORDER_DEFAULT

See Also:

Constant Field Values

ORDER_XYZCT

public static final java.lang.String ORDER_XYZCT

See Also:

Constant Field Values

ORDER_XYZTC

public static final java.lang.String ORDER_XYZTC

See Also:

Constant Field Values

ORDER_XYCZT

public static final java.lang.String ORDER_XYCZT

See Also:

Constant Field Values

ORDER_XYTCZ

public static final java.lang.String ORDER_XYTCZ

See Also:

Constant Field Values

ORDER_XYCTZ

public static final java.lang.String ORDER_XYCTZ

See Also:

Constant Field Values

ORDER_XYTZC

public static final java.lang.String ORDER_XYTZC

See Also:

Constant Field Values

DEFAULT_COLORS

private static final java.awt.Color[] DEFAULT_COLORS

Default custom colors for each channel.

seriesOn

private java.util.List<java.lang.Boolean> seriesOn

inputOrder

private java.util.List<java.lang.String> inputOrder

cBegin

private java.util.List<java.lang.Integer> cBegin

cEnd

private java.util.List<java.lang.Integer> cEnd

cStep

private java.util.List<java.lang.Integer> cStep

zBegin

private java.util.List<java.lang.Integer> zBegin

zEnd

private java.util.List<java.lang.Integer> zEnd

zStep

private java.util.List<java.lang.Integer> zStep

tBegin

private java.util.List<java.lang.Integer> tBegin

tEnd

private java.util.List<java.lang.Integer> tEnd

tStep

private java.util.List<java.lang.Integer> tStep

cropRegion

private java.util.List<loci.common.Region> cropRegion

customColors

private java.util.List<java.util.List<DoubleOption>> customColors

usePatternIds

private boolean usePatternIds

Constructor Detail

ImporterOptions

public ImporterOptions()
                throws java.io.IOException

Throws:

java.io.IOException

Method Detail

parseArg

public void parseArg(java.lang.String arg)

Parses the plugin argument for parameter values.

checkObsoleteOptions

public void checkObsoleteOptions()

Handles obsolete macro keys, for backward compatibility.

getAutoscaleInfo

public java.lang.String getAutoscaleInfo()

isAutoscale

public boolean isAutoscale()

setAutoscale

public void setAutoscale(boolean b)

getColorModeInfo

public java.lang.String getColorModeInfo()

getColorMode

public java.lang.String getColorMode()

getColorModes

public java.lang.String[] getColorModes()

isColorModeDefault

public boolean isColorModeDefault()

isColorModeComposite

public boolean isColorModeComposite()

isColorModeColorized

public boolean isColorModeColorized()

isColorModeGrayscale

public boolean isColorModeGrayscale()

isColorModeCustom

public boolean isColorModeCustom()

setColorMode

public void setColorMode(java.lang.String s)

getConcatenateInfo

public java.lang.String getConcatenateInfo()

isConcatenate

public boolean isConcatenate()

setConcatenate

public void setConcatenate(boolean b)

getCropInfo

public java.lang.String getCropInfo()

doCrop

public boolean doCrop()

setCrop

public void setCrop(boolean b)

getFirstTimeInfo

public java.lang.String getFirstTimeInfo()

isFirstTime

public boolean isFirstTime()

setFirstTime

public void setFirstTime(boolean b)

getForceThumbnailsInfo

public java.lang.String getForceThumbnailsInfo()

isForceThumbnails

public boolean isForceThumbnails()

setForceThumbnails

public void setForceThumbnails(boolean b)

getGroupFilesInfo

public java.lang.String getGroupFilesInfo()

isGroupFiles

public boolean isGroupFiles()

setGroupFiles

public void setGroupFiles(boolean b)

getUngroupFilesInfo

public java.lang.String getUngroupFilesInfo()

isUngroupFiles

public boolean isUngroupFiles()

setUngroupFiles

public void setUngroupFiles(boolean b)

getIdInfo

public java.lang.String getIdInfo()

getId

public java.lang.String getId()

setId

public void setId(java.lang.String s)

getLocationInfo

public java.lang.String getLocationInfo()

getLocation

public java.lang.String getLocation()

getLocations

public java.lang.String[] getLocations()

isLocal

public boolean isLocal()

isHTTP

public boolean isHTTP()

isOMERO

public boolean isOMERO()

setLocation

public void setLocation(java.lang.String s)

getOpenAllSeriesInfo

public java.lang.String getOpenAllSeriesInfo()

openAllSeries

public boolean openAllSeries()

setOpenAllSeries

public void setOpenAllSeries(boolean b)

getQuietInfo

public java.lang.String getQuietInfo()

isQuiet

public boolean isQuiet()

setQuiet

public void setQuiet(boolean b)

getShowMetadataInfo

public java.lang.String getShowMetadataInfo()

isShowMetadata

public boolean isShowMetadata()

setShowMetadata

public void setShowMetadata(boolean b)

getShowOMEXMLInfo

public java.lang.String getShowOMEXMLInfo()

isShowOMEXML

public boolean isShowOMEXML()

setShowOMEXML

public void setShowOMEXML(boolean b)

getShowROIsInfo

public java.lang.String getShowROIsInfo()

showROIs

public boolean showROIs()

