Class ViewSequence
- All Implemented Interfaces:
Serializable
,Annotatable
,FeatureHolder
,RealizingFeatureHolder
,Sequence
,SymbolList
,Changeable
- Direct Known Subclasses:
CircularView
SequenceTools.view(Sequence seq)
instead of instantiating this
class directly.- Author:
- Thomas Down, Matthew Pocock
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
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Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Constructor Summary
ConstructorsConstructorDescriptionViewSequence
(Sequence seq) Construct a view onto an existing sequence which takes on that sequence's name.ViewSequence
(Sequence seq, String name) Construct a view onto an existing sequence and give it a new name.ViewSequence
(Sequence seq, FeatureRealizer fr) Construct a view onto a sequence, using a specific FeatureRealizer. -
Method Summary
Modifier and TypeMethodDescriptionboolean
Check if the feature is present in this holder.int
Count how many features are contained.createFeature
(Feature.Template template) Create a new Feature, and add it to this FeatureHolder.void
Apply an edit to the SymbolList as specified by the edit object.features()
Iterate over the features in no well defined order.filter
(FeatureFilter fc) Query this set of features using a suppliedFeatureFilter
.filter
(FeatureFilter fc, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.The alphabet that this SymbolList is over.Should return the associated annotation object.getName()
The name of this sequence.Return a schema-filter for thisFeatureHolder
.getURN()
A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.iterator()
An Iterator over all Symbols in this SymbolList.int
length()
The number of symbols in this SymbolList.realizeFeature
(FeatureHolder parent, Feature.Template template) Realize a feature template.void
Remove a feature from this sequence.Stringify this symbol list.subList
(int start, int end) Return a new SymbolList for the symbols start to end inclusive.subStr
(int start, int end) Return a region of this symbol list as a String.symbolAt
(int indx) Return the symbol at index, counting from 1.toList()
Returns a List of symbols.Methods inherited from class org.biojava.utils.Unchangeable
addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Constructor Details
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ViewSequence
Construct a view onto an existing sequence and give it a new name.The prefered method is SequenceTools.view(Sequence seq, String name)
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ViewSequence
Construct a view onto an existing sequence which takes on that sequence's name.The prefered method is SequenceTools.view(Sequence seq)
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ViewSequence
Construct a view onto a sequence, using a specific FeatureRealizer.The prefered method is SequenceTools.view(Sequence seq, FeatureRealizer fr)
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Method Details
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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
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
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
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
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
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
Description copied from interface:SymbolList
Return the symbol at index, counting from 1.- Specified by:
symbolAt
in interfaceSymbolList
- Parameters:
indx
- the offset into this SymbolList- Returns:
- the Symbol at that index
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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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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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getName
Description copied from interface:Sequence
The name of this sequence.The name may contain spaces or odd characters.
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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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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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filter
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:
fc
- 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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filter
Description copied from interface:FeatureHolder
Query this set of features using a suppliedFeatureFilter
.- Specified by:
filter
in interfaceFeatureHolder
- Parameters:
fc
- theFeatureFilter
to apply.- Returns:
- all features in this container which match
filter
.
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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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removeFeature
Remove a feature from this sequence. NOTE: This method will only succeed for features which were added to this ViewSequence. Trying to remove a Feature from the underlying sequence will cause an IllegalArgumentException. I think this is the correct behaviour.- 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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containsFeature
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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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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realizeFeature
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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createFeature
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:
BioException
- if something went wrong during creating the featureChangeVetoException
- if this FeatureHolder does not support creation of new features, or if the change was vetoed
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getAddedFeatures
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edit
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:
edit
- 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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