com.pacbio.secondary.vis.common.utils

Class PropertiesHelper

java.lang.Object

com.pacbio.secondary.vis.common.utils.PropertiesHelper

All Implemented Interfaces:

java.io.Serializable

public class PropertiesHelper
extends java.lang.Object
implements java.io.Serializable

App preferences and default properties

Author:

mmilletti

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ALWAYS_SHOW_MEM_STATS_VALUE
protected boolean	alwaysShowMemoryInfo
protected static int	APP_INFO_PANEL_FONT_SIZE
protected static boolean	APP_SHOW_WHATS_NEW_HELP
protected java.lang.String	appVisualFilter
static java.lang.String	AUTO_IDEO_BAND_SIZE
static java.lang.String	AUTO_IDEO_MAX_NUM_BANDS
static java.lang.String	AUTO_IDEO_NUM_BANDS
static java.lang.String	COARSE_MODE
static java.lang.String	DETAILS_METRICS_MODE
static java.lang.String	DETAILS_VIEW_LIMITING_MODE
static java.lang.String	DNA_COLOR_0
static java.lang.String	DNA_COLOR_1
static java.lang.String	DNA_COLOR_2
static java.lang.String	DNA_COLOR_3
static boolean	DRAW_MIN_BASE_MOD_WIDTH
static boolean	DRAW_MODS_SUMMARY
static boolean	DRAW_PANEL_ICONS
static java.lang.String	ENABLE_GRAPH_STRUCTURE_VALUE
static java.lang.String	EPIPRO_CUTOFF_FILTER_VALUE
static java.lang.String	EVENTS_FILTER_VALUE
static java.lang.String	FIT_DENOVO_TABLE_TO_PANEL_VALUE
static java.lang.String	FIT_TABLE_TO_PANEL_VALUE
protected boolean	fitGenomicTableToPanel
static java.lang.String	GRAPH_STRUCTURE_TYPE_VALUE
static java.lang.String	HIGH_KIN_FILTER
static java.lang.String	HIGH_QV_FILTER
static java.lang.String	KIN_FWD_COLOR
static java.lang.String	KIN_FWD_COLOR_HEATMAP
static java.lang.String	KIN_REV_COLOR
static java.lang.String	KIN_REV_COLOR_HEATMAP
static java.lang.String	KINETICS_SCALING
static java.lang.String	LAST_USED_LAYOUT
static java.lang.String	LAST_USED_LOCAL_DIR_OPEN
static java.lang.String	LAST_USED_LOCAL_DIR_SAVE
static java.lang.String	LAST_USED_REMOTE_PATH
static java.lang.String	LOCK_RANGE_EXPANSION
protected boolean	lockGenomeRegionPanels
protected boolean	lockRangeExpand
protected boolean	lockRegionDetailsPanels
static java.lang.String	LOW_KIN_FILTER
static java.lang.String	LOW_QV_FILTER
static java.lang.String	MAX_DETAILS_COVERAGE
static java.lang.String	MAX_DETAILS_VIEW_DYNAMIC_RANGE
static java.lang.String	MAX_DETAILS_VIEW_FIXED_RANGE
static java.lang.String	MODS_FILTER_VALUE
static java.lang.String	SELECTION_PANEL_FONT_SIZE
protected static long	serialVersionUID
static java.lang.String	SHOW_DETAILS_TOOLTIP
static java.lang.String	SHOW_GRAPH_STRUCTURE_ONLY_VALUE
static java.lang.String	SHOW_IDEOGRAM_LABEL
static java.lang.String	SHOW_MARKER_LABEL
static java.lang.String	SHOW_WHATS_NEW_HELP
static java.lang.String	SMRTGROUP_OPTION
static java.lang.String	USE_EPIPRO_CUTOFF_FILTER
static java.lang.String	USE_EPIPRO_ONLY
static java.lang.String	USE_EPIPRO_UNFOLDED
static boolean	USE_FOR_TESTING_WHEN_NEEDED
static java.lang.String	USE_MAPQV_FILTER
static java.lang.String	USE_MODS_FILTER
static java.lang.String	USE_QV_FILTER
static java.lang.String	USE_VARIANT_COV_FILTER
static java.lang.String	USE_VARIANTS_CONF_FILTER
protected boolean	useLogScaling
protected boolean	useTableViewFilter
static java.lang.String	VARIANTS_CONF_FILTER_VALUE
protected boolean	viewSubReadsData

