org.biojava.bio.seq.impl
Class SubSequence

java.lang.Object
  extended by org.biojava.bio.seq.impl.SubSequence
All Implemented Interfaces:
java.io.Serializable, Annotatable, FeatureHolder, Sequence, SymbolList, Changeable

public class SubSequence
extends java.lang.Object
implements Sequence, java.io.Serializable

View a sub-section of a given sequence object, including all the features intersecting that region.

All features entirely contained within the region are projected by just translating their locations. The features that overlap the region are replaced by RemoteFeature instances with fuzzy locations that are trunchated to fit inside the sub-section. All features not contained by the region are not projected.

Since:
1.2
Author:
Thomas Down, Matthew Pocock
See Also:
Serialized Form

Nested Class Summary
static class SubSequence.SubProjectedFeatureContext
          TargetContext that implements the mapping between the parent sequence and this sub-sequence.
 
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
protected  ChangeForwarder annotationForwarder
           
 
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
SubSequence(Sequence seq, int start, int end)
          Construct a new SubSequence of the specified sequence.
SubSequence(Sequence seq, int start, int end, java.lang.String name)
          Construct a new SubSequence of the specified sequence.
 
Method Summary
 void addChangeListener(ChangeListener cl)
          Add a listener that will be informed of all changes.
 void addChangeListener(ChangeListener cl, ChangeType ct)
          Add a listener that will be informed of changes of a given type.
 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.
 void edit(Edit edit)
          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 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.
 int getEnd()
           
protected  ProjectedFeatureHolder getFeatures()
           
 java.lang.String getName()
          The name of this sequence.
 FeatureFilter getSchema()
          Return a schema-filter for this FeatureHolder.
 Sequence getSequence()
          Return the parent sequence of which this is a partial view
 int getStart()
           
 java.lang.String getURN()
          A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.
 boolean isUnchanging(ChangeType ct)
           A particular ChangeType can never be raised by this Changeable.
 java.util.Iterator iterator()
          An Iterator over all Symbols in this SymbolList.
 int length()
          The number of symbols in this SymbolList.
 void removeChangeListener(ChangeListener cl)
          Remove a listener that was interested in all types of changes.
 void removeChangeListener(ChangeListener cl, ChangeType ct)
          Remove a listener that was interested in a specific types of changes.
 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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

annotationForwarder

protected transient ChangeForwarder annotationForwarder
Constructor Detail

SubSequence

public SubSequence(Sequence seq,
                   int start,
                   int end,
                   java.lang.String name)
Construct a new SubSequence of the specified sequence. Generally you would use the SequenceTools.subSequence() methods to get an instance of this class.

Parameters:
seq - A sequence to view
start - The start of the range to view
end - The end of the range to view
name - Name for the subsequence
Throws:
java.lang.IndexOutOfBoundsException - is the start or end position is illegal.

SubSequence

public SubSequence(Sequence seq,
                   int start,
                   int end)
Construct a new SubSequence of the specified sequence. Generally you would use the SequenceTools.subSequence() methods to get an instance of this class.

Parameters:
seq - A sequence to view
start - The start of the range to view
end - The end of the range to view
Throws:
java.lang.IndexOutOfBoundsException - if the start or end position is illegal.
Method Detail

symbolAt

public Symbol symbolAt(int pos)
Description copied from interface: SymbolList
Return the symbol at index, counting from 1.

Specified by:
symbolAt in interface SymbolList
Parameters:
pos - the offset into this SymbolList
Returns:
the Symbol at that index

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 interface SymbolList
Returns:
the alphabet

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 interface SymbolList
Parameters:
start - the first symbol of the new SymbolList
end - the last symbol (inclusive) of the new SymbolList

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 interface SymbolList
Returns:
a string representation of the symbol list

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 interface SymbolList
Parameters:
start - the first symbol to include
end - the last symbol to include
Returns:
the string representation

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 interface SymbolList
Returns:
a List of Symbols

length

public int length()
Description copied from interface: SymbolList
The number of symbols in this SymbolList.

Specified by:
length in interface SymbolList
Returns:
the length

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 interface SymbolList
Returns:
an iterator

edit

public void edit(Edit edit)
          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:

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 interface SymbolList
Parameters:
edit - the Edit to perform
Throws:
ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed

countFeatures

public int countFeatures()
Description copied from interface: FeatureHolder
Count how many features are contained.

