Package htsjdk.variant.vcf
Class VCFPercentEncodedTextTransformer
- java.lang.Object
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- htsjdk.variant.vcf.VCFPercentEncodedTextTransformer
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- All Implemented Interfaces:
VCFTextTransformer
public class VCFPercentEncodedTextTransformer extends 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.
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Constructor Summary
Constructors Constructor Description VCFPercentEncodedTextTransformer()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected static String
decodePercentEncodedChars(String rawText)
Transform input strings containing embedded percent=encoded characters.String
decodeText(String rawPart)
Transform a single string, replacing % encoded values with their corresponding text.List<String>
decodeText(List<String> rawParts)
Transform a list of strings, replacing % encoded values with their corresponding text in each string.
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Method Detail
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decodeText
public String decodeText(String rawPart)
Transform a single string, replacing % encoded values with their corresponding text.- Specified by:
decodeText
in interfaceVCFTextTransformer
- Parameters:
rawPart
- the raw string to be decoded- Returns:
- the decoded string
- Throws:
TribbleException
- if the the encoding is uninterpretable
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decodeText
public List<String> decodeText(List<String> rawParts)
Transform a list of strings, replacing % encoded values with their corresponding text in each string.- Specified by:
decodeText
in interfaceVCFTextTransformer
- Parameters:
rawParts
- a list of raw strings- Returns:
- a list of decoded strings
- Throws:
TribbleException
- if the the encoding is uninterpretable
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decodePercentEncodedChars
protected static String decodePercentEncodedChars(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
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