blrevcomp
Class BioSeq.Nuchar

java.lang.Object
  blrevcomp.BioSeq.Nuchar

Enclosing class:

BioSeq

public class BioSeq.Nuchar
extends java.lang.Object

Nuchar.INuc.get() returns the character to be written if the sequence is being printed from the input strand.
Nuchar.CNuc.get() returns the character to be written if the sequence is being printed from the complementary strand.
The case of nucleotides in the input sequence is preserved in the output sequence.

Examples:

Nuchar.Inuc.get('A') returns 'A'
Nuchar.Inuc.get('a') returns 'a'
Nuchar.Cnuc.get('Y') returns 'R'
Nuchar.Cnuc.get('d') returns 'h'
Nuchar.Cnuc.get('N') returns 'N'

All standard IUPAC ambiguity characters are supported, as defined in

Cornish-Bowden (1985) Nucl. Acids Res. 13:3021-3030.

If gap characters ('-') are present in the file, they are retained in the output.

Field Summary

java.util.HashMap<java.lang.Character,java.lang.Character>	CNuc Complementary strand
java.util.HashMap<java.lang.Character,java.lang.Character>	INuc Input strand

Constructor Summary

BioSeq.Nuchar()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

INuc

public java.util.HashMap<java.lang.Character,java.lang.Character> INuc

Input strand

CNuc

public java.util.HashMap<java.lang.Character,java.lang.Character> CNuc

Complementary strand

Constructor Detail

BioSeq.Nuchar

public BioSeq.Nuchar()