org.jbei.ice.lib.parsers

Class AbstractParser

java.lang.Object

org.jbei.ice.lib.entry.HasEntry

org.jbei.ice.lib.parsers.AbstractParser

Direct Known Subclasses:

FastaParser, GenBankParser, PlainParser, SBOLParser

public abstract class AbstractParser
extends HasEntry

Field Summary

Fields

Modifier and Type	Field and Description
protected Entry	entry
protected String	fileName
protected PartData	partData
protected String	userId

Fields inherited from class org.jbei.ice.lib.entry.HasEntry

accountDAO, entryDAO

Constructor Summary

Constructors

Constructor and Description
AbstractParser()
AbstractParser(String userId, String entryId)

Method Summary

Modifier and Type	Method and Description
protected String	cleanSequence(String sequence) Replace different line termination characters with the newline character (\n).
DNASequence	parse(String textSequence)
protected SequenceInfo	save(DNASequence dnaSequence, String sequenceString)

Methods inherited from class org.jbei.ice.lib.entry.HasEntry

getEntry

Methods inherited from class java.lang.Object

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

Field Detail

entry

protected final Entry entry

userId

protected final String userId

partData

protected final PartData partData

fileName

protected String fileName

Constructor Detail

AbstractParser

public AbstractParser(String userId,
                      String entryId)

AbstractParser

public AbstractParser()

Method Detail

parse

public DNASequence parse(String textSequence)
                  throws InvalidFormatParserException

Throws:

InvalidFormatParserException

cleanSequence

protected String cleanSequence(String sequence)

Replace different line termination characters with the newline character (\n).

Parameters:

sequence - Text to clean.

Returns:

String with only newline character (\n).

save

protected SequenceInfo save(DNASequence dnaSequence,
                            String sequenceString)