org.biojava.bio.program.das
Class DASSequence

java.lang.Object
  extended byorg.biojava.utils.AbstractChangeable
      extended byorg.biojava.bio.program.das.DASSequence
All Implemented Interfaces:
Annotatable, Changeable, org.biojava.bio.program.das.DASSequenceI, FeatureHolder, RealizingFeatureHolder, Sequence, SymbolList

public class DASSequence
extends AbstractChangeable
implements org.biojava.bio.program.das.DASSequenceI

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

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.symbol.SymbolList
SymbolList.EmptySymbolList
 
Nested classes inherited from class org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
 
Nested classes inherited from class org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
protected  Annotatable.AnnotationForwarder 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
           
 
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
 
Method Summary
 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 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
 java.lang.String getName()
          The name of this sequence.
 DASSequenceDB getParentDB()
           
 FeatureFilter getSchema()
          Return a schema-filter for this FeatureHolder.
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, isUnchanging, removeChangeListener, removeChangeListener
 
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
 

Field Detail

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.


PROPERTY_ANNOTATIONSERVER

public static final java.lang.String PROPERTY_ANNOTATIONSERVER
See Also:
Constant Field Values

PROPERTY_FEATUREID

public static final java.lang.String PROPERTY_FEATUREID
See Also:
Constant Field Values

PROPERTY_FEATURELABEL

public static final java.lang.String PROPERTY_FEATURELABEL
See Also:
Constant Field Values

PROPERTY_LINKS

public static final java.lang.String PROPERTY_LINKS
See Also:
Constant Field Values

PROPERTY_SEQUENCEVERSION

public static final java.lang.String PROPERTY_SEQUENCEVERSION
See Also:
Constant Field Values

SIZE_THRESHOLD

public static final int SIZE_THRESHOLD
See Also:
Constant Field Values

annotationForwarder

protected transient Annotatable.AnnotationForwarder annotationForwarder
Method Detail

getParentDB

public DASSequenceDB getParentDB()
Specified by:
getParentDB in interface org.biojava.bio.program.das.DASSequenceI

dataSourceURLs

public java.util.Set dataSourceURLs()

addAnnotationSource

public void addAnnotationSource(java.net.URL dataSourceURL)
                         throws BioException,
                                ChangeVetoException
Throws:
BioException
ChangeVetoException

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)
Description copied from class: AbstractChangeable
Called to retrieve the ChangeSupport for this object

Overrides:
getChangeSupport in class AbstractChangeable

removeAnnotationSource

public void removeAnnotationSource(java.net.URL dataSourceURL)
                            throws ChangeVetoException,
                                   BioException
Throws:
ChangeVetoException
BioException

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

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

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

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

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

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

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

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:

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

getSymbols

protected SymbolList getSymbols()
                         throws BioException
Throws:
BioException

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

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

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

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.

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.

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

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

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 interface FeatureHolder
Throws:
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
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

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 the createFeature method of either this FeatureHolder or one of our child Features.

Specified by:
realizeFeature in interface RealizingFeatureHolder
Throws:
BioException

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