Constructor Summary

Constructors

Constructor and Description
PropertiesHelper()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	getAlwaysShowMemStats()
static boolean	getBoolean(java.lang.String property, boolean def)
static java.lang.String	getConfigurationFilePath() return path of configuration file
static double	getDouble(java.lang.String property, double def)
protected static java.lang.String	getFileComments()
boolean	getFitDeNovoTableToPanel()
boolean	getFitTableToPanel()
static int	getInfoPanelFontSize()
static int	getInt(java.lang.String property, int def)
static boolean	getIsSMRTGroup(java.lang.String url) Returns true if host requires group-level access control
static java.io.File	getLastLocalDataFolderOpen(java.lang.String type)
static java.io.File	getLastLocalDataFolderSave(java.lang.String type)
static java.lang.String	getLastRemoteDataFiles(java.lang.String type)
static int	getLastusedLayout()
boolean	getLockGenomeRegionPanels()
boolean	getLockRangeExpand()
boolean	getLockRegionDetailsPanels()
protected static java.util.Properties	getProperties(java.lang.String file_path)
static boolean	getShowBaseModsInfo()
static java.io.File	getSMRTViewLocalHome(java.lang.String type) return path of smrtview local data directory
static java.lang.String	getString(java.lang.String property, java.lang.String def_value)
boolean	getUseLogScaling()
boolean	getUseVisualFilter()
boolean	getViewSubreads()
java.lang.String	getVisualFilter()
void	readApplicationProperties() Read generic app properties
static void	readIdeogramProperties(IdeogramDB ideogram)
void	saveApplicationProperties() Save generic app properties
static void	saveIdeogramProperties(IdeogramDB ideogram)
void	setAlwaysShowMemStats(boolean b)
static void	setBoolean(java.lang.String property, boolean b)
static void	setDouble(java.lang.String property, double d)
void	setFitDeNovoTableToPanel(boolean b)
void	setFitTableToPanel(boolean b)
static void	setInfoPanelFontSize(int aPP_INFO_PANEL_FONT_SIZE)
static void	setInt(java.lang.String property, int i)
static void	setIsSMRTGroup(java.lang.String url, boolean b) Adds/removes host to list of systems requiring group-level access control
static void	setLastLocalDataFolderOpen(java.io.File folder, java.lang.String type)
static void	setLastLocalDataFolderSave(java.io.File folder, java.lang.String type)
static void	setLastRemoteDataFiles(java.lang.String folder, java.lang.String type)
static void	setLastusedLayout(int layout_idx)
void	setLockGenomeRegionPanels(boolean b)
void	setLockRangeExpand(boolean b)
void	setLockRegionDetailsPanels(boolean b)
static void	setShowBaseModsInfo(boolean b)
static void	setString(java.lang.String property, java.lang.String str)
void	setUseLogScaling(boolean b)
void	setUseVisualFilter(boolean b)
void	setViewSubreads(boolean b)
void	setVisualFilter(java.lang.String s)

Methods inherited from class java.lang.Object

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

Field Detail

serialVersionUID

protected static final long serialVersionUID

See Also:

Constant Field Values

USE_MODS_FILTER

public static final java.lang.String USE_MODS_FILTER

See Also:

Constant Field Values

MODS_FILTER_VALUE

public static final java.lang.String MODS_FILTER_VALUE

See Also:

Constant Field Values

USE_VARIANTS_CONF_FILTER

public static final java.lang.String USE_VARIANTS_CONF_FILTER

See Also:

Constant Field Values

VARIANTS_CONF_FILTER_VALUE

public static final java.lang.String VARIANTS_CONF_FILTER_VALUE

See Also:

Constant Field Values

USE_VARIANT_COV_FILTER

public static final java.lang.String USE_VARIANT_COV_FILTER

See Also:

Constant Field Values

EVENTS_FILTER_VALUE

public static final java.lang.String EVENTS_FILTER_VALUE

See Also:

