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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.seq.impl.SimpleSequence
public class SimpleSequence
A basic implementation of the Sequence
interface.
This class now implements all methods in the SymbolList interface by delegating to another SymbolList object. This avoids unnecessary copying, but means that any changes in the underlying SymbolList will be silently reflected in the SimpleSequence. In general, SimpleSequences should only be constructed from SymbolLists which are known to be immutable.
By default, features attached to a SimpleSequence are
realized as simple in-memory implementations using
SimpleFeatureRealizer.DEFAULT
. If you need
alternative feature realization behaviour, any
FeatureRealizer
implementation may be
supplied at construction-time.
SimpleRichSequence
Nested Class Summary |
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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 |
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder |
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FeatureHolder.EmptyFeatureHolder |
Field Summary |
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Fields inherited from interface org.biojava.bio.symbol.SymbolList |
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EDIT, EMPTY_LIST |
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 |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
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EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA |
Constructor Summary | |
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SimpleSequence(SymbolList sym,
String urn,
String name,
Annotation annotation)
Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed. |
|
SimpleSequence(SymbolList sym,
String urn,
String name,
Annotation annotation,
FeatureRealizer realizer)
Create a SimpleSequence using a specified FeatureRealizer. |
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 template)
Create a new Feature, and add it to this FeatureHolder. |
Feature |
createFeature(FeatureHolder fh,
Feature.Template template)
Deprecated. Please use new 1-arg createFeature instead. |
void |
edit(Edit edit)
Apply an edit to the SymbolList as specified by the edit object. |
protected boolean |
featureHolderAllocated()
|
Iterator |
features()
Iterate over the features in no well defined order. |
FeatureHolder |
filter(FeatureFilter filter)
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. |
Alphabet |
getAlphabet()
The alphabet that this SymbolList is over. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
protected ChangeSupport |
getChangeSupport(ChangeType ct)
Called to retrieve the ChangeSupport for this object. |
protected SimpleFeatureHolder |
getFeatureHolder()
|
String |
getName()
The name of this sequence. |
FeatureFilter |
getSchema()
Return a schema-filter for this FeatureHolder . |
String |
getURN()
A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. |
Iterator |
iterator()
An Iterator over all Symbols in this SymbolList. |
int |
length()
The number of symbols in this SymbolList. |
Feature |
realizeFeature(FeatureHolder parent,
Feature.Template template)
Realize a feature template. |
void |
removeFeature(Feature f)
Remove a feature attached to this sequence. |
String |
seqString()
Stringify this symbol list. |
void |
setName(String name)
Assign a name to this sequence |
void |
setURN(String urn)
Provide the URN for this sequence |
SymbolList |
subList(int start,
int end)
Return a new SymbolList for the symbols start to end inclusive. |
String |
subStr(int start,
int end)
Return a region of this symbol list as a String. |
Symbol |
symbolAt(int index)
Return the symbol at index, counting from 1. |
List |
toList()
Returns a List of symbols. |
String |
toString()
|
Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from interface org.biojava.utils.Changeable |
---|
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from interface org.biojava.utils.Changeable |
---|
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from interface org.biojava.utils.Changeable |
---|
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Constructor Detail |
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public SimpleSequence(SymbolList sym, String urn, String name, Annotation annotation)
sym
- the SymbolList to wrap as a sequenceurn
- the URNname
- the name - should be unique if practicalannotation
- the annotation object to use or nullpublic SimpleSequence(SymbolList sym, String urn, String name, Annotation annotation, FeatureRealizer realizer)
sym
- the SymbolList to wrap as a sequenceurn
- the URNname
- the name - should be unique if practicalannotation
- the annotation object to use or nullrealizer
- the FeatureRealizer implemetation to use when adding featuresMethod Detail |
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public Alphabet getAlphabet()
SymbolList
Every symbol within this SymbolList is a member of this alphabet.
alphabet.contains(symbol) == true
for each symbol that is within this sequence.
