net.maizegenetics.prefs

Class TasselPrefs

net.maizegenetics.prefs.TasselPrefs

public class TasselPrefs

Field Detail

TASSEL_TOP

public static java.lang.String TASSEL_TOP

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Constant Field Values

TASSEL_SAVE_DIR

public static java.lang.String TASSEL_SAVE_DIR

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Constant Field Values

TASSEL_SAVE_DIR_DEFAULT

public static java.lang.String TASSEL_SAVE_DIR_DEFAULT

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Constant Field Values

TASSEL_OPEN_DIR

public static java.lang.String TASSEL_OPEN_DIR

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Constant Field Values

TASSEL_OPEN_DIR_DEFAULT

public static java.lang.String TASSEL_OPEN_DIR_DEFAULT

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Constant Field Values

TASSEL_X_DIM

public static java.lang.String TASSEL_X_DIM

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Constant Field Values

TASSEL_X_DIM_DEFAULT

public static int TASSEL_X_DIM_DEFAULT

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Constant Field Values

TASSEL_Y_DIM

public static java.lang.String TASSEL_Y_DIM

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Constant Field Values

TASSEL_Y_DIM_DEFAULT

public static int TASSEL_Y_DIM_DEFAULT

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Constant Field Values

TASSEL_LOG_SEND_TO_CONSOLE

public static java.lang.String TASSEL_LOG_SEND_TO_CONSOLE

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Constant Field Values

TASSEL_LOG_SEND_TO_CONSOLE_DEFAULT

public static boolean TASSEL_LOG_SEND_TO_CONSOLE_DEFAULT

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Constant Field Values

TASSEL_LOG_DEBUG

public static java.lang.String TASSEL_LOG_DEBUG

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Constant Field Values

TASSEL_LOG_DEBUG_DEFAULT

public static boolean TASSEL_LOG_DEBUG_DEFAULT

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Constant Field Values

TASSEL_LOG_X_DIM

public static java.lang.String TASSEL_LOG_X_DIM

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Constant Field Values

TASSEL_LOG_X_DIM_DEFAULT

public static int TASSEL_LOG_X_DIM_DEFAULT

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Constant Field Values

TASSEL_LOG_Y_DIM

public static java.lang.String TASSEL_LOG_Y_DIM

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Constant Field Values

TASSEL_LOG_Y_DIM_DEFAULT

public static int TASSEL_LOG_Y_DIM_DEFAULT

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Constant Field Values

TASSEL_MAX_THREADS

public static java.lang.String TASSEL_MAX_THREADS

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Constant Field Values

TASSEL_MAX_THREADS_DEFAULT

public static int TASSEL_MAX_THREADS_DEFAULT

TASSEL_CONFIG_FILE

public static java.lang.String TASSEL_CONFIG_FILE

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Constant Field Values

TASSEL_CONFIG_FILE_DEFAULT

public static java.lang.String TASSEL_CONFIG_FILE_DEFAULT

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Constant Field Values

TASSEL_LOCALE

public static java.lang.String TASSEL_LOCALE

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Constant Field Values

EXPORT_PLUGIN_TOP

public static java.lang.String EXPORT_PLUGIN_TOP

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Constant Field Values

EXPORT_PLUGIN_EXPORT_DIPLOIDS

public static java.lang.String EXPORT_PLUGIN_EXPORT_DIPLOIDS

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Constant Field Values

EXPORT_PLUGIN_EXPORT_DIPLOIDS_DEFAULT

public static boolean EXPORT_PLUGIN_EXPORT_DIPLOIDS_DEFAULT

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Constant Field Values

EXPORT_PLUGIN_INCLUDE_TAXA_ANNOTATIONS

public static java.lang.String EXPORT_PLUGIN_INCLUDE_TAXA_ANNOTATIONS

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Constant Field Values

EXPORT_PLUGIN_INCLUDE_TAXA_ANNOTATIONS_DEFAULT

public static boolean EXPORT_PLUGIN_INCLUDE_TAXA_ANNOTATIONS_DEFAULT

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Constant Field Values

FILTER_ALIGN_PLUGIN_TOP

public static java.lang.String FILTER_ALIGN_PLUGIN_TOP

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Constant Field Values

FILTER_ALIGN_PLUGIN_MIN_FREQ

public static java.lang.String FILTER_ALIGN_PLUGIN_MIN_FREQ

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Constant Field Values

FILTER_ALIGN_PLUGIN_MIN_FREQ_DEFAULT

