org.biojava.bio.seq.impl
Class SimpleStrandedFeature
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.impl.SimpleFeature
org.biojava.bio.seq.impl.SimpleStrandedFeature
- All Implemented Interfaces:
- java.io.Serializable, Annotatable, Feature, FeatureHolder, RealizingFeatureHolder, StrandedFeature, Changeable
- Direct Known Subclasses:
- SimpleFramedFeature, SimpleHomologyFeature, SimpleRemoteFeature, SimpleRestrictionSite, SimpleSimilarityPairFeature
public class SimpleStrandedFeature
- extends SimpleFeature
- implements StrandedFeature
A no-frills implementation of StrandedFeature.
- Author:
- Matthew Pocock, Thomas Down
- See Also:
- Serialized Form
Methods inherited from class org.biojava.bio.seq.impl.SimpleFeature |
containsFeature, countFeatures, createFeature, equals, featureHolderAllocated, features, fillTemplate, filter, filter, getAnnotation, getChangeSupport, getFeatureHolder, getLocation, getParent, getSchema, getSequence, getSource, getSourceTerm, getType, getTypeTerm, hashCode, realizeFeature, removeFeature, setLocation, setSource, setSourceTerm, setType, setTypeTerm |
Methods inherited from class java.lang.Object |
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.biojava.bio.seq.Feature |
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, setLocation, setSource, setSourceTerm, setType, setTypeTerm |
SimpleStrandedFeature
public SimpleStrandedFeature(Sequence sourceSeq,
FeatureHolder parent,
StrandedFeature.Template template)
throws java.lang.IllegalArgumentException
- Throws:
java.lang.IllegalArgumentException
getStrand
public StrandedFeature.Strand getStrand()
- Description copied from interface:
StrandedFeature
- Retrieve the strand that this feature lies upon.
This will be one of StrandedFeature.POSITIVE or NEGATIVE.
- Specified by:
getStrand
in interface StrandedFeature
- Returns:
- one of the Strand constants
getSymbols
public SymbolList getSymbols()
- Description copied from interface:
Feature
- Return a list of symbols that are contained in this feature.
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 location is modified then this does not modify any
SymbolList produced by earlier invocations of this method.
- Specified by:
getSymbols
in interface Feature
- Specified by:
getSymbols
in interface StrandedFeature
- Overrides:
getSymbols
in class SimpleFeature
- Returns:
- a SymbolList containing each symbol of the parent sequence contained
within this feature in the order they appear in the parent
setStrand
public void setStrand(StrandedFeature.Strand strand)
throws ChangeVetoException
- Description copied from interface:
StrandedFeature
- Set the strand that this feature lies upon.
This will be one of StrandedFeature.POSITIVE or NEGATIVE.
- Specified by:
setStrand
in interface StrandedFeature
- Parameters:
strand
- a Strand
.
- Throws:
ChangeVetoException
- if the strand may not be
changed.
makeTemplate
public Feature.Template makeTemplate()
- Description copied from interface:
Feature
- Create a new Template that could be used to generate a feature identical
to this one. The fields of the template can be edited without changing
the feature.
- Specified by:
makeTemplate
in interface Feature
- Overrides:
makeTemplate
in class SimpleFeature
- Returns:
- a new Template that would make a feature like this one
fillTemplate
protected void fillTemplate(StrandedFeature.Template ft)
toString
public java.lang.String toString()
- Overrides:
toString
in class SimpleFeature