org.jbei.ice.lib.entry.sequence

Class PartSequence

java.lang.Object

org.jbei.ice.lib.entry.HasEntry

org.jbei.ice.lib.entry.sequence.PartSequence

public class PartSequence
extends HasEntry

Biological part with associated sequence information

Author:

Hector Plahar

Field Summary

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

accountDAO, entryDAO

Constructor Summary

Constructors

Constructor and Description
PartSequence(String userId, EntryType type) Constructor for creating a new part to associate a sequence with
PartSequence(String userId, String entryId)

Method Summary

Modifier and Type	Method and Description
protected SequenceFormat	detectFormat(String sequenceString) Attempts to detect the sequence format from the first line of a stream using the following heuristics If line starts with LOCUS then assumed to be a genbank file If line starts with > then assumed to be a fasta file If line starts with < then assumed to be an sbol file Anything else is assumed to be plain nucleotides
FeaturedDNASequence	get()
protected FeaturedDNASequence	getFeaturedSequence(Entry entry, boolean canEdit)
SequenceInfo	parseSequenceFile(InputStream inputStream, String fileName, boolean extractHierarchy) Parses a sequence in a file and associates it with the current entry
protected SequenceInfo	save(DNASequence dnaSequence, String sequenceString, String fileName)
protected FeaturedDNASequence	sequenceToDNASequence(Sequence sequence)

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

Constructor Detail

PartSequence

public PartSequence(String userId,
                    EntryType type)

Constructor for creating a new part to associate a sequence with

Parameters:

userId - unique identifier for user creating new part

type - type of part to create.

PartSequence

public PartSequence(String userId,
                    String entryId)

Method Detail

get

public FeaturedDNASequence get()

parseSequenceFile

public SequenceInfo parseSequenceFile(InputStream inputStream,
                                      String fileName,
                                      boolean extractHierarchy)
                               throws IOException

Parses a sequence in a file and associates it with the current entry

Parameters:

inputStream - input stream of bytes representing the file

fileName - name of file being parsed

Returns:

wrapper around the internal model used to represent sequence information

Throws:

IOException - on Exception parsing the contents of the file

save

protected SequenceInfo save(DNASequence dnaSequence,
                            String sequenceString,
                            String fileName)

detectFormat

protected SequenceFormat detectFormat(String sequenceString)
                               throws IOException

Attempts to detect the sequence format from the first line of a stream using the following heuristics

• If line starts with LOCUS then assumed to be a genbank file
• If line starts with > then assumed to be a fasta file
• If line starts with < then assumed to be an sbol file
• Anything else is assumed to be plain nucleotides

Parameters:

sequenceString - input sequence

Returns:

detected format

Throws:

IOException

getFeaturedSequence

protected FeaturedDNASequence getFeaturedSequence(Entry entry,
                                                  boolean canEdit)

sequenceToDNASequence

protected FeaturedDNASequence sequenceToDNASequence(Sequence sequence)