htsjdk.samtools

Class TextTagCodec

java.lang.Object

htsjdk.samtools.TextTagCodec

public class TextTagCodec
extends java.lang.Object

Converter between SAM text representation of a tag, and in-memory Object representation. Note that this class is not thread-safe, in that some local variables have been made into instance variables in order to reduce object creation, but it should not ever be the case that the same instance is used in multiple threads.

Constructor Summary

Constructors

Constructor and Description
TextTagCodec()

Method Summary

Methods

Modifier and Type	Method and Description
java.util.Map.Entry<java.lang.String,java.lang.Object>	decode(java.lang.String tag) Convert typed tag in SAM text format (name:type:value) into tag name and Object value representation.
java.lang.String	encode(java.lang.String tagName, java.lang.Object value) Convert in-memory representation of tag to SAM text representation.
java.lang.String	encodeUntypedTag(java.lang.String tagName, java.lang.Object value) Encode a standard header tag, which should not have a type field.

Methods inherited from class java.lang.Object

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

Constructor Detail

TextTagCodec

public TextTagCodec()

Method Detail

encode

public java.lang.String encode(java.lang.String tagName,
                      java.lang.Object value)

Convert in-memory representation of tag to SAM text representation.

Parameters:

tagName - Two-character tag name.

value - Tag value as approriate Object subclass.

Returns:

SAM text String representation, i.e. name:type:value

encodeUntypedTag

public java.lang.String encodeUntypedTag(java.lang.String tagName,
                                java.lang.Object value)

Encode a standard header tag, which should not have a type field.

Parameters:

tagName - 2-character String.

value - Not necessarily a String. Some of these are integers but the type is implied by the tagName. Converted to String with toString().

Returns:

Colon-separated text representation suitable for a SAM header, i.e. name:value.

decode

public java.util.Map.Entry<java.lang.String,java.lang.Object> decode(java.lang.String tag)

Convert typed tag in SAM text format (name:type:value) into tag name and Object value representation.

Parameters:

tag - SAM text format name:type:value tag.

Returns:

Tag name as 2-character String, and tag value in appropriate class based on tag type. If value is an unsigned array, then the value is a TagValueAndUnsignedArrayFlag object.