org.jbei.ice.lib.entry.sequence

Class SequenceAnalysisController

java.lang.Object

org.jbei.ice.lib.entry.sequence.SequenceAnalysisController

public class SequenceAnalysisController
extends Object

ABI to manipulate DNA sequence trace analysis

Author:

Zinovii Dmytriv

Field Summary

Fields

Modifier and Type	Field and Description
static String	SHOTGUN_DIR_NAME
static String	TRACES_DIR_NAME

Constructor Summary

Constructors

Constructor and Description
SequenceAnalysisController()

Method Summary

Modifier and Type	Method and Description
void	buildOrRebuildAlignment(TraceSequence traceSequence, Sequence sequence) Calculate sequence alignment between the given TraceSequence and Sequence using bl2seq, and save the result into the database.
File	getFile(TraceSequence traceSequence) Retrieve the File associated with the given TraceSequence.
TraceSequence	getTraceSequenceByFileId(String fileId)
List<TraceSequence>	getTraceSequences(Entry entry) Retrieve the TraceSequence associated with the given Entry entry.
void	rebuildAllAlignments(Entry entry) Calculate sequence alignments between the sequence associated with an Entry entry with all the TraceSequences associated with that entry.
void	removeShotgunSequence(ShotgunSequence shotgunSequence)
void	removeTraceSequence(TraceSequence traceSequence) Remove a TraceSequence from the database and disk.

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

SHOTGUN_DIR_NAME

public static final String SHOTGUN_DIR_NAME

See Also:

Constant Field Values

Constructor Detail

SequenceAnalysisController

public SequenceAnalysisController()

Method Detail

removeTraceSequence

public void removeTraceSequence(TraceSequence traceSequence)

Remove a TraceSequence from the database and disk.

Parameters:

traceSequence - dto for trace sequence information

removeShotgunSequence

public void removeShotgunSequence(ShotgunSequence shotgunSequence)

getTraceSequences

public List<TraceSequence> getTraceSequences(Entry entry)

Retrieve the TraceSequence associated with the given Entry entry.

Parameters:

entry - entry object

Returns:

Retrieved TraceSequence

getTraceSequenceByFileId

public TraceSequence getTraceSequenceByFileId(String fileId)

getFile

public File getFile(TraceSequence traceSequence)

Retrieve the File associated with the given TraceSequence.

Parameters:

traceSequence - dto for trace sequence information

Returns:

File object.

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

rebuildAllAlignments

public void rebuildAllAlignments(Entry entry)

Calculate sequence alignments between the sequence associated with an Entry entry with all the TraceSequences associated with that entry.

Calls buildOrReplaceAlignment on each TraceSequence.

Parameters:

entry - entry object