public static double FILTER_ALIGN_PLUGIN_MIN_FREQ_DEFAULT

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Constant Field Values

FILTER_ALIGN_PLUGIN_MAX_FREQ

public static java.lang.String FILTER_ALIGN_PLUGIN_MAX_FREQ

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Constant Field Values

FILTER_ALIGN_PLUGIN_MAX_FREQ_DEFAULT

public static double FILTER_ALIGN_PLUGIN_MAX_FREQ_DEFAULT

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Constant Field Values

FILTER_ALIGN_PLUGIN_MIN_COUNT

public static java.lang.String FILTER_ALIGN_PLUGIN_MIN_COUNT

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Constant Field Values

FILTER_ALIGN_PLUGIN_MIN_COUNT_DEFAULT

public static int FILTER_ALIGN_PLUGIN_MIN_COUNT_DEFAULT

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Constant Field Values

FILTER_TAXA_PROPS_PLUGIN_TOP

public static java.lang.String FILTER_TAXA_PROPS_PLUGIN_TOP

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Constant Field Values

FILTER_TAXA_PROPS_PLUGIN_MIN_NOT_MISSING

public static java.lang.String FILTER_TAXA_PROPS_PLUGIN_MIN_NOT_MISSING

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Constant Field Values

FILTER_TAXA_PROPS_PLUGIN_MIN_NOT_MISSING_DEFAULT

public static double FILTER_TAXA_PROPS_PLUGIN_MIN_NOT_MISSING_DEFAULT

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Constant Field Values

FILTER_TAXA_PROPS_PLUGIN_MIN_HET

public static java.lang.String FILTER_TAXA_PROPS_PLUGIN_MIN_HET

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Constant Field Values

FILTER_TAXA_PROPS_PLUGIN_MIN_HET_DEFAULT

public static double FILTER_TAXA_PROPS_PLUGIN_MIN_HET_DEFAULT

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Constant Field Values

FILTER_TAXA_PROPS_PLUGIN_MAX_HET

public static java.lang.String FILTER_TAXA_PROPS_PLUGIN_MAX_HET

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Constant Field Values

FILTER_TAXA_PROPS_PLUGIN_MAX_HET_DEFAULT

public static double FILTER_TAXA_PROPS_PLUGIN_MAX_HET_DEFAULT

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Constant Field Values

ALIGNMENT_TOP

public static java.lang.String ALIGNMENT_TOP

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Constant Field Values

ALIGNMENT_RETAIN_RARE_ALLELES

public static java.lang.String ALIGNMENT_RETAIN_RARE_ALLELES

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Constant Field Values

ALIGNMENT_RETAIN_RARE_ALLELES_DEFAULT

public static boolean ALIGNMENT_RETAIN_RARE_ALLELES_DEFAULT

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Constant Field Values

GOBII_TOP

public static java.lang.String GOBII_TOP

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Constant Field Values

GOBII_USER

public static java.lang.String GOBII_USER

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Constant Field Values

GOBII_USER_DEFAULT

public static java.lang.String GOBII_USER_DEFAULT

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Constant Field Values

GOBII_DB

public static java.lang.String GOBII_DB

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Constant Field Values

GOBII_DB_DEFAULT

public static java.lang.String GOBII_DB_DEFAULT

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Constant Field Values

BMS_USER

public static java.lang.String BMS_USER

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Constant Field Values

BMS_USER_DEFAULT

public static java.lang.String BMS_USER_DEFAULT

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Constant Field Values

BMS_HOST

public static java.lang.String BMS_HOST

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Constant Field Values

BMS_HOST_DEFAULT

public static java.lang.String BMS_HOST_DEFAULT

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Constant Field Values

BMS_DB

public static java.lang.String BMS_DB

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Constant Field Values

BMS_DB_DEFAULT

public static java.lang.String BMS_DB_DEFAULT

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Constant Field Values

Method Detail

getPersistPreferences

public static boolean getPersistPreferences()

setPersistPreferences

public static void setPersistPreferences(boolean persist)

Whether to Persist Preferences. Preference changes should be persisted when executing GUI and set only temporarily from Command Line Flags. Also getting preferences should use stored values when executing GUI. And should use default values (if not temporarily set) when executing from Command Line.