Specified by:
countFeatures in interface FeatureHolder
Returns:
a positive integer or zero, equal to the number of features contained

features

public java.util.Iterator features()
Description copied from interface: FeatureHolder
Iterate over the features in no well defined order.

Specified by:
features in interface FeatureHolder
Returns:
an Iterator

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 interface FeatureHolder
Parameters:
ff - the FeatureFilter to apply
recurse - 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.

filter

public FeatureHolder filter(FeatureFilter ff)
Description copied from interface: FeatureHolder
Query this set of features using a supplied FeatureFilter.

Specified by:
filter in interface FeatureHolder
Parameters:
ff - the FeatureFilter to apply.
Returns:
all features in this container which match filter.

containsFeature

public boolean containsFeature(Feature f)
Description copied from interface: FeatureHolder
Check if the feature is present in this holder.

Specified by:
containsFeature in interface FeatureHolder
Parameters:
f - the Feature to check
Returns:
true if f is in this set

createFeature

public Feature createFeature(Feature.Template templ)
                      throws BioException,
                             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 interface FeatureHolder
Throws:
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 vetoed

removeFeature

public void removeFeature(Feature f)
                   throws ChangeVetoException,
                          BioException
Description copied from interface: FeatureHolder
Remove a feature from this FeatureHolder.

Specified by:
removeFeature in interface FeatureHolder
Throws:
ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed
BioException - if there was an error removing the feature

getSchema

public FeatureFilter getSchema()
Description copied from interface: FeatureHolder
Return a schema-filter for this FeatureHolder. This is a filter which all Features 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)).

Specified by:
getSchema in interface FeatureHolder
Returns:
the schema filter

getFeatures

protected ProjectedFeatureHolder getFeatures()

getName

public java.lang.String getName()
Description copied from interface: Sequence
The name of this sequence.

The name may contain spaces or odd characters.

Specified by:
getName in interface Sequence
Returns:
the name as a String

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 network
 file:///home/thomas/myseq.fa|seq22
 http://www.mysequences.net/chr22.seq
 

Specified by:
getURN in interface Sequence
Returns:
the URI as a String

getAnnotation

public Annotation getAnnotation()
Description copied from interface: Annotatable
Should return the associated annotation object.

Specified by:
getAnnotation in interface Annotatable
Returns:
an Annotation object, never null

getSequence

public Sequence getSequence()
Return the parent sequence of which this is a partial view

Since:
1.3

getStart

public int getStart()

getEnd

public int getEnd()

addChangeListener

public void addChangeListener(ChangeListener cl,
                              ChangeType ct)
Description copied from interface: Changeable
Add a listener that will be informed of changes of a given type.

Specified by:
addChangeListener in interface Changeable
Parameters:
cl - the ChangeListener
ct - the ChangeType it is to be informed of

addChangeListener

public void addChangeListener(ChangeListener cl)
Description copied from interface: Changeable
Add a listener that will be informed of all changes.

Specified by:
addChangeListener in interface Changeable
Parameters:
cl - the ChangeListener to add

removeChangeListener

public void removeChangeListener(ChangeListener cl,
                                 ChangeType ct)
Description copied from interface: Changeable
Remove a listener that was interested in a specific types of changes.

Specified by:
removeChangeListener in interface Changeable
Parameters:
cl - a ChangeListener to remove
ct - the ChangeType that it was interested in

removeChangeListener

public void removeChangeListener(ChangeListener cl)
Description copied from interface: Changeable
Remove a listener that was interested in all types of changes.

Specified by:
removeChangeListener in interface Changeable
Parameters:
cl - a ChangeListener to remove

isUnchanging

public boolean isUnchanging(ChangeType ct)
Description copied from interface: Changeable

A particular ChangeType can never be raised by this Changeable.

If this returns true, then it is guaranteed that change events of this type (and all child types) can never under any circumstances be fired by this Changeable instance. If it returns false, that does not mean that this type of event will or even can be raised, but that it is worth registering listeners incase.

Specified by:
isUnchanging in interface Changeable
Parameters:
ct - the ChangeType to check
Returns:
true if ChangeEvents of this type are guaranteed to never be fired