VCFCompoundHeaderLine (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.variant.vcf.VCFHeaderLine
- - htsjdk.variant.vcf.VCFCompoundHeaderLine

All Implemented Interfaces:

VCFIDHeaderLine, Serializable, Comparable

Direct Known Subclasses:

VCFFormatHeaderLine, VCFInfoHeaderLine
```
public abstract class VCFCompoundHeaderLine
extends VCFHeaderLine
implements VCFIDHeaderLine
```
a base class for compound header lines, which include info lines and format lines (so far)

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class VCFCompoundHeaderLine.SupportedHeaderLineType

Nested Classes
Modifier and Type	Class and Description
`static class`	`VCFCompoundHeaderLine.SupportedHeaderLineType`

Field Summary
- Fields inherited from class htsjdk.variant.vcf.VCFHeaderLine
  ALLOW_UNBOUND_DESCRIPTIONS, serialVersionUID, UNBOUND_DESCRIPTION

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType)` create a VCF format header line
`protected`	`VCFCompoundHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType)` create a VCF format header line
`protected`	`VCFCompoundHeaderLine(String line, VCFHeaderVersion version, VCFCompoundHeaderLine.SupportedHeaderLineType lineType)` create a VCF format header line

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`equals(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()`
`String`	`getDescription()`
`String`	`getID()`
`VCFHeaderLineType`	`getType()`
`int`	`hashCode()`
`boolean`	`isFixedCount()`
`boolean`	`sameLineTypeAndName(VCFCompoundHeaderLine other)`
`void`	`setNumberToUnbounded()`
`protected String`	`toStringEncoding()` make a string representation of this header line

Methods inherited from class htsjdk.variant.vcf.VCFHeaderLine
compareTo, getKey, getValue, isHeaderLine, shouldBeAddedToDictionary, toString, toStringEncoding

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - VCFCompoundHeaderLine
```
protected VCFCompoundHeaderLine(String name,
                                int count,
                                VCFHeaderLineType type,
                                String description,
                                VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
```
    create a VCF format header line
    
    Parameters:
    
    name - the name for this header line
    
    count - the count for this header line
    
    type - the type for this header line
    
    description - the description for this header line
    
    lineType - the header line type
  - VCFCompoundHeaderLine
```
protected VCFCompoundHeaderLine(String name,
                                VCFHeaderLineCount count,
                                VCFHeaderLineType type,
                                String description,
                                VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
```
    create a VCF format header line
    
    Parameters:
    
    name - the name for this header line
    
    count - the count type for this header line
    
    type - the type for this header line
    
    description - the description for this header line
    
    lineType - the header line type
  - VCFCompoundHeaderLine
```
protected VCFCompoundHeaderLine(String line,
                                VCFHeaderVersion version,
                                VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
```
    create a VCF format header line
    
    Parameters:
    
    line - the header line
    
    version - the VCF header version
    
    lineType - the header line type
- Method Detail
  - getID
```
public String getID()
```
    Specified by:
    
    getID in interface VCFIDHeaderLine
  - getDescription
```
public String getDescription()
```
  - getType
```
public VCFHeaderLineType getType()
```
  - getCountType
```
public VCFHeaderLineCount getCountType()
```
  - isFixedCount
```
public boolean isFixedCount()
```
  - getCount
```
public int getCount()
```
  - getCount
```
public 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. For example, a field with size of 1 in the header returns 1 If the count is of type A, return vc.getNAlleles - 1 If the count is of type R, return vc.getNAlleles If the count is of type G, return the expected number of genotypes given the number of alleles in VC and the max ploidy among all samples. Note that if the max ploidy of the VC is 0 (there's no GT information at all, then implicitly assume diploid samples when computing G values. If the count is UNBOUNDED return -1
    
    Parameters:
    
    vc -
    
    Returns:
  - setNumberToUnbounded
```
public void setNumberToUnbounded()
```
  - toStringEncoding
```
protected String toStringEncoding()
```
    make a string representation of this header line
    
    Overrides:
    
    toStringEncoding in class VCFHeaderLine
    
    Returns:
    
    a string representation
  - equals
```
public boolean equals(Object o)
```
    returns true if we're equal to another compound header line
    
    Overrides:
    
    equals in class VCFHeaderLine
    
    Parameters:
    
    o - a compound header line
    
    Returns:
    
    true if equal
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class VCFHeaderLine
  - equalsExcludingDescription
```
public boolean equalsExcludingDescription(VCFCompoundHeaderLine other)
```
  - sameLineTypeAndName
```
public boolean sameLineTypeAndName(VCFCompoundHeaderLine other)
```

Class VCFCompoundHeaderLine

Nested Class Summary

Field Summary

Fields inherited from class htsjdk.variant.vcf.VCFHeaderLine

Constructor Summary

Method Summary

Methods inherited from class htsjdk.variant.vcf.VCFHeaderLine

Methods inherited from class java.lang.Object

Constructor Detail

VCFCompoundHeaderLine

VCFCompoundHeaderLine

VCFCompoundHeaderLine

Method Detail

getID

getDescription

getType

getCountType

isFixedCount

getCount

getCount

setNumberToUnbounded

toStringEncoding

equals

hashCode

equalsExcludingDescription

sameLineTypeAndName