Parameters:

persist - whether to persist preferences

getPref

public static java.lang.String getPref(java.lang.String path,
                                       java.lang.String key,
                                       java.lang.String def)

putPref

public static void putPref(java.lang.String path,
                           java.lang.String key,
                           java.lang.String value)

getDoublePref

public static double getDoublePref(java.lang.String path,
                                   java.lang.String key,
                                   double def)

putDoublePref

public static void putDoublePref(java.lang.String path,
                                 java.lang.String key,
                                 double value)

getIntPref

public static int getIntPref(java.lang.String path,
                             java.lang.String key,
                             int def)

putIntPref

public static void putIntPref(java.lang.String path,
                              java.lang.String key,
                              int value)

getBooleanPref

public static boolean getBooleanPref(java.lang.String path,
                                     java.lang.String key,
                                     boolean def)

putBooleanPref

public static void putBooleanPref(java.lang.String path,
                                  java.lang.String key,
                                  boolean value)

getSaveDir

public static java.lang.String getSaveDir()

putSaveDir

public static void putSaveDir(java.lang.String value)

getOpenDir

public static java.lang.String getOpenDir()

putOpenDir

public static void putOpenDir(java.lang.String value)

getXDim

public static int getXDim()

putXDim

public static void putXDim(int value)

getYDim

public static int getYDim()

putYDim

public static void putYDim(int value)

getLogSendToConsole

public static boolean getLogSendToConsole()

putLogSendToConsole

public static void putLogSendToConsole(boolean value)

getLogDebug

public static boolean getLogDebug()

putLogDebug

public static void putLogDebug(boolean value)

getLogXDim

public static int getLogXDim()

putLogXDim

public static void putLogXDim(int value)

getLogYDim

public static int getLogYDim()

putLogYDim

public static void putLogYDim(int value)

getMaxThreads

public static int getMaxThreads()

putMaxThreads

public static void putMaxThreads(int value)

getConfigFile

public static java.lang.String getConfigFile()

putConfigFile

public static void putConfigFile(java.lang.String value)

getLocale

public static java.util.Locale getLocale()

putLocale

public static void putLocale(java.util.Locale value)

getExportPluginExportDiploids

public static boolean getExportPluginExportDiploids()

putExportPluginExportDiploids

public static void putExportPluginExportDiploids(boolean value)

getExportPluginIncludeTaxaAnnotations

public static boolean getExportPluginIncludeTaxaAnnotations()

putExportPluginIncludeTaxaAnnotations

public static void putExportPluginIncludeTaxaAnnotations(boolean value)

getFilterAlignPluginMinFreq

public static double getFilterAlignPluginMinFreq()

putFilterAlignPluginMinFreq

public static void putFilterAlignPluginMinFreq(double value)

getFilterAlignPluginMaxFreq

public static double getFilterAlignPluginMaxFreq()

putFilterAlignPluginMaxFreq

public static void putFilterAlignPluginMaxFreq(double value)

getFilterAlignPluginMinCount

public static int getFilterAlignPluginMinCount()

putFilterAlignPluginMinCount

public static void putFilterAlignPluginMinCount(int value)

getFilterTaxaPropsMinNotMissingFreq

public static double getFilterTaxaPropsMinNotMissingFreq()

putFilterTaxaPropsMinNotMissingFreq

public static void putFilterTaxaPropsMinNotMissingFreq(double value)

getFilterTaxaPropsMinHetFreq

public static double getFilterTaxaPropsMinHetFreq()

putFilterTaxaPropsMinHetFreq

public static void putFilterTaxaPropsMinHetFreq(double value)

getFilterTaxaPropsMaxHetFreq

public static double getFilterTaxaPropsMaxHetFreq()

putFilterTaxaPropsMaxHetFreq

public static void putFilterTaxaPropsMaxHetFreq(double value)

getAlignmentRetainRareAlleles

public static boolean getAlignmentRetainRareAlleles()

putAlignmentRetainRareAlleles

public static void putAlignmentRetainRareAlleles(boolean value)

getGOBIIDB

public static java.lang.String getGOBIIDB()

putGOBIIDB

public static void putGOBIIDB(java.lang.String value)

getGOBIIUser

public static java.lang.String getGOBIIUser()

putGOBIIUser

public static void putGOBIIUser(java.lang.String value)

getBMSHost

public static java.lang.String getBMSHost()

putBMSHost

public static void putBMSHost(java.lang.String value)

getBMSDB

public static java.lang.String getBMSDB()

putBMSDB

public static void putBMSDB(java.lang.String value)

getBMSUser

public static java.lang.String getBMSUser()

putBMSUser

public static void putBMSUser(java.lang.String value)