Constant Field Values

LAST_USED_LOCAL_DIR_OPEN

public static final java.lang.String LAST_USED_LOCAL_DIR_OPEN

See Also:

Constant Field Values

LAST_USED_LOCAL_DIR_SAVE

public static final java.lang.String LAST_USED_LOCAL_DIR_SAVE

See Also:

Constant Field Values

LAST_USED_REMOTE_PATH

public static final java.lang.String LAST_USED_REMOTE_PATH

See Also:

Constant Field Values

ALWAYS_SHOW_MEM_STATS_VALUE

public static final java.lang.String ALWAYS_SHOW_MEM_STATS_VALUE

See Also:

Constant Field Values

FIT_TABLE_TO_PANEL_VALUE

public static final java.lang.String FIT_TABLE_TO_PANEL_VALUE

See Also:

Constant Field Values

FIT_DENOVO_TABLE_TO_PANEL_VALUE

public static final java.lang.String FIT_DENOVO_TABLE_TO_PANEL_VALUE

See Also:

Constant Field Values

SHOW_MARKER_LABEL

public static final java.lang.String SHOW_MARKER_LABEL

See Also:

Constant Field Values

SHOW_IDEOGRAM_LABEL

public static final java.lang.String SHOW_IDEOGRAM_LABEL

See Also:

Constant Field Values

AUTO_IDEO_NUM_BANDS

public static final java.lang.String AUTO_IDEO_NUM_BANDS

See Also:

Constant Field Values

AUTO_IDEO_BAND_SIZE

public static final java.lang.String AUTO_IDEO_BAND_SIZE

See Also:

Constant Field Values

AUTO_IDEO_MAX_NUM_BANDS

public static final java.lang.String AUTO_IDEO_MAX_NUM_BANDS

See Also:

Constant Field Values

USE_MAPQV_FILTER

public static final java.lang.String USE_MAPQV_FILTER

See Also:

Constant Field Values

USE_QV_FILTER

public static final java.lang.String USE_QV_FILTER

See Also:

Constant Field Values

LOW_QV_FILTER

public static final java.lang.String LOW_QV_FILTER

See Also:

Constant Field Values

HIGH_QV_FILTER

public static final java.lang.String HIGH_QV_FILTER

See Also:

Constant Field Values

LOW_KIN_FILTER

public static final java.lang.String LOW_KIN_FILTER

See Also:

Constant Field Values

HIGH_KIN_FILTER

public static final java.lang.String HIGH_KIN_FILTER

See Also:

Constant Field Values

KINETICS_SCALING

public static final java.lang.String KINETICS_SCALING

See Also:

Constant Field Values

COARSE_MODE

public static final java.lang.String COARSE_MODE

See Also:

Constant Field Values

LAST_USED_LAYOUT

public static final java.lang.String LAST_USED_LAYOUT

See Also:

Constant Field Values

KIN_FWD_COLOR

public static final java.lang.String KIN_FWD_COLOR

See Also:

Constant Field Values

KIN_REV_COLOR

public static final java.lang.String KIN_REV_COLOR

See Also:

Constant Field Values

KIN_FWD_COLOR_HEATMAP

public static final java.lang.String KIN_FWD_COLOR_HEATMAP

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Constant Field Values

KIN_REV_COLOR_HEATMAP

public static final java.lang.String KIN_REV_COLOR_HEATMAP

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Constant Field Values

SHOW_WHATS_NEW_HELP

public static final java.lang.String SHOW_WHATS_NEW_HELP

See Also:

Constant Field Values

USE_EPIPRO_UNFOLDED

public static final java.lang.String USE_EPIPRO_UNFOLDED

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Constant Field Values

USE_EPIPRO_ONLY

public static final java.lang.String USE_EPIPRO_ONLY

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Constant Field Values

USE_EPIPRO_CUTOFF_FILTER

public static final java.lang.String USE_EPIPRO_CUTOFF_FILTER

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Constant Field Values

EPIPRO_CUTOFF_FILTER_VALUE

public static final java.lang.String EPIPRO_CUTOFF_FILTER_VALUE

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Constant Field Values

SHOW_DETAILS_TOOLTIP

public static final java.lang.String SHOW_DETAILS_TOOLTIP

See Also:

Constant Field Values

DETAILS_METRICS_MODE

public static final java.lang.String DETAILS_METRICS_MODE

See Also:

Constant Field Values

ENABLE_GRAPH_STRUCTURE_VALUE

public static final java.lang.String ENABLE_GRAPH_STRUCTURE_VALUE

See Also:

Constant Field Values

SHOW_GRAPH_STRUCTURE_ONLY_VALUE

public static final java.lang.String SHOW_GRAPH_STRUCTURE_ONLY_VALUE

See Also:

Constant Field Values

GRAPH_STRUCTURE_TYPE_VALUE

public static final java.lang.String GRAPH_STRUCTURE_TYPE_VALUE

See Also:

Constant Field Values

SELECTION_PANEL_FONT_SIZE

public static final java.lang.String SELECTION_PANEL_FONT_SIZE

See Also:

Constant Field Values

DNA_COLOR_0

public static final java.lang.String DNA_COLOR_0

See Also:

Constant Field Values

DNA_COLOR_1

public static final java.lang.String DNA_COLOR_1

See Also:

Constant Field Values

DNA_COLOR_2

public static final java.lang.String DNA_COLOR_2

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Constant Field Values

DNA_COLOR_3

public static final java.lang.String DNA_COLOR_3

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Constant Field Values

DETAILS_VIEW_LIMITING_MODE

public static final java.lang.String DETAILS_VIEW_LIMITING_MODE

See Also:

Constant Field Values

MAX_DETAILS_VIEW_FIXED_RANGE

public static final java.lang.String MAX_DETAILS_VIEW_FIXED_RANGE

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Constant Field Values

MAX_DETAILS_VIEW_DYNAMIC_RANGE

public static final java.lang.String MAX_DETAILS_VIEW_DYNAMIC_RANGE

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Constant Field Values

MAX_DETAILS_COVERAGE

public static final java.lang.String MAX_DETAILS_COVERAGE

See Also:

Constant Field Values

LOCK_RANGE_EXPANSION

public static final java.lang.String LOCK_RANGE_EXPANSION

See Also:

Constant Field Values

SMRTGROUP_OPTION

public static final java.lang.String SMRTGROUP_OPTION

See Also:

Constant Field Values

APP_INFO_PANEL_FONT_SIZE

protected static int APP_INFO_PANEL_FONT_SIZE

APP_SHOW_WHATS_NEW_HELP

protected static boolean APP_SHOW_WHATS_NEW_HELP

DRAW_MODS_SUMMARY

public static final boolean DRAW_MODS_SUMMARY

See Also:

Constant Field Values

DRAW_MIN_BASE_MOD_WIDTH

public static final boolean DRAW_MIN_BASE_MOD_WIDTH

See Also:

Constant Field Values

DRAW_PANEL_ICONS

public static final boolean DRAW_PANEL_ICONS

See Also:

Constant Field Values

USE_FOR_TESTING_WHEN_NEEDED

public static transient boolean USE_FOR_TESTING_WHEN_NEEDED

appVisualFilter

protected java.lang.String appVisualFilter

useTableViewFilter

protected boolean useTableViewFilter

alwaysShowMemoryInfo

protected boolean alwaysShowMemoryInfo

fitGenomicTableToPanel

protected boolean fitGenomicTableToPanel

lockGenomeRegionPanels

protected boolean lockGenomeRegionPanels

lockRegionDetailsPanels

protected boolean lockRegionDetailsPanels

viewSubReadsData

protected boolean viewSubReadsData

lockRangeExpand

protected boolean lockRangeExpand

useLogScaling

protected boolean useLogScaling

Constructor Detail

PropertiesHelper

public PropertiesHelper()

Method Detail

getLastLocalDataFolderOpen

public static java.io.File getLastLocalDataFolderOpen(java.lang.String type)

setLastLocalDataFolderOpen

public static void setLastLocalDataFolderOpen(java.io.File folder,
                              java.lang.String type)

getLastLocalDataFolderSave

public static java.io.File getLastLocalDataFolderSave(java.lang.String type)

setLastLocalDataFolderSave

public static void setLastLocalDataFolderSave(java.io.File folder,
                              java.lang.String type)

getLastRemoteDataFiles

public static java.lang.String getLastRemoteDataFiles(java.lang.String type)

setLastRemoteDataFiles

public static void setLastRemoteDataFiles(java.lang.String folder,
                          java.lang.String type)

setLastusedLayout

public static void setLastusedLayout(int layout_idx)

getLastusedLayout

public static int getLastusedLayout()

