org.pharmgkb.parser.vcf.model

Class VcfMetadata

java.lang.Object

org.pharmgkb.parser.vcf.model.VcfMetadata

public class VcfMetadata
extends java.lang.Object

This class captures all of the VCF metadata from a VCF file.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	VcfMetadata.Builder

Method Summary

Modifier and Type	Method and Description
void	addAlt(IdDescriptionMetadata value) Adds value to the map of ALT metadata, using its ID as the key.
void	addAssembly(java.lang.String value) Adds value to the list of assembly metadata.
void	addContig(ContigMetadata value) Adds value to the map of CONTIG metadata, using its ID as the key.
void	addFilter(IdDescriptionMetadata value) Adds value to the map of FILTER metadata, using its ID as the key.
void	addFormat(FormatMetadata value) Adds value to the map of FORMAT metadata, using its ID as the key.
void	addInfo(InfoMetadata value) Adds value to the map of INFO metadata, using its ID as the key.
void	addPedigreeDatabase(java.lang.String value) Adds value to the list of pedigreeDB.
IdDescriptionMetadata	getAlt(java.lang.String id) Gets the ALT metadata for the given ID.
java.util.Map<java.lang.String,IdDescriptionMetadata>	getAlts()
java.util.List<java.lang.String>	getAssemblies()
int	getColumnIndex(java.lang.String column)
java.util.Map<java.lang.String,ContigMetadata>	getContigs()
java.lang.String	getFileFormat()
java.util.Map<java.lang.String,IdDescriptionMetadata>	getFilters()
java.util.Map<java.lang.String,FormatMetadata>	getFormats()
java.util.Map<java.lang.String,InfoMetadata>	getInfo()
int	getNumSamples() Gets the number of samples in the VCF file.
java.util.List<java.lang.String>	getPedigreeDatabases()
java.util.List<BaseMetadata>	getPedigrees()
com.google.common.collect.ListMultimap<java.lang.String,java.lang.String>	getRawProperties() Returns a map from every property key to each of its values.
java.util.SortedSet<java.lang.String>	getRawPropertyKeys() Returns a list of the properties defined.
java.util.List<java.lang.String>	getRawValuesOfProperty(java.lang.String propertyKey) Returns the value of a property, or null if the property is not set or has no value.
int	getSampleIndex(java.lang.String sampleId) Sample numbering starts at 0.
java.lang.String	getSampleName(int idx) Gets the sample name (column name).
java.util.Map<java.lang.String,IdDescriptionMetadata>	getSamples()
void	removeAlt(IdDescriptionMetadata value)
void	removeAssembly(java.lang.String value)
void	removeContig(ContigMetadata value)
void	removeFilter(IdDescriptionMetadata value)
void	removeFormat(FormatMetadata value)
void	removeInfo(InfoMetadata value)
void	removePedigreeDb(java.lang.String value) Adds value to the list of pedigreeDB.
void	setFileFormat(java.lang.String fileFormat)

Methods inherited from class java.lang.Object

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

Method Detail

getFileFormat

@Nonnull
public java.lang.String getFileFormat()

setFileFormat

public void setFileFormat(@Nonnull
                          java.lang.String fileFormat)

getAlts

@Nonnull
public java.util.Map<java.lang.String,IdDescriptionMetadata> getAlts()

getAlt

@Nullable
public IdDescriptionMetadata getAlt(@Nonnull
                                               java.lang.String id)

Gets the ALT metadata for the given ID.

Parameters:

id - the ID to lookup, will unwrap ID's enclosed in angle brackets (e.g. <CN1> will get converted to CN1)

getInfo

@Nonnull
public java.util.Map<java.lang.String,InfoMetadata> getInfo()

getFilters

@Nonnull
public java.util.Map<java.lang.String,IdDescriptionMetadata> getFilters()

getFormats

@Nonnull
public java.util.Map<java.lang.String,FormatMetadata> getFormats()

getContigs

@Nonnull
public java.util.Map<java.lang.String,ContigMetadata> getContigs()

getPedigrees

@Nonnull
public java.util.List<BaseMetadata> getPedigrees()

getSamples

@Nonnull
public java.util.Map<java.lang.String,IdDescriptionMetadata> getSamples()

getAssemblies

@Nonnull
public java.util.List<java.lang.String> getAssemblies()

