htsjdk.variant.vcf

Class VCFPercentEncodedTextTransformer

java.lang.Object

htsjdk.variant.vcf.VCFPercentEncodedTextTransformer

All Implemented Interfaces:

VCFTextTransformer

public class VCFPercentEncodedTextTransformer
extends java.lang.Object
implements VCFTextTransformer

Text transformer for attribute values embedded in VCF. VCF version 4.3 supports percent-encoding of characters that have special meaning in VCF.

Constructor Summary

Constructors

Constructor and Description
VCFPercentEncodedTextTransformer()

Method Summary

Modifier and Type	Method and Description
protected static java.lang.String	decodePercentEncodedChars(java.lang.String rawText) Transform input strings containing embedded percent=encoded characters.
java.util.List<java.lang.String>	decodeText(java.util.List<java.lang.String> rawParts) Transform a list of strings, replacing % encoded values with their corresponding text in each string.
java.lang.String	decodeText(java.lang.String rawPart) Transform a single string, replacing % encoded values with their corresponding text.

Methods inherited from class java.lang.Object

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

Constructor Detail

VCFPercentEncodedTextTransformer

public VCFPercentEncodedTextTransformer()

Method Detail

decodeText

public java.lang.String decodeText(java.lang.String rawPart)

Transform a single string, replacing % encoded values with their corresponding text.

Specified by:

decodeText in interface VCFTextTransformer

Parameters:

rawPart - the raw string to be decoded

Returns:

the decoded string

Throws:

TribbleException - if the the encoding is uninterpretable

decodeText

public java.util.List<java.lang.String> decodeText(java.util.List<java.lang.String> rawParts)

Transform a list of strings, replacing % encoded values with their corresponding text in each string.

Specified by:

decodeText in interface VCFTextTransformer

Parameters:

rawParts - a list of raw strings

Returns:

a list of decoded strings

Throws:

TribbleException - if the the encoding is uninterpretable

decodePercentEncodedChars

protected static java.lang.String decodePercentEncodedChars(java.lang.String rawText)

Transform input strings containing embedded percent=encoded characters. For example, when given the string '%3D%41' will return the string '=A'.

Parameters:

rawText - a string containing zero or more embedded encodings

Returns:

a string with all encoded characters replaced with the corresponding character

Throws:

TribbleException - if the the encoding is uninterpretable