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
Constructor Summary |
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 |
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 |
NO_LOG10_PERROR
public static final double NO_LOG10_PERROR
- See Also:
- Constant Field Values
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)
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)