| Package | Description |
|---|---|
| io.repseq.cli | |
| io.repseq.core | |
| io.repseq.gen | |
| io.repseq.gen.dist |
| Modifier and Type | Field and Description |
|---|---|
GeneFeature |
CLIUtils.GeneFeatureWithOriginalName.feature |
| Modifier and Type | Method and Description |
|---|---|
GeneFeature |
InferAnchorPointsAction.Params.getGeneFeature() |
GeneFeature |
FastaAction.Params.getGeneFeature() |
GeneFeature |
ExportCloneSequencesAction.Params.getGeneFeature() |
| Constructor and Description |
|---|
CLIUtils.GeneFeatureWithOriginalName(GeneFeature feature,
String originalName) |
TsvAction.NameAndGeneFeature(String name,
GeneFeature feature) |
| Modifier and Type | Field and Description |
|---|---|
static GeneFeature |
GeneFeature.CDR1 |
static GeneFeature |
GeneFeature.CDR2 |
static GeneFeature |
GeneFeature.CDR3 |
static GeneFeature |
GeneFeature.CExon1 |
static GeneFeature |
GeneFeature.CRegion |
static GeneFeature |
GeneFeature.DCDR3Part |
static GeneFeature |
GeneFeature.DJJunction |
static GeneFeature |
GeneFeature.DLeftPSegment |
static GeneFeature |
GeneFeature.DRegion |
static GeneFeature |
GeneFeature.DRegionTrimmed |
static GeneFeature |
GeneFeature.DRegionWithP |
static GeneFeature |
GeneFeature.DRightPSegment |
static GeneFeature |
GeneFeature.Exon1 |
static GeneFeature |
GeneFeature.Exon2 |
static GeneFeature |
GeneFeature.FR1 |
static GeneFeature |
GeneFeature.FR2 |
static GeneFeature |
GeneFeature.FR3 |
static GeneFeature |
GeneFeature.FR4 |
static GeneFeature |
GeneFeature.GermlineDPSegment |
static GeneFeature |
GeneFeature.GermlineJCDR3Part |
static GeneFeature |
GeneFeature.GermlineJPSegment |
static GeneFeature |
GeneFeature.GermlineVCDR3Part |
static GeneFeature |
GeneFeature.GermlineVPSegment |
static GeneFeature |
GeneFeature.JCDR3Part |
static GeneFeature |
GeneFeature.JPSegment |
static GeneFeature |
GeneFeature.JRegion |
static GeneFeature |
GeneFeature.JRegionTrimmed |
static GeneFeature |
GeneFeature.JRegionWithP |
static GeneFeature |
GeneFeature.L |
static GeneFeature |
GeneFeature.L1 |
static GeneFeature |
GeneFeature.L2 |
static GeneFeature |
GeneFeature.ShortCDR3 |
static GeneFeature |
GeneFeature.V5UTR |
static GeneFeature |
GeneFeature.V5UTRGermline |
static GeneFeature |
GeneFeature.VCDR3Part |
static GeneFeature |
GeneFeature.VDJRegion |
static GeneFeature |
GeneFeature.VDJTranscript |
static GeneFeature |
GeneFeature.VDJTranscriptWithout5UTR |
static GeneFeature |
GeneFeature.VDJunction |
static GeneFeature |
GeneFeature.VExon2 |
static GeneFeature |
GeneFeature.VExon2Trimmed |
static GeneFeature |
GeneFeature.VGene |
static GeneFeature |
GeneFeature.VGeneWithP |
static GeneFeature |
GeneFeature.VIntron |
static GeneFeature |
GeneFeature.VJJunction |
static GeneFeature |
GeneFeature.VLIntronL |
static GeneFeature |
GeneFeature.VPSegment |
static GeneFeature |
GeneFeature.VRegion |
static GeneFeature |
GeneFeature.VRegionTrimmed |
static GeneFeature |
GeneFeature.VRegionWithP |
static GeneFeature |
GeneFeature.VTranscript |
static GeneFeature |
GeneFeature.VTranscriptWithout5UTR |
static GeneFeature |
GeneFeature.VTranscriptWithout5UTRWithP |
static GeneFeature |
GeneFeature.VTranscriptWithP |
| Modifier and Type | Method and Description |
|---|---|
GeneFeature |
GeneFeature.append(GeneFeature gf) |
GeneFeature |
GeneFeature.Deserializer.deserialize(com.fasterxml.jackson.core.JsonParser jp,
com.fasterxml.jackson.databind.DeserializationContext ctxt) |
static GeneFeature |
GeneFeature.getCodingGeneFeature(GeneFeature feature)
Returns coding gene feature contained in input gene feature
|
static GeneFeature |
GeneFeature.getFeatureByName(String pointName) |
static GeneFeature |
GeneFeature.getRegion(GeneType type) |
static GeneFeature |
GeneFeature.intersection(GeneFeature gf1,
GeneFeature gf2) |
static GeneFeature |
GeneFeature.intersection(GeneFeature gf1,
GeneFeature gf2,
boolean strict) |
static GeneFeature |
GeneFeature.intersectionStrict(GeneFeature gf1,
GeneFeature gf2) |
static GeneFeature |
GeneFeature.parse(String string) |
