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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.seq.impl.SimpleSequence
org.biojava.bio.seq.impl.RevCompSequence
A reverse complement view onto Sequence
interface.
All features of the underlying sequence are reflected onto the RevCompSequence using a ProjectedFeatureHolder
calling createFeature() on a RevCompSequence creates a feature on the underlying sequence. Non-Stranded features will return the reverse compemented view of the sequence when getSymbols() is called that is to say if you get what you expect as if your RevCompSequence was a regular Sequence.
Nested Class Summary |
Nested classes inherited from class org.biojava.bio.symbol.SymbolList |
SymbolList.EmptySymbolList |
Nested classes inherited from class org.biojava.bio.seq.FeatureHolder |
FeatureHolder.EmptyFeatureHolder |
Nested classes inherited from class org.biojava.bio.Annotatable |
Annotatable.AnnotationForwarder |
Field Summary | |
protected Sequence |
origSeq
|
Fields inherited from interface org.biojava.bio.symbol.SymbolList |
EDIT, EMPTY_LIST |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA |
Fields inherited from interface org.biojava.bio.Annotatable |
ANNOTATION |
Constructor Summary | |
RevCompSequence(Sequence seq)
URN, Name and Annotation are copied as is from the original Sequence, unless you use the the other contructor that sets these. |
|
RevCompSequence(Sequence seq,
java.lang.String urn,
java.lang.String name,
Annotation annotation)
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Method Summary | |
java.lang.Object |
clone()
clone() should make a complete copy of the Sequence with all features (and children) and return a SimpleSequence that is unconnected from the original sequence. |
boolean |
containsFeature(Feature f)
containsFeature() will return true if this seq contains the feature in question, or if if the original (non reverse complement) sequence contains the feature; |
int |
countFeatures()
Count how many features are contained. |
Feature |
createFeature(Feature.Template ft)
createFeature() will call createFeature() on the underlying Sequence. |
void |
edit(Edit e)
edit() will try to edit the underlying Sequence. |
java.util.Iterator |
features()
Iterate over the features in no well defined order. |
Feature |
getFeatureFromOriginal(Feature f)
getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am including this method so that you can get the corresponding feature from the original sequence. |
void |
removeFeature(Feature f)
Remove a feature attached to this sequence. |
Methods inherited from class org.biojava.bio.seq.impl.SimpleSequence |
createFeature, featureHolderAllocated, filter, filter, getAlphabet, getAnnotation, getChangeSupport, getFeatureHolder, getName, getSchema, getURN, iterator, length, realizeFeature, seqString, setName, setURN, subList, subStr, symbolAt, toList |
Methods inherited from class org.biojava.utils.AbstractChangeable |
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
protected Sequence origSeq
Constructor Detail |
public RevCompSequence(Sequence seq) throws IllegalAlphabetException
public RevCompSequence(Sequence seq, java.lang.String urn, java.lang.String name, Annotation annotation) throws IllegalAlphabetException
Method Detail |
public void edit(Edit e) throws ChangeVetoException, java.lang.IndexOutOfBoundsException
Since I have not seen and editable Sequence I have not tested this
edit
in interface SymbolList
edit
in class SimpleSequence
ChangeVetoException
java.lang.IndexOutOfBoundsException
public java.util.Iterator features()
FeatureHolder
features
in interface FeatureHolder
features
in class SimpleSequence
public int countFeatures()
FeatureHolder
countFeatures
in interface FeatureHolder
countFeatures
in class SimpleSequence
public boolean containsFeature(Feature f)
containsFeature
in interface FeatureHolder
containsFeature
in class SimpleSequence
public void removeFeature(Feature f) throws ChangeVetoException
SimpleSequence
removeFeature
in interface FeatureHolder
removeFeature
in class SimpleSequence
ChangeVetoException
public Feature createFeature(Feature.Template ft) throws ChangeVetoException, BioException
createFeature
in interface FeatureHolder
createFeature
in class SimpleSequence
ChangeVetoException
BioException
public Feature getFeatureFromOriginal(Feature f)
public java.lang.Object clone()
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