Package org.pharmgkb.parser.vcf.model

Class ContigMetadata

java.lang.Object

org.pharmgkb.parser.vcf.model.BaseMetadata

org.pharmgkb.parser.vcf.model.IdMetadata

org.pharmgkb.parser.vcf.model.ContigMetadata

public class ContigMetadata
extends IdMetadata

VCF metadata for contig=<> elements.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ASSEMBLY
static final String	ID
static final String	LENGTH
static final String	MD5
static final String	SPECIES
static final String	TAXONOMY
static final String	URL

Constructor Summary

Constructors

Constructor	Description
ContigMetadata(String id, long length, String assembly, String md5, String species, String taxonomy, String url)
ContigMetadata(Map<String,String> properties)

Method Summary

Modifier and Type	Method	Description
String	getAssembly()
long	getLength()
String	getMd5()
String	getSpecies()
String	getTaxonomy()
String	getUrl()

Methods inherited from class org.pharmgkb.parser.vcf.model.IdMetadata

getId

Methods inherited from class org.pharmgkb.parser.vcf.model.BaseMetadata

ensureNoExtras, getPropertiesRaw, getPropertiesUnquoted, getPropertyKeys, getPropertyRaw, getPropertyUnquoted, putAndQuoteProperty, putPropertyRaw

Methods inherited from class java.lang.Object

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

Field Details

ID

public static final String ID

See Also:

• Constant Field Values

LENGTH

public static final String LENGTH

See Also:

• Constant Field Values

ASSEMBLY

public static final String ASSEMBLY

See Also:

• Constant Field Values

MD5

public static final String MD5

See Also:

• Constant Field Values

SPECIES

public static final String SPECIES

See Also:

• Constant Field Values

TAXONOMY

public static final String TAXONOMY

See Also:

• Constant Field Values

URL

public static final String URL

See Also:

• Constant Field Values

Constructor Details

ContigMetadata

public ContigMetadata(@Nonnull
 String id,
 long length,
 @Nonnull
 String assembly,
 @Nullable
 String md5,
 @Nullable
 String species,
 @Nullable
 String taxonomy,
 @Nullable
 String url)

ContigMetadata

public ContigMetadata(@Nonnull
 Map<String,String> properties)

Method Details

getLength

public long getLength()

getAssembly

@Nullable
public String getAssembly()

Returns:

Null only when invalid

getTaxonomy

@Nullable
public String getTaxonomy()

getSpecies

@Nullable
public String getSpecies()

getMd5

@Nullable
public String getMd5()

getUrl

@Nullable
public String getUrl()