de.jstacs.utils

Class LargeSequenceReader

java.lang.Object

de.jstacs.utils.LargeSequenceReader

public class LargeSequenceReader
extends Object

Class for reading large DNA sequences (e.g. genomes) from disk sequentially.

Author:

Jan Grau

Constructor Summary

Constructors

Constructor and Description
LargeSequenceReader()

Method Summary

Modifier and Type	Method and Description
static Pair<IntList,ArrayList<Sequence>>	readNextSequences(BufferedReader read, StringBuffer lastHeader, int minimumLength) Returns the next chunk of input sequences.

Methods inherited from class java.lang.Object

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

Constructor Detail

LargeSequenceReader

public LargeSequenceReader()

Method Detail

readNextSequences

public static Pair<IntList,ArrayList<Sequence>> readNextSequences(BufferedReader read,
                                                                  StringBuffer lastHeader,
                                                                  int minimumLength)
                                                           throws IOException

Returns the next chunk of input sequences. Input sequences are split at non-ACGT characters and parts between those are returned independently. For longer sequences that are split in this manner, the offsets of the individual chunks within the complete sequence are also returned.

Parameters:

read - the source of the sequence data

lastHeader - the header of previous chunk, may be empty initially and is modified internally

minimumLength - the minimum length of sequences or chunks considered, shorter sequences are skipped

Returns:

a Pair with the offsets of the individual chunks and the sequences

Throws:

IOException - if the sequence could not be read from read