public class TasselPrefs
public static java.lang.String TASSEL_TOP
public static java.lang.String TASSEL_SAVE_DIR
public static java.lang.String TASSEL_SAVE_DIR_DEFAULT
public static java.lang.String TASSEL_OPEN_DIR
public static java.lang.String TASSEL_OPEN_DIR_DEFAULT
public static java.lang.String TASSEL_X_DIM
public static int TASSEL_X_DIM_DEFAULT
public static java.lang.String TASSEL_Y_DIM
public static int TASSEL_Y_DIM_DEFAULT
public static java.lang.String TASSEL_LOG_SEND_TO_CONSOLE
public static boolean TASSEL_LOG_SEND_TO_CONSOLE_DEFAULT
public static java.lang.String TASSEL_LOG_DEBUG
public static boolean TASSEL_LOG_DEBUG_DEFAULT
public static java.lang.String TASSEL_LOG_X_DIM
public static int TASSEL_LOG_X_DIM_DEFAULT
public static java.lang.String TASSEL_LOG_Y_DIM
public static int TASSEL_LOG_Y_DIM_DEFAULT
public static java.lang.String TASSEL_MAX_THREADS
public static int TASSEL_MAX_THREADS_DEFAULT
public static java.lang.String TASSEL_CONFIG_FILE
public static java.lang.String TASSEL_CONFIG_FILE_DEFAULT
public static java.lang.String TASSEL_LOCALE
public static java.lang.String EXPORT_PLUGIN_TOP
public static java.lang.String EXPORT_PLUGIN_EXPORT_DIPLOIDS
public static boolean EXPORT_PLUGIN_EXPORT_DIPLOIDS_DEFAULT
public static java.lang.String EXPORT_PLUGIN_INCLUDE_TAXA_ANNOTATIONS
public static boolean EXPORT_PLUGIN_INCLUDE_TAXA_ANNOTATIONS_DEFAULT
public static java.lang.String FILTER_ALIGN_PLUGIN_TOP
public static java.lang.String FILTER_ALIGN_PLUGIN_MIN_FREQ
public static double FILTER_ALIGN_PLUGIN_MIN_FREQ_DEFAULT
public static java.lang.String FILTER_ALIGN_PLUGIN_MAX_FREQ
public static double FILTER_ALIGN_PLUGIN_MAX_FREQ_DEFAULT
public static java.lang.String FILTER_ALIGN_PLUGIN_MIN_COUNT
public static int FILTER_ALIGN_PLUGIN_MIN_COUNT_DEFAULT
public static java.lang.String FILTER_TAXA_PROPS_PLUGIN_TOP
public static java.lang.String FILTER_TAXA_PROPS_PLUGIN_MIN_NOT_MISSING
public static double FILTER_TAXA_PROPS_PLUGIN_MIN_NOT_MISSING_DEFAULT
public static java.lang.String FILTER_TAXA_PROPS_PLUGIN_MIN_HET
public static double FILTER_TAXA_PROPS_PLUGIN_MIN_HET_DEFAULT
public static java.lang.String FILTER_TAXA_PROPS_PLUGIN_MAX_HET
public static double FILTER_TAXA_PROPS_PLUGIN_MAX_HET_DEFAULT
public static java.lang.String ALIGNMENT_TOP
public static java.lang.String ALIGNMENT_RETAIN_RARE_ALLELES
public static boolean ALIGNMENT_RETAIN_RARE_ALLELES_DEFAULT
public static java.lang.String GOBII_TOP
public static java.lang.String GOBII_USER
public static java.lang.String GOBII_USER_DEFAULT
public static java.lang.String GOBII_DB
public static java.lang.String GOBII_DB_DEFAULT
public static java.lang.String BMS_USER
public static java.lang.String BMS_USER_DEFAULT
public static java.lang.String BMS_HOST
public static java.lang.String BMS_HOST_DEFAULT
public static java.lang.String BMS_DB
public static java.lang.String BMS_DB_DEFAULT
public static boolean getPersistPreferences()
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.
persist - whether to persist preferencespublic static java.lang.String getPref(java.lang.String path,
java.lang.String key,
java.lang.String def)
public static void putPref(java.lang.String path,
java.lang.String key,
java.lang.String value)
public static double getDoublePref(java.lang.String path,
java.lang.String key,
double def)
public static void putDoublePref(java.lang.String path,
java.lang.String key,
double value)
public static int getIntPref(java.lang.String path,
java.lang.String key,
int def)
public static void putIntPref(java.lang.String path,
java.lang.String key,
int value)
public static boolean getBooleanPref(java.lang.String path,
java.lang.String key,
boolean def)
public static void putBooleanPref(java.lang.String path,
java.lang.String key,
boolean value)
public static java.lang.String getSaveDir()
public static void putSaveDir(java.lang.String value)
public static java.lang.String getOpenDir()
public static void putOpenDir(java.lang.String value)
public static int getXDim()
public static void putXDim(int value)
public static int getYDim()
public static void putYDim(int value)
public static boolean getLogSendToConsole()
public static void putLogSendToConsole(boolean value)
public static boolean getLogDebug()
public static void putLogDebug(boolean value)
public static int getLogXDim()
public static void putLogXDim(int value)
public static int getLogYDim()
public static void putLogYDim(int value)
public static int getMaxThreads()
public static void putMaxThreads(int value)
public static java.lang.String getConfigFile()
public static void putConfigFile(java.lang.String value)
public static java.util.Locale getLocale()
public static void putLocale(java.util.Locale value)
public static boolean getExportPluginExportDiploids()
public static void putExportPluginExportDiploids(boolean value)
public static boolean getExportPluginIncludeTaxaAnnotations()
public static void putExportPluginIncludeTaxaAnnotations(boolean value)
public static double getFilterAlignPluginMinFreq()
public static void putFilterAlignPluginMinFreq(double value)
public static double getFilterAlignPluginMaxFreq()
public static void putFilterAlignPluginMaxFreq(double value)
public static int getFilterAlignPluginMinCount()
public static void putFilterAlignPluginMinCount(int value)
public static double getFilterTaxaPropsMinNotMissingFreq()
public static void putFilterTaxaPropsMinNotMissingFreq(double value)
public static double getFilterTaxaPropsMinHetFreq()
public static void putFilterTaxaPropsMinHetFreq(double value)
public static double getFilterTaxaPropsMaxHetFreq()
public static void putFilterTaxaPropsMaxHetFreq(double value)
public static boolean getAlignmentRetainRareAlleles()
public static void putAlignmentRetainRareAlleles(boolean value)
public static java.lang.String getGOBIIDB()
public static void putGOBIIDB(java.lang.String value)
public static java.lang.String getGOBIIUser()
public static void putGOBIIUser(java.lang.String value)
public static java.lang.String getBMSHost()
public static void putBMSHost(java.lang.String value)
public static java.lang.String getBMSDB()
public static void putBMSDB(java.lang.String value)
public static java.lang.String getBMSUser()
public static void putBMSUser(java.lang.String value)