public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCFIDHeaderLine
Modifier and Type | Class and Description |
---|---|
static class |
VCFCompoundHeaderLine.SupportedHeaderLineType |
ALLOW_UNBOUND_DESCRIPTIONS, serialVersionUID, UNBOUND_DESCRIPTION
Modifier | Constructor and Description |
---|---|
protected |
VCFCompoundHeaderLine(java.lang.String name,
int count,
VCFHeaderLineType type,
java.lang.String description,
VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
create a VCF format header line
|
protected |
VCFCompoundHeaderLine(java.lang.String name,
int count,
VCFHeaderLineType type,
java.lang.String description,
VCFCompoundHeaderLine.SupportedHeaderLineType lineType,
java.lang.String source,
java.lang.String version)
create a VCF format header line
|
protected |
VCFCompoundHeaderLine(java.lang.String name,
VCFHeaderLineCount count,
VCFHeaderLineType type,
java.lang.String description,
VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
create a VCF format header line
|
protected |
VCFCompoundHeaderLine(java.lang.String name,
VCFHeaderLineCount count,
VCFHeaderLineType type,
java.lang.String description,
VCFCompoundHeaderLine.SupportedHeaderLineType lineType,
java.lang.String source,
java.lang.String version)
create a VCF format header line
|
protected |
VCFCompoundHeaderLine(java.lang.String line,
VCFHeaderVersion version,
VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
create a VCF format header line
|
Modifier and Type | Method and Description |
---|---|
boolean |
equals(java.lang.Object o)
returns true if we're equal to another compound header line
|
boolean |
equalsExcludingDescription(VCFCompoundHeaderLine other) |
int |
getCount() |
int |
getCount(VariantContext vc)
Get the number of values expected for this header field, given the properties of VariantContext vc
If the count is a fixed count, return that.
|
VCFHeaderLineCount |
getCountType() |
java.lang.String |
getDescription() |
java.lang.String |
getID() |
java.lang.String |
getSource() |
VCFHeaderLineType |
getType() |
java.lang.String |
getVersion() |
int |
hashCode() |
boolean |
isFixedCount() |
boolean |
sameLineTypeAndName(VCFCompoundHeaderLine other) |
void |
setNumberToUnbounded() |
void |
setSource(java.lang.String source)
Specify annotation source
|
void |
setVersion(java.lang.String version)
Specify annotation version
|
protected java.lang.String |
toStringEncoding()
make a string representation of this header line
|
compareTo, getKey, getValue, isHeaderLine, shouldBeAddedToDictionary, toString, toStringEncoding
protected VCFCompoundHeaderLine(java.lang.String name, int count, VCFHeaderLineType type, java.lang.String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
name
- the name for this header linecount
- the count for this header linetype
- the type for this header linedescription
- the description for this header linelineType
- the header line typeprotected VCFCompoundHeaderLine(java.lang.String name, VCFHeaderLineCount count, VCFHeaderLineType type, java.lang.String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
name
- the name for this header linecount
- the count type for this header linetype
- the type for this header linedescription
- the description for this header linelineType
- the header line typeprotected VCFCompoundHeaderLine(java.lang.String name, int count, VCFHeaderLineType type, java.lang.String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType, java.lang.String source, java.lang.String version)
name
- the name for this header linecount
- the count for this header linetype
- the type for this header linedescription
- the description for this header linelineType
- the header line typesource
- annotation source (case-insensitive, e.g. "dbsnp")version
- exact version (e.g. "138")protected VCFCompoundHeaderLine(java.lang.String name, VCFHeaderLineCount count, VCFHeaderLineType type, java.lang.String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType, java.lang.String source, java.lang.String version)
name
- the name for this header linecount
- the count type for this header linetype
- the type for this header linedescription
- the description for this header linelineType
- the header line typesource
- annotation source (case-insensitive, e.g. "dbsnp")version
- exact version (e.g. "138")protected VCFCompoundHeaderLine(java.lang.String line, VCFHeaderVersion version, VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
line
- the header lineversion
- the VCF header versionlineType
- the header line typepublic java.lang.String getID()
getID
in interface VCFIDHeaderLine
public java.lang.String getDescription()
public VCFHeaderLineType getType()
public VCFHeaderLineCount getCountType()
public boolean isFixedCount()
public int getCount()
public java.lang.String getSource()
public java.lang.String getVersion()
public int getCount(VariantContext vc)
vc
- public void setNumberToUnbounded()
protected java.lang.String toStringEncoding()
toStringEncoding
in class VCFHeaderLine
public boolean equals(java.lang.Object o)
equals
in class VCFHeaderLine
o
- a compound header linepublic int hashCode()
hashCode
in class VCFHeaderLine
public boolean equalsExcludingDescription(VCFCompoundHeaderLine other)
public boolean sameLineTypeAndName(VCFCompoundHeaderLine other)
public void setSource(java.lang.String source)
This value is optional starting with VCFv4.2.
source
- annotation source (case-insensitive, e.g. "dbsnp")public void setVersion(java.lang.String version)
This value is optional starting with VCFv4.2.
version
- exact version (e.g. "138")