Package | Description |
---|---|
eu.etaxonomy.cdm.api.service | |
eu.etaxonomy.cdm.api.service.dto | |
eu.etaxonomy.cdm.api.service.molecular | |
eu.etaxonomy.cdm.model.molecular |
Provides classes for DNA samples and related sequences.
|
Modifier and Type | Method and Description |
---|---|
UpdateResult |
IOccurrenceService.moveSequence(DnaSample from,
DnaSample to,
Sequence sequence)
|
UpdateResult |
OccurrenceServiceImpl.moveSequence(DnaSample from,
DnaSample to,
Sequence sequence) |
Constructor and Description |
---|
SequenceDTO(Sequence seq) |
Modifier and Type | Method and Description |
---|---|
java.util.Map<SingleRead,java.util.Collection<Sequence>> |
ISequenceService.getSingleReadSequencesMap()
Creates and returns a map with
SingleRead s as keys. |
java.util.Map<SingleRead,java.util.Collection<Sequence>> |
SequenceServiceImpl.getSingleReadSequencesMap() |
Modifier and Type | Method and Description |
---|---|
DeleteResult |
SequenceServiceImpl.delete(Sequence sequence) |
DeleteResult |
ISequenceService.deleteSingleRead(SingleRead singleRead,
Sequence sequence)
|
DeleteResult |
SequenceServiceImpl.deleteSingleRead(SingleRead singleRead,
Sequence sequence) |
UpdateResult |
ISequenceService.moveSingleRead(Sequence from,
Sequence to,
SingleRead singleRead)
Moves the given
SingleRead from one Sequence to another. |
UpdateResult |
SequenceServiceImpl.moveSingleRead(Sequence from,
Sequence to,
SingleRead singleRead) |
Modifier and Type | Method and Description |
---|---|
Sequence |
SingleReadAlignment.getConsensusSequence() |
static Sequence |
Sequence.NewInstance(DnaSample dnaSample,
java.lang.String consensusSequence,
java.lang.Integer length) |
static Sequence |
Sequence.NewInstance(java.lang.String consensusSequence) |
static Sequence |
Sequence.NewInstance(java.lang.String consensusSequence,
java.lang.Integer length) |
Modifier and Type | Method and Description |
---|---|
java.util.Set<Sequence> |
DnaSample.getSequences() |
java.util.Set<Sequence> |
PhylogeneticTree.getUsedSequences() |
Modifier and Type | Method and Description |
---|---|
void |
DnaSample.addSequence(Sequence sequence) |
void |
PhylogeneticTree.addUsedSequences(Sequence usedSequence) |
static SingleReadAlignment |
SingleReadAlignment.NewInstance(Sequence consensusSequence,
SingleRead singleRead) |
static SingleReadAlignment |
SingleReadAlignment.NewInstance(Sequence consensusSequence,
SingleRead singleRead,
SingleReadAlignment.Shift[] shifts,
java.lang.String editedSequence) |
void |
DnaSample.removeSequence(Sequence sequence) |
void |
PhylogeneticTree.removeUsedSequences(Sequence usedSequence) |
void |
SingleReadAlignment.setConsensusAlignment(Sequence consensusAlignment) |
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