Returns:

getIsSMRTGroup

public static boolean getIsSMRTGroup(java.lang.String url)

Returns true if host requires group-level access control

Parameters:

host -

Returns:

setIsSMRTGroup

public static void setIsSMRTGroup(java.lang.String url,
                  boolean b)

Adds/removes host to list of systems requiring group-level access control

Parameters:

host -

b -

getFitTableToPanel

public boolean getFitTableToPanel()

setFitTableToPanel

public void setFitTableToPanel(boolean b)

getFitDeNovoTableToPanel

public boolean getFitDeNovoTableToPanel()

setFitDeNovoTableToPanel

public void setFitDeNovoTableToPanel(boolean b)

getInfoPanelFontSize

public static int getInfoPanelFontSize()

setInfoPanelFontSize

public static void setInfoPanelFontSize(int aPP_INFO_PANEL_FONT_SIZE)

getShowBaseModsInfo

public static boolean getShowBaseModsInfo()

setShowBaseModsInfo

public static void setShowBaseModsInfo(boolean b)

getUseVisualFilter

public boolean getUseVisualFilter()

setUseVisualFilter

public void setUseVisualFilter(boolean b)

getVisualFilter

public java.lang.String getVisualFilter()

setVisualFilter

public void setVisualFilter(java.lang.String s)

getUseLogScaling

public boolean getUseLogScaling()

setUseLogScaling

public void setUseLogScaling(boolean b)

getLockGenomeRegionPanels

public boolean getLockGenomeRegionPanels()

setLockGenomeRegionPanels

public void setLockGenomeRegionPanels(boolean b)

getLockRegionDetailsPanels

public boolean getLockRegionDetailsPanels()

setLockRegionDetailsPanels

public void setLockRegionDetailsPanels(boolean b)

getLockRangeExpand

public boolean getLockRangeExpand()

setLockRangeExpand

public void setLockRangeExpand(boolean b)

getViewSubreads

public boolean getViewSubreads()

setViewSubreads

public void setViewSubreads(boolean b)

getAlwaysShowMemStats

public boolean getAlwaysShowMemStats()

setAlwaysShowMemStats

public void setAlwaysShowMemStats(boolean b)

saveApplicationProperties

public void saveApplicationProperties()

Save generic app properties

readApplicationProperties

public void readApplicationProperties()

Read generic app properties

saveIdeogramProperties

public static void saveIdeogramProperties(IdeogramDB ideogram)

readIdeogramProperties

public static void readIdeogramProperties(IdeogramDB ideogram)

getConfigurationFilePath

public static java.lang.String getConfigurationFilePath()

return path of configuration file

Returns:

getSMRTViewLocalHome

public static java.io.File getSMRTViewLocalHome(java.lang.String type)

return path of smrtview local data directory

Returns:

getProperties

protected static java.util.Properties getProperties(java.lang.String file_path)

Parameters:

file_path -

Returns:

getString

public static java.lang.String getString(java.lang.String property,
                         java.lang.String def_value)

Parameters:

property -

def_value -

Returns:

setString

public static void setString(java.lang.String property,
             java.lang.String str)

Parameters:

property -

str -

getBoolean

public static boolean getBoolean(java.lang.String property,
                 boolean def)

Parameters:

property -

def -

Returns:

setBoolean

public static void setBoolean(java.lang.String property,
              boolean b)

Parameters:

property -

b -

getInt

public static int getInt(java.lang.String property,
         int def)

Parameters:

property -

def -

Returns:

setInt

public static void setInt(java.lang.String property,
          int i)

Parameters:

property -

i -

getDouble

public static double getDouble(java.lang.String property,
               double def)

Parameters:

property -

def -

Returns:

setDouble

public static void setDouble(java.lang.String property,
             double d)

Parameters:

property -

i -

getFileComments

protected static java.lang.String getFileComments()

Returns: