public class SettingsHolder extends Object
Modifier and Type | Class and Description |
---|---|
static class |
SettingsHolder.GeneScoreMethod
For the gene set resampling method, how are scores computed for the group?
|
static class |
SettingsHolder.Method
Which gene set scoring method to use.
|
static class |
SettingsHolder.MultiProbeHandling
What to do when there are multiple values for a gene.
|
static class |
SettingsHolder.MultiTestCorrMethod
How to correct for multiple tests.
|
Modifier | Constructor and Description |
---|---|
protected |
SettingsHolder() |
|
SettingsHolder(org.apache.commons.configuration.PropertiesConfiguration oldConfig) |
public static final String GEMMA_URL_BASE
protected static final String ALWAYS_USE_EMPIRICAL
protected static final String ANNOT_FILE
protected static final String ANNOT_FORMAT
protected static final String BIG_IS_BETTER
protected static final String CLASS_FILE
protected static final String CLASS_SCORE_METHOD
protected static final String DATA_DIRECTORY
protected static final String DO_LOG
protected static final String GENE_REP_TREATMENT
protected static final String GOLD_STANDARD_FILE
protected static final String IS_TESTER
protected static final String ITERATIONS
protected static final String MAX_CLASS_SIZE
protected static final String MIN_CLASS_SIZE
protected static final String MTC_CONFIG_NAME
protected static final String USE_MULTIFUNCTIONALITY_CORRECTION
protected static final String OUTPUT_FILE
protected static final String GENE_SCORE_THRESHOLD_KEY
protected static final String GENE_SCORE_THRESHOLD_LEGACY_KEY
protected static final String PREFERENCES_FILE_NAME
protected static final String QUANTILE_CONFIG_NAME
protected static final String RAW_FILE_CONFIG_NAME
protected static final String GENE_SET_RESAMPLING_SCORE_METHOD
protected static final String SCORE_COL
protected static final String SCORE_FILE
protected static final String DATA_COL
protected static final String SELECTED_CUSTOM_GENESETS
protected static final String CUSTOM_GENESET_FILES
protected static final String FILTER_NONSPECIFIC
protected static final String USE_BIOL_PROC
protected static final String USE_MOL_FUNC
protected static final String USE_CELL_COMP
protected static final String USE_USER_DEFINED_GROUPS
protected static final String CUSTOM_GENE_SET_DIRECTORY_PROPERTY
protected static final String SAVE_ALL_GENES_IN_OUTPUT
public static final String GENE_URL_BASE
protected static final String DEFAULT_CUSTOM_GENE_SET_DIR_NAME
protected static final String DEFAULT_USER_DATA_DIR_NAME
protected org.apache.commons.configuration.PropertiesConfiguration config
public SettingsHolder(org.apache.commons.configuration.PropertiesConfiguration oldConfig)
oldConfig
- protected SettingsHolder()
protected static String getDefaultUserClassesDirPath()
protected static String getDefaultUserDataDirPath()
public boolean getAlwaysUseEmpirical()
public String getAnnotFile()
public GeneAnnotationParser.Format getAnnotFormat()
public boolean getBigIsBetter()
public String getClassFile()
public SettingsHolder.Method getClassScoreMethod()
public String getClassScoreMethodName()
public String getCustomGeneSetDirectory()
public int getDataCol()
public String getDataDirectory()
public String getDefaultGeneUrl()
public boolean getDoLog()
public boolean getFilterNonSpecific()
public SettingsHolder.MultiProbeHandling getGeneRepTreatment()
public String getGeneScoreFileDirectory()
public double getGeneScoreThreshold()
public SettingsHolder.GeneScoreMethod getGeneSetResamplingScoreMethod()
public String getGeneUrlBase()
public String getGoldStandardFile()
public String getHelpUrl()
public int getIterations()
public int getMaxClassSize()
public int getMinClassSize()
public SettingsHolder.MultiTestCorrMethod getMtc()
public int getQuantile()
public String getRawDataFileDirectory()
public String getRawDataFileName()
public boolean getSaveAllGenesInOutput()
public int getScoreCol()
public String getScoreFile()
public String getStringProperty(String propertyName)
propertyName
- public boolean getUseBiologicalProcess()
public boolean getUseCellularComponent()
public boolean getUseLog()
public boolean getUseMolecularFunction()
public String getUserGeneSetDirectory()
public boolean getUseUserDefined()
public boolean isTester()
public boolean loadUserDefined()
public void setCustomGeneSetFiles(Collection<String> filePaths)
public void setLoadUserDefined(boolean b)
public void setRawFile(String val)
public void setScoreFile(String val)
public void setUseUserDefined(boolean b)
public boolean upperTail()
public boolean useMultifunctionalityCorrection()
protected org.apache.commons.configuration.PropertiesConfiguration getConfig()
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