Returns:

The URLs from the field(s) in the assembly metadata line(s)

getPedigreeDatabases

@Nonnull
public java.util.List<java.lang.String> getPedigreeDatabases()

Returns:

The URLs from the field(s) in the pedigreeDB metadata line(s), including angle brackets if any

addAlt

public void addAlt(@Nonnull
                   IdDescriptionMetadata value)

Adds value to the map of ALT metadata, using its ID as the key.

addInfo

public void addInfo(@Nonnull
                    InfoMetadata value)

Adds value to the map of INFO metadata, using its ID as the key.

addFormat

public void addFormat(@Nonnull
                      FormatMetadata value)

Adds value to the map of FORMAT metadata, using its ID as the key.

addContig

public void addContig(@Nonnull
                      ContigMetadata value)

Adds value to the map of CONTIG metadata, using its ID as the key.

addFilter

public void addFilter(@Nonnull
                      IdDescriptionMetadata value)

Adds value to the map of FILTER metadata, using its ID as the key.

addAssembly

public void addAssembly(@Nonnull
                        java.lang.String value)

Adds value to the list of assembly metadata.

Parameters:

value - Should not be wrapped in angle brackets

addPedigreeDatabase

public void addPedigreeDatabase(@Nonnull
                                java.lang.String value)

Adds value to the list of pedigreeDB.

Parameters:

value - Must be wrapped in angle brackets

Throws:

java.lang.IllegalArgumentException - If value is not wrapped in angle brackets

removeAlt

public void removeAlt(@Nonnull
                      IdDescriptionMetadata value)

removeInfo

public void removeInfo(@Nonnull
                       InfoMetadata value)

removeFormat

public void removeFormat(@Nonnull
                         FormatMetadata value)

removeContig

public void removeContig(@Nonnull
                         ContigMetadata value)

removeFilter

public void removeFilter(@Nonnull
                         IdDescriptionMetadata value)

removeAssembly

public void removeAssembly(@Nonnull
                           java.lang.String value)

removePedigreeDb

public void removePedigreeDb(@Nonnull
                             java.lang.String value)

Adds value to the list of pedigreeDB.

Parameters:

value - Must be wrapped in angle brackets

Throws:

java.lang.IllegalArgumentException - If value is not wrapped in angle brackets

getRawProperties

@Nonnull
public com.google.common.collect.ListMultimap<java.lang.String,java.lang.String> getRawProperties()

Returns a map from every property key to each of its values. Call ListMultimap.asMap() to get a Map<String, Collection<String>>.

Returns:

Contains every property except those contained in:

• getInfo()
• getFilters()
• getFormats()
• getContigs()
• getPedigrees()
• getInfo()
• getSamples()

However, contains any in getAssemblies() and getPedigreeDatabases().

getRawValuesOfProperty

@Nonnull
public java.util.List<java.lang.String> getRawValuesOfProperty(@Nonnull
                                                                         java.lang.String propertyKey)

Returns the value of a property, or null if the property is not set or has no value. This method will return null for a reserved property of the form XX=<ID=value,ID=value,...>; assembly and pedigreeDB are still included.

getRawPropertyKeys

@Nonnull
public java.util.SortedSet<java.lang.String> getRawPropertyKeys()

Returns a list of the properties defined. Reserved properties of the form XX=<ID=value,ID=value,...> are excluded, though assembly and pedigreeDB are still included.

Returns:

Contains every property except those contained in:

• getInfo()
• getFilters()
• getFormats()
• getContigs()
• getPedigrees()
• getInfo()
• getSamples()

However, contains any in getAssemblies() and getPedigreeDatabases().

getColumnIndex

public int getColumnIndex(@Nonnull
                          java.lang.String column)

getSampleIndex

public int getSampleIndex(@Nonnull
                          java.lang.String sampleId)

Sample numbering starts at 0.

getNumSamples

public int getNumSamples()

Gets the number of samples in the VCF file.

getSampleName

@Nonnull
public java.lang.String getSampleName(int idx)

Gets the sample name (column name).

Parameters:

idx - sample index, first sample is at index 0

Throws:

java.lang.ArrayIndexOutOfBoundsException - If the sample doesn't exist