com.hfg.bio.seq.format

Interface ReadableSeqFormat<T extends BioSequence>

All Known Implementing Classes:

EMBL, FASTA, FASTQ, GenBank, IlluminaFASTQ, ReadableSeqFormatBase

public interface ReadableSeqFormat<T extends BioSequence>

Interface for readable sequence formats.

Method Summary

Modifier and Type	Method and Description
boolean	hasJanusDelimiter() A format has a Janus delimiter if the line that indicates that the previous record is over is also part of the next record.
boolean	isEndOfRecord(String inLine)
List<T>	read(BufferedReader inFile)
List<T>	read(File inFile)
T	readRecord(BufferedReader inReader)
T	readRecord(CharSequence inString)

Method Detail

read

List<T> read(File inFile)
      throws SeqIOException

Throws:

SeqIOException

read

List<T> read(BufferedReader inFile)
      throws SeqIOException

Throws:

SeqIOException

readRecord

T readRecord(CharSequence inString)
      throws SeqIOException

Throws:

SeqIOException

readRecord

T readRecord(BufferedReader inReader)
      throws SeqIOException

Throws:

SeqIOException

isEndOfRecord

boolean isEndOfRecord(String inLine)

hasJanusDelimiter

boolean hasJanusDelimiter()

A format has a Janus delimiter if the line that indicates that the previous record is over is also part of the next record. Will return true for formats like FASTA.

Returns:

whether or not this format's record delimiter is also part of the next record