htsjdk.variant.variantcontext

Class CommonInfo

java.lang.Object

htsjdk.variant.variantcontext.CommonInfo

public final class CommonInfo
extends java.lang.Object

Common utility routines for VariantContext and Genotype

Field Summary

Fields

Modifier and Type	Field and Description
static double	NO_LOG10_PERROR

Constructor Summary

Constructors

Constructor and Description
CommonInfo(java.lang.String name, double log10PError, java.util.Set<java.lang.String> filters, java.util.Map<java.lang.String,java.lang.Object> attributes)

Method Summary

Methods

Modifier and Type	Method and Description
void	addFilter(java.lang.String filter)
void	addFilters(java.util.Collection<java.lang.String> filters)
void	clearAttributes()
boolean	filtersWereApplied()
java.lang.Object	getAttribute(java.lang.String key)
java.lang.Object	getAttribute(java.lang.String key, java.lang.Object defaultValue)
boolean	getAttributeAsBoolean(java.lang.String key, boolean defaultValue)
double	getAttributeAsDouble(java.lang.String key, double defaultValue)
int	getAttributeAsInt(java.lang.String key, int defaultValue)
java.lang.String	getAttributeAsString(java.lang.String key, java.lang.String defaultValue)
java.util.Map<java.lang.String,java.lang.Object>	getAttributes()
java.util.Set<java.lang.String>	getFilters()
java.util.Set<java.lang.String>	getFiltersMaybeNull()
double	getLog10PError()
java.lang.String	getName()
int	getNumAttributes()
double	getPhredScaledQual()
boolean	hasAttribute(java.lang.String key)
boolean	hasLog10PError()
boolean	isFiltered()
boolean	isNotFiltered()
void	putAttribute(java.lang.String key, java.lang.Object value)
void	putAttribute(java.lang.String key, java.lang.Object value, boolean allowOverwrites)
void	putAttributes(java.util.Map<java.lang.String,?> map)
void	removeAttribute(java.lang.String key)
void	setAttributes(java.util.Map<java.lang.String,?> map)
void	setLog10PError(double log10PError)
void	setName(java.lang.String name) Sets the name

Methods inherited from class java.lang.Object

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

Field Detail

NO_LOG10_PERROR

public static final double NO_LOG10_PERROR

See Also:

Constant Field Values

Constructor Detail

CommonInfo

public CommonInfo(java.lang.String name,
          double log10PError,
          java.util.Set<java.lang.String> filters,
          java.util.Map<java.lang.String,java.lang.Object> attributes)

Method Detail

getName

public java.lang.String getName()

Returns:

the name

setName

public void setName(java.lang.String name)

Sets the name

Parameters:

name - the name associated with this information

getFiltersMaybeNull

public java.util.Set<java.lang.String> getFiltersMaybeNull()

getFilters

public java.util.Set<java.lang.String> getFilters()

filtersWereApplied

public boolean filtersWereApplied()

isFiltered

public boolean isFiltered()

isNotFiltered

public boolean isNotFiltered()

addFilter

public void addFilter(java.lang.String filter)

addFilters

public void addFilters(java.util.Collection<java.lang.String> filters)

hasLog10PError

public boolean hasLog10PError()

getLog10PError

public double getLog10PError()

Returns:

the -1 * log10-based error estimate

getPhredScaledQual

public double getPhredScaledQual()

setLog10PError

public void setLog10PError(double log10PError)

clearAttributes

public void clearAttributes()

getAttributes

public java.util.Map<java.lang.String,java.lang.Object> getAttributes()

Returns:

the attribute map

setAttributes

public void setAttributes(java.util.Map<java.lang.String,?> map)

putAttribute

public void putAttribute(java.lang.String key,
                java.lang.Object value)

putAttribute

public void putAttribute(java.lang.String key,
                java.lang.Object value,
                boolean allowOverwrites)

removeAttribute

public void removeAttribute(java.lang.String key)

putAttributes

public void putAttributes(java.util.Map<java.lang.String,?> map)

hasAttribute

public boolean hasAttribute(java.lang.String key)

getNumAttributes

public int getNumAttributes()

getAttribute

public java.lang.Object getAttribute(java.lang.String key)

Parameters:

key - the attribute key

Returns:

the attribute value for the given key (or null if not set)

getAttribute

public java.lang.Object getAttribute(java.lang.String key,
                            java.lang.Object defaultValue)

getAttributeAsString

public java.lang.String getAttributeAsString(java.lang.String key,
                                    java.lang.String defaultValue)

getAttributeAsInt

public int getAttributeAsInt(java.lang.String key,
                    int defaultValue)

getAttributeAsDouble

public double getAttributeAsDouble(java.lang.String key,
                          double defaultValue)

getAttributeAsBoolean

public boolean getAttributeAsBoolean(java.lang.String key,
                            boolean defaultValue)