setShowROIs

public void setShowROIs(boolean b)

getROIsModeInfo

public java.lang.String getROIsModeInfo()

getROIsMode

public java.lang.String getROIsMode()

getROIsModes

public java.lang.String[] getROIsModes()

setROIsMode

public void setROIsMode(java.lang.String s)

getSpecifyRangesInfo

public java.lang.String getSpecifyRangesInfo()

isSpecifyRanges

public boolean isSpecifyRanges()

setSpecifyRanges

public void setSpecifyRanges(boolean b)

getSplitFocalPlanesInfo

public java.lang.String getSplitFocalPlanesInfo()

isSplitFocalPlanes

public boolean isSplitFocalPlanes()

setSplitFocalPlanes

public void setSplitFocalPlanes(boolean b)

getSplitTimepointsInfo

public java.lang.String getSplitTimepointsInfo()

isSplitTimepoints

public boolean isSplitTimepoints()

setSplitTimepoints

public void setSplitTimepoints(boolean b)

getSplitChannelsInfo

public java.lang.String getSplitChannelsInfo()

isSplitChannels

public boolean isSplitChannels()

setSplitChannels

public void setSplitChannels(boolean b)

getStackFormatInfo

public java.lang.String getStackFormatInfo()

getStackFormat

public java.lang.String getStackFormat()

getStackFormats

public java.lang.String[] getStackFormats()

isViewNone

public boolean isViewNone()

isViewStandard

public boolean isViewStandard()

isViewHyperstack

public boolean isViewHyperstack()

isViewBrowser

public boolean isViewBrowser()

isViewImage5D

public boolean isViewImage5D()

isViewView5D

public boolean isViewView5D()

setStackFormat

public void setStackFormat(java.lang.String s)

getStackOrderInfo

public java.lang.String getStackOrderInfo()

getStackOrder

public java.lang.String getStackOrder()

getStackOrders

public java.lang.String[] getStackOrders()

setStackOrder

public void setStackOrder(java.lang.String s)

getSwapDimensionsInfo

public java.lang.String getSwapDimensionsInfo()

isSwapDimensions

public boolean isSwapDimensions()

setSwapDimensions

public void setSwapDimensions(boolean b)

getUpgradeCheckInfo

public java.lang.String getUpgradeCheckInfo()

doUpgradeCheck

public boolean doUpgradeCheck()

setUpgradeCheck

public void setUpgradeCheck(boolean b)

getVirtualInfo

public java.lang.String getVirtualInfo()

isVirtual

public boolean isVirtual()

setVirtual

public void setVirtual(boolean b)

getWindowlessInfo

public java.lang.String getWindowlessInfo()

isWindowless

public boolean isWindowless()

setWindowless

public void setWindowless(boolean b)

getStitchTilesInfo

public java.lang.String getStitchTilesInfo()

doStitchTiles

public boolean doStitchTiles()

setStitchTiles

public void setStitchTiles(boolean b)

getMustGroupInfo

public java.lang.String getMustGroupInfo()

doMustGroup

public boolean doMustGroup()

setMustGroup

public void setMustGroup(boolean b)

isSeriesOn

public boolean isSeriesOn(int s)

setSeriesOn

public void setSeriesOn(int s,
                        boolean value)

clearSeries

public void clearSeries()

getInputOrder

public java.lang.String getInputOrder(int s)

setInputOrder

public void setInputOrder(int s,
                          java.lang.String value)

getCBegin

public int getCBegin(int s)

setCBegin

public void setCBegin(int s,
                      int value)

getCEnd

public int getCEnd(int s)

setCEnd

public void setCEnd(int s,
                    int value)

getCStep

public int getCStep(int s)

setCStep

public void setCStep(int s,
                     int value)

getZBegin

public int getZBegin(int s)

setZBegin

public void setZBegin(int s,
                      int value)

getZEnd

public int getZEnd(int s)

setZEnd

public void setZEnd(int s,
                    int value)

getZStep

public int getZStep(int s)

setZStep

public void setZStep(int s,
                     int value)

getTBegin

public int getTBegin(int s)

setTBegin

public void setTBegin(int s,
                      int value)

getTEnd

public int getTEnd(int s)

setTEnd

public void setTEnd(int s,
                    int value)

getTStep

public int getTStep(int s)

setTStep

public void setTStep(int s,
                     int value)

getCropRegion

public loci.common.Region getCropRegion(int s)

setCropRegion

public void setCropRegion(int s,
                          loci.common.Region r)

getCustomColor

public java.awt.Color getCustomColor(int s,
                                     int c)

setCustomColor

public void setCustomColor(int s,
                           int c,
                           java.awt.Color color)

getDefaultCustomColor

public java.awt.Color getDefaultCustomColor(int c)

getCustomColorKey

public java.lang.String getCustomColorKey(int s,
                                          int c)

isUsingPatternIds

public boolean isUsingPatternIds()

setUsingPatternIds

public void setUsingPatternIds(boolean b)

set

private <T> void set(java.util.List<T> list,
                     int index,
                     T value,
                     T fillValue)

get

private <T> T get(java.util.List<T> list,
                  int index,
                  T defaultValue)

checkKey

protected boolean checkKey(java.lang.String options,
                           java.lang.String key)

Tests whether the given boolean key is set in the specified options.