getAlphabet
in interface SymbolList
public Iterator iterator()
SymbolList
This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
iterator
in interface SymbolList
public int length()
SymbolList
length
in interface SymbolList
public String seqString()
SymbolList
It is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.
seqString
in interface SymbolList
public String subStr(int start, int end)
SymbolList
This should use the same rules as seqString.
subStr
in interface SymbolList
start
- the first symbol to includeend
- the last symbol to include
public SymbolList subList(int start, int end)
SymbolList
The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.
subList
in interface SymbolList
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolListpublic Symbol symbolAt(int index)
SymbolList
symbolAt
in interface SymbolList
index
- the offset into this SymbolList
public List toList()
SymbolList
This is an immutable list of symbols. Do not edit it.
toList
in interface SymbolList
protected SimpleFeatureHolder getFeatureHolder()
protected boolean featureHolderAllocated()
public 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 void setURN(String urn)
public String getName()
Sequence
The name may contain spaces or odd characters.
getName
in interface Sequence
public void setName(String name)
public Annotation getAnnotation()
Annotatable
getAnnotation
in interface Annotatable
public int countFeatures()
FeatureHolder
countFeatures
in interface FeatureHolder
public Iterator features()
FeatureHolder
features
in interface FeatureHolder
public FeatureHolder filter(FeatureFilter filter)
FeatureHolder
FeatureFilter
.
filter
in interface FeatureHolder
filter
- 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 boolean containsFeature(Feature f)
FeatureHolder
containsFeature
in interface FeatureHolder
f
- the Feature to check
public Feature realizeFeature(FeatureHolder parent, Feature.Template template) throws BioException
RealizingFeatureHolder
createFeature
method of either
this FeatureHolder
or one of our child Features.
realizeFeature
in interface RealizingFeatureHolder
BioException
public Feature createFeature(Feature.Template template) throws BioException, ChangeVetoException
FeatureHolder
createFeature
in interface FeatureHolder
BioException
- if something went wrong during creating the feature
ChangeVetoException
- if this FeatureHolder does not support
creation of new features, or if the change was vetoedpublic 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 Feature createFeature(FeatureHolder fh, Feature.Template template) throws BioException, ChangeVetoException
BioException
ChangeVetoException
public void removeFeature(Feature f) throws ChangeVetoException, BioException
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 void edit(Edit edit) throws ChangeVetoException
SymbolList
All edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.
When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).
The pos and pos+length should always be valid positions on the SymbolList to:
SymbolList seq = DNATools.createDNA("atcaaaaacgctagc");
System.out.println(seq.seqString());
// delete 5 bases from position 4
Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
seq.edit(ed);
System.out.println(seq.seqString());
// delete one base from the start
ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
seq.edit(ed);
// delete one base from the end
ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
seq.edit(ed);
System.out.println(seq.seqString());
// overwrite 2 bases from position 3 with "tt"
ed = new Edit(3, 2, DNATools.createDNA("tt"));
seq.edit(ed);
System.out.println(seq.seqString());
// add 6 bases to the start
ed = new Edit(1, 0, DNATools.createDNA("aattgg");
seq.edit(ed);
System.out.println(seq.seqString());
// add 4 bases to the end
ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
seq.edit(ed);
System.out.println(seq.seqString());
// full edit
ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
seq.edit(ed);
System.out.println(seq.seqString());
edit
in interface SymbolList
edit
- the Edit to perform
ChangeVetoException
- if either the SymboList does not support the
edit, or if the change was vetoedpublic String toString()
toString
in class Object
protected ChangeSupport getChangeSupport(ChangeType ct)
AbstractChangeable
Your implementation of this method should have the following structure:
It is usual for the forwarding listeners (someForwarder in this example) to
be transient and lazily instantiated. Be sure to register & unregister the
forwarder in the code that does the ChangeEvent handling in setter methods.
ChangeSupport cs = super.getChangeSupport(ct);
if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
someForwarder = new ChangeForwarder(...
this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
}
return cs;
getChangeSupport
in class AbstractChangeable
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