charite.christo.protein
Class NumberedSequence_Parser

java.lang.Object
  charite.christo.protein.NumberedSequence_Parser

All Implemented Interfaces:

ProteinParser

public class NumberedSequence_Parser
extends java.lang.Object
implements ProteinParser

HELP Sequence files where the sequence block is at the end of the file. This sequence block might have preceding or trailing position numbers. In case there is no numbering then the sequence block must be indented by space of any length. To identify the first and last line of this sequence block the program starts looking from the end of the file. This is because files usually start with annotations and references which might be mistaken for the sequence if started from the first line.
GenBank sample: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt

Field Summary

Fields inherited from interface charite.christo.protein.ProteinParser

IGNORE_SEQRES, SEQUENCE_FEATURES, SIDE_CHAIN_ATOMS

Constructor Summary

NumberedSequence_Parser()

Method Summary

boolean	parse(Protein prot, long options, BA byteArray)
static int	parseMultipleSwiss(BA ba, Protein[] pp)

Methods inherited from class java.lang.Object

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

Constructor Detail

NumberedSequence_Parser

public NumberedSequence_Parser()

Method Detail

parse

public boolean parse(Protein prot,
                     long options,
                     BA byteArray)

Specified by:

parse in interface ProteinParser

byteArray - the entire file contents It is a byte array and not a String Object for performance reasons.

Returns:

true: success, false: inappropriate file format

parseMultipleSwiss

public static int parseMultipleSwiss(BA ba,
                                     Protein[] pp)