com.hfg.bio.seq.format

Interface ReadableSeqFormat<T extends BioSequence>

All Known Implementing Classes:

EMBL, FASTA, FASTQ, GenBank, 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(java.lang.String inLine)
java.util.List<T>	read(java.io.BufferedReader inFile)
java.util.List<T>	read(java.io.File inFile)
T	readRecord(java.io.BufferedReader inReader)
T	readRecord(java.lang.CharSequence inString)

Method Detail

read

java.util.List<T> read(java.io.File inFile)
                throws SeqIOException

Throws:

SeqIOException

read

java.util.List<T> read(java.io.BufferedReader inFile)
                throws SeqIOException

Throws:

SeqIOException

readRecord

T readRecord(java.lang.CharSequence inString)
      throws SeqIOException

Throws:

SeqIOException

readRecord

T readRecord(java.io.BufferedReader inReader)
      throws SeqIOException

Throws:

SeqIOException

isEndOfRecord

boolean isEndOfRecord(java.lang.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