|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractSymbolList
org.biojava.bio.symbol.SimpleGappedSymbolList
org.biojava.bio.seq.impl.SimpleGappedSequence
public class SimpleGappedSequence
Simple implementation of GappedSequence. Please note that this is a view onto another Sequence. Gaps created and removed are only in the view not the underlying original. This means that any gaps present in the original cannot be manipulated in this view. To manipulate the original you would need to use Edit objects.
Nested Class Summary | |
---|---|
class |
SimpleGappedSequence.GappedContext
|
Nested classes/interfaces inherited from class org.biojava.bio.symbol.SimpleGappedSymbolList |
---|
SimpleGappedSymbolList.Block |
Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList |
---|
AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater |
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder |
---|
FeatureHolder.EmptyFeatureHolder |
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
---|
Annotatable.AnnotationForwarder |
Field Summary |
---|
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
---|
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA |
Fields inherited from interface org.biojava.bio.Annotatable |
---|
ANNOTATION |
Fields inherited from interface org.biojava.bio.symbol.SymbolList |
---|
EDIT, EMPTY_LIST |
Constructor Summary | |
---|---|
SimpleGappedSequence(GappedSequence seq)
|
|
SimpleGappedSequence(Sequence seq)
|
Method Summary | |
---|---|
boolean |
containsFeature(Feature f)
Check if the feature is present in this holder. |
int |
countFeatures()
Count how many features are contained. |
Feature |
createFeature(Feature.Template templ)
Create a new Feature, and add it to this FeatureHolder. |
java.util.Iterator |
features()
Iterate over the features in no well defined order. |
FeatureHolder |
filter(FeatureFilter ff)
Query this set of features using a supplied FeatureFilter . |
FeatureHolder |
filter(FeatureFilter ff,
boolean recurse)
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
boolean |
getCreateOnUnderlyingSequence()
|
java.lang.String |
getName()
The name of this sequence. |
FeatureFilter |
getSchema()
Return a schema-filter for this FeatureHolder . |
java.lang.String |
getURN()
A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. |
void |
removeFeature(Feature f)
Remove a feature from this FeatureHolder. |
void |
setCreateOnUnderlyingSequence(boolean underlying)
|
Methods inherited from class org.biojava.bio.symbol.SimpleGappedSymbolList |
---|
addGapInSource, addGapInView, addGapsInSource, addGapsInView, BlockIterator, dumpBlocks, findSourceBlock, findSourceGap, findViewBlock, findViewGap, firstNonGap, gappedToLocation, getAlphabet, getSourceSymbolList, getUngappedLocation, isSane, lastNonGap, length, locationToGapped, removeGap, removeGaps, renumber, sourceToView, sourceToView, symbolAt, viewToSource, viewToSource |
Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList |
---|
edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString |
Methods inherited from class org.biojava.utils.AbstractChangeable |
---|
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
---|
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.biojava.bio.symbol.GappedSymbolList |
---|
addGapInSource, addGapInView, addGapsInSource, addGapsInView, firstNonGap, getSourceSymbolList, getUngappedLocation, lastNonGap, removeGap, removeGaps, sourceToView, viewToSource |
Methods inherited from interface org.biojava.bio.symbol.SymbolList |
---|
edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList |
Methods inherited from interface org.biojava.utils.Changeable |
---|
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Constructor Detail |
---|
public SimpleGappedSequence(Sequence seq)
public SimpleGappedSequence(GappedSequence seq)
Method Detail |
---|
public boolean getCreateOnUnderlyingSequence()
public void setCreateOnUnderlyingSequence(boolean underlying)
public Annotation getAnnotation()
Annotatable
getAnnotation
in interface Annotatable
public java.lang.String getName()
Sequence
The name may contain spaces or odd characters.
getName
in interface Sequence
public java.lang.String getURN()
Sequence
urn:sequence/embl:AL121903It may also be a URL identifying a specific resource, either locally or over the network
file:///home/thomas/myseq.fa|seq22 http://www.mysequences.net/chr22.seq
getURN
in interface Sequence
public java.util.Iterator features()
FeatureHolder
features
in interface FeatureHolder
public FeatureHolder filter(FeatureFilter ff)
FeatureHolder
FeatureFilter
.
filter
in interface FeatureHolder
ff
- the FeatureFilter
to apply.
filter
.public FeatureHolder filter(FeatureFilter ff, boolean recurse)
FeatureHolder
filter
in interface FeatureHolder
ff
- the FeatureFilter to applyrecurse
- true if all features-of-features should be scanned, and a
single flat collection of features returned, or false if
just immediate children should be filtered.public int countFeatures()
FeatureHolder
countFeatures
in interface FeatureHolder
public boolean containsFeature(Feature f)
FeatureHolder
containsFeature
in interface FeatureHolder
f
- the Feature to check
public FeatureFilter getSchema()
FeatureHolder
FeatureHolder
. This is a filter
which all Feature
s immediately contained by this FeatureHolder
will match. It need not directly match their child features, but it can (and should!) provide
information about them using FeatureFilter.OnlyChildren
filters. In cases where there
is no feature hierarchy, this can be indicated by including FeatureFilter.leaf
in
the schema filter.
For the truly non-informative case, it is possible to return FeatureFilter.all
. However,
it is almost always possible to provide slightly more information that this. For example, Sequence
objects should, at a minimum, return FeatureFilter.top_level
. Feature
objects
should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this))
.
getSchema
in interface FeatureHolder
public void removeFeature(Feature f) throws ChangeVetoException, BioException
FeatureHolder
removeFeature
in interface FeatureHolder
ChangeVetoException
- if this FeatureHolder does not support
feature removal or if the change was vetoed
BioException
- if there was an error removing the featurepublic Feature createFeature(Feature.Template templ) throws ChangeVetoException, BioException
FeatureHolder
createFeature
in interface FeatureHolder
ChangeVetoException
- if this FeatureHolder does not support
creation of new features, or if the change was vetoed
BioException
- if something went wrong during creating the feature
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |