blrevcomp
Class BioSeq

java.lang.Object
  blrevcomp.BioSeq

public class BioSeq
extends java.lang.Object

Biological sequence

Nested Class Summary

class

BioSeq.Nuchar 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.

Field Summary

int	LEN Length of sequence
int	MAXSEQ Maximum number of sequence elements
java.lang.String	Name Sequence name
char[]	seq Sequence
char	SFlag Flag character that indicates beginning of a sequence

Constructor Summary

BioSeq()

Method Summary

boolean	readFasta(BufferedTextInputFile In) Read a sequence in Pearson format:
void	writeFasta(BufferedTextOutputFile Out, java.lang.String SUFFIX, char STRAND, int SENSE, int WIDTH) Write sequence in Pearson/FASTA format
void	writeRAW(BufferedTextOutputFile Out, char STRAND, int SENSE, java.util.HashMap N, int WIDTH) Write sequence in raw format.

Methods inherited from class java.lang.Object

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

Field Detail

MAXSEQ

public int MAXSEQ

Maximum number of sequence elements

Name

public java.lang.String Name

Sequence name

SFlag

public char SFlag

Flag character that indicates beginning of a sequence

seq

public char[] seq

Sequence

LEN

public int LEN

Length of sequence

Constructor Detail

BioSeq

public BioSeq()

Method Detail

readFasta

public boolean readFasta(BufferedTextInputFile In)

Read a sequence in Pearson format:

    >name
    sequence
    sequence
    ...
    

Parameters:

In - Input file

writeRAW

public void writeRAW(BufferedTextOutputFile Out,
                     char STRAND,
                     int SENSE,
                     java.util.HashMap N,
                     int WIDTH)

Write sequence in raw format.

Parameters:

Out - BufferedTextOutputFile

STRAND - 'i': input strand 'c': complimentary strand

SENSE - 1 : original direction, -1 : reverse direction

N - - Nuchar.INuc for input strand; Nuchar.CNuc for complimentary strand

WIDTH - number of characters in output line

writeFasta

public void writeFasta(BufferedTextOutputFile Out,
                       java.lang.String SUFFIX,
                       char STRAND,
                       int SENSE,
                       int WIDTH)

Write sequence in Pearson/FASTA format

Parameters:

Out - - Output fie

SUFFIX - - Add SUFFIX to name of sequence:

• inverse complement - .opp
• complement - .comp
• reverse strand - .flip

STRAND - - 'i' - input; 'c' - complement

SENSE - 1 - forward direction; -1 reverse direction

WIDTH - - number of nucleotides to print per line