Class DASSequence
- java.lang.Object
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- org.biojava.utils.AbstractChangeable
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- org.biojava.bio.program.das.DASSequence
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- All Implemented Interfaces:
Annotatable
,FeatureHolder
,RealizingFeatureHolder
,Sequence
,SymbolList
,Changeable
public class DASSequence extends AbstractChangeable
Sequence reflecting a DAS reference sequence, possibly decorated with one of more annotation sets.This is an first-pass implementation. In future, I hope to add query optimization for better performance on large sequences, and pluggable transducers to parameterize the creation of BioJava features.
- Since:
- 1.1
- Author:
- Thomas Down, Matthew Pocock, David Huen
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
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Field Summary
Fields Modifier and Type Field Description protected ChangeForwarder
annotationForwarder
static ChangeType
ANNOTATIONS
Change type which indicates that the set of annotation servers used by this DASSequence has been changed.static java.lang.String
PROPERTY_ANNOTATIONSERVER
static java.lang.String
PROPERTY_FEATUREID
static java.lang.String
PROPERTY_FEATURELABEL
static java.lang.String
PROPERTY_LINKS
static java.lang.String
PROPERTY_SEQUENCEVERSION
static int
SIZE_THRESHOLD
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Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
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Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addAnnotationSource(java.net.URL dataSourceURL)
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 temp)
Create a new Feature, and add it to this FeatureHolder.java.util.Set
dataSourceURLs()
void
edit(Edit e)
Apply an edit to the SymbolList as specified by the edit object.java.util.Iterator
features()
Iterate over the features in no well defined order.FeatureHolder
filter(FeatureFilter ff)
Query this set of features using a suppliedFeatureFilter
.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.java.lang.String
getName()
The name of this sequence.DASSequenceDB
getParentDB()
FeatureFilter
getSchema()
Return a schema-filter for thisFeatureHolder
.protected SymbolList
getSymbols()
java.lang.String
getURN()
A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.java.util.Iterator
iterator()
An Iterator over all Symbols in this SymbolList.int
length()
The number of symbols in this SymbolList.Feature
realizeFeature(FeatureHolder dest, Feature.Template temp)
Realize a feature template.void
removeAnnotationSource(java.net.URL dataSourceURL)
void
removeFeature(Feature f)
Remove a feature from this FeatureHolder.java.lang.String
seqString()
Stringify this symbol list.SymbolList
subList(int start, int end)
Return a new SymbolList for the symbols start to end inclusive.java.lang.String
subStr(int start, int end)
Return a region of this symbol list as a String.Symbol
symbolAt(int pos)
Return the symbol at index, counting from 1.java.util.List
toList()
Returns a List of symbols.-
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Field Detail
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ANNOTATIONS
public static final ChangeType ANNOTATIONS
Change type which indicates that the set of annotation servers used by this DASSequence has been changed. This extends Feature.FEATURES as the addition and removal of annotation servers adds and removes features.
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PROPERTY_ANNOTATIONSERVER
public static final java.lang.String PROPERTY_ANNOTATIONSERVER
- See Also:
- Constant Field Values
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PROPERTY_FEATUREID
public static final java.lang.String PROPERTY_FEATUREID
- See Also:
- Constant Field Values
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PROPERTY_FEATURELABEL
public static final java.lang.String PROPERTY_FEATURELABEL
- See Also:
- Constant Field Values
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PROPERTY_LINKS
public static final java.lang.String PROPERTY_LINKS
- See Also:
- Constant Field Values
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PROPERTY_SEQUENCEVERSION
public static final java.lang.String PROPERTY_SEQUENCEVERSION
- See Also:
- Constant Field Values
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SIZE_THRESHOLD
public static final int SIZE_THRESHOLD
- See Also:
- Constant Field Values
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annotationForwarder
protected transient ChangeForwarder annotationForwarder
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Method Detail
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getParentDB
public DASSequenceDB getParentDB()
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dataSourceURLs
public java.util.Set dataSourceURLs()
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addAnnotationSource
public void addAnnotationSource(java.net.URL dataSourceURL) throws BioException, ChangeVetoException
- Throws:
BioException
ChangeVetoException
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getChangeSupport
protected ChangeSupport getChangeSupport(ChangeType ct)
Description copied from class:AbstractChangeable
Called to retrieve the ChangeSupport for this object.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;
- Overrides:
getChangeSupport
in classAbstractChangeable
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removeAnnotationSource
public void removeAnnotationSource(java.net.URL dataSourceURL) throws ChangeVetoException, BioException
- Throws:
ChangeVetoException
BioException
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getAlphabet
public Alphabet getAlphabet()
Description copied from interface:SymbolList
The alphabet that this SymbolList is over.Every symbol within this SymbolList is a member of this alphabet.
alphabet.contains(symbol) == true
for each symbol that is within this sequence.- Specified by:
getAlphabet
in interfaceSymbolList
- Returns:
- the alphabet
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iterator
public java.util.Iterator iterator()
Description copied from interface:SymbolList
An Iterator over all Symbols in this SymbolList.This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
- Specified by:
iterator
in interfaceSymbolList
- Returns:
- an iterator
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length
public int length()
Description copied from interface:SymbolList
The number of symbols in this SymbolList.- Specified by:
length
in interfaceSymbolList
- Returns:
- the length
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seqString
public java.lang.String seqString()
Description copied from interface:SymbolList
Stringify this symbol list.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.
