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public interface StrandedFeature
Adds the concept of 'strand' to features.
Strandedness only applies to some types of sequence, such as DNA. Any
implementation should blow chunks to avoid being added to a sequence for
which strand is a foreign concept.
Strand is intrinsicly part of all RichFeatures
We strongly recommend using this interface.
RichFeature
Nested Class Summary | |
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static class |
StrandedFeature.Strand
Class to represent the 'strandedness' of a feature. |
static class |
StrandedFeature.Template
Template class for parameterizing the creation of a new StrandedFeature . |
Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature |
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Feature.ByLocationComparator |
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder |
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FeatureHolder.EmptyFeatureHolder |
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
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Annotatable.AnnotationForwarder |
Field Summary | |
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static StrandedFeature.Strand |
NEGATIVE
Flag to indicate that a feature is on the negative strand. |
static StrandedFeature.Strand |
POSITIVE
Flag to indicate that a feature is on the positive strand. |
static ChangeType |
STRAND
The strand of this feature is being altered. |
static StrandedFeature.Strand |
UNKNOWN
Flag to indicate that a feature has an unknown strand. |
Fields inherited from interface org.biojava.bio.seq.Feature |
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byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
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EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA |
Fields inherited from interface org.biojava.bio.Annotatable |
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ANNOTATION |
Method Summary | |
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StrandedFeature.Strand |
getStrand()
Retrieve the strand that this feature lies upon. |
SymbolList |
getSymbols()
Return a list of symbols that are contained in this feature. |
void |
setStrand(StrandedFeature.Strand strand)
Set the strand that this feature lies upon. |
Methods inherited from interface org.biojava.bio.seq.Feature |
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features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm |
Methods inherited from interface org.biojava.bio.seq.FeatureHolder |
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containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature |
Methods inherited from interface org.biojava.bio.Annotatable |
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getAnnotation |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
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static final ChangeType STRAND
static final StrandedFeature.Strand POSITIVE
static final StrandedFeature.Strand NEGATIVE
static final StrandedFeature.Strand UNKNOWN
Method Detail |
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StrandedFeature.Strand getStrand()
This will be one of StrandedFeature.POSITIVE or NEGATIVE.
void setStrand(StrandedFeature.Strand strand) throws ChangeVetoException
This will be one of StrandedFeature.POSITIVE or NEGATIVE.
strand
- a Strand
.
ChangeVetoException
- if the strand may not be
changed.SymbolList getSymbols()
The symbols may not be contiguous in the original sequence, but they will be concatenated together in the resulting SymbolList.
The order of the Symbols within the resulting symbol list will be according to the concept of ordering within the location object.
If the feature is on the negative strand then the SymbolList will be reverse-complemented as appropriate.
getSymbols
in interface Feature
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