GeneFeature |
GeneFeatureSerializer.read(com.milaboratory.primitivio.PrimitivI input) |
GeneFeature |
GeneFeature.reverse() |
| Modifier and Type | Method and Description |
|---|---|
static Map<String,GeneFeature> |
GeneFeature.getFeaturesByName() |
static Map<GeneFeature,String> |
GeneFeature.getNameByFeature() |
| Modifier and Type | Method and Description |
|---|---|
GeneFeature |
GeneFeature.append(GeneFeature gf) |
int |
GeneFeature.compareTo(GeneFeature o) |
boolean |
GeneFeature.contains(GeneFeature geneFeature) |
static String |
GeneFeature.encode(GeneFeature feature) |
int |
SequencePartitioning.getAbsolutePosition(GeneFeature feature,
int positionInFeature)
Returns absolute position in reference sequence for the specified local position in specified
feature
or -1 if this position can't be projected. |
static GeneFeature |
GeneFeature.getCodingGeneFeature(GeneFeature feature)
Returns coding gene feature contained in input gene feature
|
S |
PartitionedSequenceCached.getFeature(GeneFeature feature) |
S |
PartitionedSequence.getFeature(GeneFeature feature) |
static ReferencePoint |
GeneFeature.getFrameReference(GeneFeature feature)
Returns reference point that is triplet boundary (so defines reading frame) inside provided gene feature or
returns null.
|
int |
SequencePartitioning.getLength(GeneFeature feature) |
static String |
GeneFeature.getNameByFeature(GeneFeature point) |
com.milaboratory.core.Range |
SequencePartitioning.getRange(GeneFeature feature)
Return sequence range for non-composite gene features
|
com.milaboratory.core.Range[] |
SequencePartitioning.getRanges(GeneFeature feature) |
int |
SequencePartitioning.getRelativePosition(GeneFeature feature,
ReferencePoint referencePoint)
Returns a relative position of specified
referencePoint in specified feature or -1 if this
position is not available. |
com.milaboratory.core.Range |
SequencePartitioning.getRelativeRange(GeneFeature feature,
GeneFeature subFeature)
Returns a relative range of specified
subFeature in specified feature or null if this is not
available. |
com.milaboratory.core.sequence.TranslationParameters |
SequencePartitioning.getTranslationParameters(GeneFeature feature)
Calculates translation parameters ( ~ translation frame ) for given gene feature using current sequence
partitioning.
|
static GeneFeature |
GeneFeature.intersection(GeneFeature gf1,
GeneFeature gf2) |
static GeneFeature |
GeneFeature.intersection(GeneFeature gf1,
GeneFeature gf2,
boolean strict) |
static GeneFeature |
GeneFeature.intersectionStrict(GeneFeature gf1,
GeneFeature gf2) |
boolean |
SequencePartitioning.isAvailable(GeneFeature feature)
Checks if position of gene feature can be obtained using this partitioning
|
static boolean |
GeneFeature.match(GeneFeature.ReferenceRange a,
GeneFeature b) |
void |
GeneFeature.Serializer.serialize(GeneFeature value,
com.fasterxml.jackson.core.JsonGenerator jgen,
com.fasterxml.jackson.databind.SerializerProvider provider) |
void |
GeneFeatureSerializer.write(com.milaboratory.primitivio.PrimitivO output,
GeneFeature object) |
| Constructor and Description |
|---|
GeneFeature(GeneFeature... features) |
GeneFeature(GeneFeature feature,
int leftOffset,
int rightOffset) |
| Modifier and Type | Field and Description |
|---|---|
GeneFeature |
GGene.definedIn
Gene region where this gene is defined.
|
| Constructor and Description |
|---|
GGene(GeneFeature definedIn,
VDJCGenes vdjcGenes,
VDJTrimming vdjTrimming,
com.milaboratory.core.sequence.NucleotideSequence vInsert,
com.milaboratory.core.sequence.NucleotideSequence djInsert) |
GGene(GeneFeature definedIn,
VDJCGene v,
VDJCGene d,
VDJCGene j,
VDJCGene c,
int vTrimming,
int jTrimming,
Integer d5Trimming,
Integer d3Trimming,
com.milaboratory.core.sequence.NucleotideSequence vInsert,
com.milaboratory.core.sequence.NucleotideSequence djInsert) |
| Modifier and Type | Method and Description |
|---|---|
static GeneFeature |
CommonNormalGeneTrimmingModel.cdr3Part(GeneType geneType) |
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