org.jbei.ice.lib.entry.sequence

Class TraceSequences

java.lang.Object

org.jbei.ice.lib.entry.sequence.TraceSequences

public class TraceSequences
extends Object

Trace sequence for alignment against a specific sequence

Author:

Hector Plahar

Field Summary

Fields

Modifier and Type	Field and Description
static String	TRACES_DIR_NAME

Constructor Summary

Constructors

Constructor and Description
TraceSequences(String userId, long partId)

Method Summary

Modifier and Type	Method and Description
boolean	addTraceSequence(File file, String uploadFileName)
void	buildOrRebuildAlignment(TraceSequence traceSequence, Sequence sequence) Calculate sequence alignment between the given TraceSequence and Sequence using bl2seq, and save the result into the database.
protected boolean	canEdit(String userId, String depositor, Entry entry)
ByteArrayOutputStream	getAll() Retrieves all the trace sequence files, for the specified part, and places them in a zip file
Results<TraceSequenceAnalysis>	getTraces(int start, int limit)
TraceSequence	importTraceSequence(String filename, String sequence, InputStream inputStream) Create a new TraceSequence record and associated with the Entry entry.

Methods inherited from class java.lang.Object

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

Field Detail

TRACES_DIR_NAME

public static final String TRACES_DIR_NAME

See Also:

Constant Field Values

Constructor Detail

TraceSequences

public TraceSequences(String userId,
                      long partId)

Method Detail

getAll

public ByteArrayOutputStream getAll()
                             throws IOException

Retrieves all the trace sequence files, for the specified part, and places them in a zip file

Returns:

output stream for zip file bytes

Throws:

IOException - on exception creating zip file or retrieving bytes for it

addTraceSequence

public boolean addTraceSequence(File file,
                                String uploadFileName)

getTraces

public Results<TraceSequenceAnalysis> getTraces(int start,
                                                int limit)

importTraceSequence

public TraceSequence importTraceSequence(String filename,
                                         String sequence,
                                         InputStream inputStream)

Create a new TraceSequence record and associated with the Entry entry.

Unlike importTraceSequence this method auto generates uuid and timestamp.

Parameters:

filename - name of the file uploaded by the user

sequence - sequence string

inputStream - input stream for uploaded file

Returns:

Saved traceSequence

buildOrRebuildAlignment

public void buildOrRebuildAlignment(TraceSequence traceSequence,
                                    Sequence sequence)

Calculate sequence alignment between the given TraceSequence and Sequence using bl2seq, and save the result into the database.

Parameters:

traceSequence - traceSequence

sequence - sequence

canEdit

protected boolean canEdit(String userId,
                          String depositor,
                          Entry entry)