org.pharmgkb.parser.vcf.model

Class AltStructuralVariant

java.lang.Object

org.pharmgkb.parser.vcf.model.AltStructuralVariant

public class AltStructuralVariant
extends java.lang.Object

A strictly validated VCF metadata ALT code of the form: ##ALT=<ID=type,Description=description> Where ID is a colon-delimited list of identifiers. Some of these identifiers are reserved, as coded in the ReservedStructuralVariantCode class. The first identifier (at level 0) is required to be reserved. As explicitly stated in the spec, these codes are case-sensitive.

Example:

   AltStructuralVariant alt = new AltStructuralVariant("INS:ME:LINE");
   alt.getReservedComponent(0); // ReservedStructuralVariantCode.Insertion
   alt.getReservedComponent(1); // ReservedStructuralVariantCode.MobileElement
   alt.getReservedComponent(2); // null, because it's not a reserved code
   alt.getComponent(); // "LINE"
 
 

Constructor Summary

Constructors

Constructor and Description
AltStructuralVariant(java.lang.String string)

Method Summary

Modifier and Type	Method and Description
java.lang.String	getComponent(int level)
java.util.List<java.lang.String>	getComponents()
ReservedStructuralVariantCode	getReservedComponent(int level)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

AltStructuralVariant

public AltStructuralVariant(@Nonnull
                            java.lang.String string)

Parameters:

string - The full code (e.g. INS:ME:LINE:type-a1)

Method Detail

getComponents

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

Returns:

The list of codes in order from level 0 to level n; for example ("INS", "ME", "LINE")

getComponent

@Nonnull
public java.lang.String getComponent(int level)

Returns:

The code at the specified level (e.g. CNV)

Throws:

java.lang.ArrayIndexOutOfBoundsException

getReservedComponent

@Nullable
public ReservedStructuralVariantCode getReservedComponent(int level)

Returns:

The code at the specified level (e.g. CNV), or null if it is not a reserved code

Throws:

java.lang.ArrayIndexOutOfBoundsException

toString

@Nonnull
public java.lang.String toString()

Overrides:

toString in class java.lang.Object

Returns:

The original string (e.g. INS:ME:LINE:type-a1)