- Specified by:
seqString
in interfaceSymbolList
- Returns:
- a string representation of the symbol list
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subStr
public java.lang.String subStr(int start, int end)
Description copied from interface:SymbolList
Return a region of this symbol list as a String.This should use the same rules as seqString.
- Specified by:
subStr
in interfaceSymbolList
- Parameters:
start
- the first symbol to includeend
- the last symbol to include- Returns:
- the string representation
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subList
public SymbolList subList(int start, int end)
Description copied from interface:SymbolList
Return a new SymbolList for the symbols start to end inclusive.The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.
- Specified by:
subList
in interfaceSymbolList
- Parameters:
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolList
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symbolAt
public Symbol symbolAt(int pos)
Description copied from interface:SymbolList
Return the symbol at index, counting from 1.- Specified by:
symbolAt
in interfaceSymbolList
- Parameters:
pos
- the offset into this SymbolList- Returns:
- the Symbol at that index
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toList
public java.util.List toList()
Description copied from interface:SymbolList
Returns a List of symbols.This is an immutable list of symbols. Do not edit it.
- Specified by:
toList
in interfaceSymbolList
- Returns:
- a List of Symbols
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edit
public void edit(Edit e) throws ChangeVetoException
Description copied from interface:SymbolList
Apply an edit to the SymbolList as specified by the edit object.Description
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:
- be edited (between 0 and symL.length()+1).
- To append to a sequence, pos=symL.length()+1, pos=0.
- To insert something at the beginning of the sequence, set pos=1 and length=0.
Examples
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());
- Specified by:
edit
in interfaceSymbolList
- Parameters:
e
- the Edit to perform- Throws:
ChangeVetoException
- if either the SymboList does not support the edit, or if the change was vetoed
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getSymbols
protected SymbolList getSymbols() throws BioException
- Throws:
BioException
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getName
public java.lang.String getName()
Description copied from interface:Sequence
The name of this sequence.The name may contain spaces or odd characters.
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getURN
public java.lang.String getURN()
Description copied from interface:Sequence
A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. For sequences in well-known database, this may be a URN, e.g.urn:sequence/embl:AL121903
It may also be a URL identifying a specific resource, either locally or over the networkfile:///home/thomas/myseq.fa|seq22 http://www.mysequences.net/chr22.seq
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features
public java.util.Iterator features()
Description copied from interface:FeatureHolder
Iterate over the features in no well defined order.- Specified by:
features
in interfaceFeatureHolder
- Returns:
- an Iterator
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containsFeature
public boolean containsFeature(Feature f)
Description copied from interface:FeatureHolder
Check if the feature is present in this holder.- Specified by:
containsFeature
in interfaceFeatureHolder
- Parameters:
f
- the Feature to check- Returns:
- true if f is in this set
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filter
public FeatureHolder filter(FeatureFilter ff)
Description copied from interface:FeatureHolder
Query this set of features using a suppliedFeatureFilter
.- Specified by:
filter
in interfaceFeatureHolder
- Parameters:
ff
- theFeatureFilter
to apply.- Returns:
- all features in this container which match
filter
.
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filter
public FeatureHolder filter(FeatureFilter ff, boolean recurse)
Description copied from interface:FeatureHolder
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.- Specified by:
filter
in interfaceFeatureHolder
- Parameters:
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.
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getSchema
public FeatureFilter getSchema()
Description copied from interface:FeatureHolder
Return a schema-filter for thisFeatureHolder
. This is a filter which allFeature
s immediately contained by thisFeatureHolder
will match. It need not directly match their child features, but it can (and should!) provide information about them usingFeatureFilter.OnlyChildren
filters. In cases where there is no feature hierarchy, this can be indicated by includingFeatureFilter.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, returnFeatureFilter.top_level
.Feature
objects should, as a minimum, returnFeatureFilter.ByParent(new FeatureFilter.ByFeature(this))
.- Specified by:
getSchema
in interfaceFeatureHolder
- Returns:
- the schema filter
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countFeatures
public int countFeatures()
Description copied from interface:FeatureHolder
Count how many features are contained.- Specified by:
countFeatures
in interfaceFeatureHolder
- Returns:
- a positive integer or zero, equal to the number of features contained
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createFeature
public Feature createFeature(Feature.Template temp) throws ChangeVetoException
Description copied from interface:FeatureHolder
Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.- Specified by:
createFeature
in interfaceFeatureHolder
- Throws:
ChangeVetoException
- if this FeatureHolder does not support creation of new features, or if the change was vetoed
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removeFeature
public void removeFeature(Feature f) throws ChangeVetoException
Description copied from interface:FeatureHolder
Remove a feature from this FeatureHolder.- Specified by:
removeFeature
in interfaceFeatureHolder
- Throws:
ChangeVetoException
- if this FeatureHolder does not support feature removal or if the change was vetoed
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realizeFeature
public Feature realizeFeature(FeatureHolder dest, Feature.Template temp) throws BioException
Description copied from interface:RealizingFeatureHolder
Realize a feature template. This will be a template which has been passed to thecreateFeature
method of either thisFeatureHolder
or one of our child Features.- Specified by:
realizeFeature
in interfaceRealizingFeatureHolder
- Throws:
BioException
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getAnnotation
public Annotation getAnnotation()
Description copied from interface:Annotatable
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
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