Uses of Class
org.jbei.ice.storage.model.TraceSequence

Packages that use TraceSequence

Package	Description
org.jbei.ice.lib.entry.sequence
org.jbei.ice.storage.hibernate.dao
org.jbei.ice.storage.model	Data models for ice objects.

Uses of TraceSequence in org.jbei.ice.lib.entry.sequence

Methods in org.jbei.ice.lib.entry.sequence that return TraceSequence

Modifier and Type	Method and Description
TraceSequence	SequenceAnalysisController.getTraceSequenceByFileId(String fileId)
TraceSequence	TraceSequences.importTraceSequence(String filename, String sequence, InputStream inputStream) Create a new TraceSequence record and associated with the Entry entry.

Methods in org.jbei.ice.lib.entry.sequence that return types with arguments of type TraceSequence

Modifier and Type	Method and Description
List<TraceSequence>	SequenceAnalysisController.getTraceSequences(Entry entry) Retrieve the TraceSequence associated with the given Entry entry.

Methods in org.jbei.ice.lib.entry.sequence with parameters of type TraceSequence

Modifier and Type	Method and Description
void	TraceSequences.buildOrRebuildAlignment(TraceSequence traceSequence, Sequence sequence) Calculate sequence alignment between the given TraceSequence and Sequence using bl2seq, and save the result into the database.
void	SequenceAnalysisController.buildOrRebuildAlignment(TraceSequence traceSequence, Sequence sequence) Calculate sequence alignment between the given TraceSequence and Sequence using bl2seq, and save the result into the database.
File	SequenceAnalysisController.getFile(TraceSequence traceSequence) Retrieve the File associated with the given TraceSequence.
void	SequenceAnalysisController.removeTraceSequence(TraceSequence traceSequence) Remove a TraceSequence from the database and disk.

Uses of TraceSequence in org.jbei.ice.storage.hibernate.dao

Methods in org.jbei.ice.storage.hibernate.dao that return TraceSequence

Modifier and Type	Method and Description
TraceSequence	TraceSequenceDAO.create(Path traceDir, TraceSequence traceSequence, InputStream inputStream) Create a new TraceSequence object in the database, and write the file data to disk.
TraceSequence	TraceSequenceDAO.get(long id)
TraceSequence	TraceSequenceDAO.save(TraceSequence traceSequence) Save the given TraceSequence object in the database.

Methods in org.jbei.ice.storage.hibernate.dao that return types with arguments of type TraceSequence

Modifier and Type	Method and Description
List<TraceSequence>	TraceSequenceDAO.getByEntry(Entry entry, int start, int limit) Retrieve all TraceSequence objects associated with the given Entry object using the paging parameters, ordered by creation time in ascending order
Optional<TraceSequence>	TraceSequenceDAO.getByFileId(String fileId) Retrieve the TraceSequence object by its fileId.

Methods in org.jbei.ice.storage.hibernate.dao with parameters of type TraceSequence

Modifier and Type	Method and Description
TraceSequence	TraceSequenceDAO.create(Path traceDir, TraceSequence traceSequence, InputStream inputStream) Create a new TraceSequence object in the database, and write the file data to disk.
void	TraceSequenceDAO.delete(Path tracesDir, TraceSequence traceSequence) Delete the trace file from the referenced directory and if that succeeds, deletes the given TraceSequence object in the database
TraceSequence	TraceSequenceDAO.save(TraceSequence traceSequence) Save the given TraceSequence object in the database.

Uses of TraceSequence in org.jbei.ice.storage.model

Methods in org.jbei.ice.storage.model that return TraceSequence

Modifier and Type	Method and Description
TraceSequence	TraceSequenceAlignment.getTraceSequence()

Methods in org.jbei.ice.storage.model with parameters of type TraceSequence

Modifier and Type	Method and Description
void	TraceSequenceAlignment.setTraceSequence(TraceSequence traceSequence)

Constructors in org.jbei.ice.storage.model with parameters of type TraceSequence

Constructor and Description
TraceSequenceAlignment(TraceSequence traceSequence, int score, int strand, int queryStart, int queryEnd, int subjectStart, int subjectEnd, String queryAlignment, String subjectAlignment, String sequenceHash, Date modificationTime)