SimpleSequence (biojava-legacy 1.9.3 API)

java.lang.Object
- org.biojava.utils.AbstractChangeable
- - org.biojava.bio.seq.impl.SimpleSequence

All Implemented Interfaces:

Serializable, Annotatable, FeatureHolder, RealizingFeatureHolder, Sequence, SymbolList, Changeable

Direct Known Subclasses:

PhredSequence, RevCompSequence
```
public class SimpleSequence
extends AbstractChangeable
implements Sequence, RealizingFeatureHolder, Serializable
```
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.
More functionality and better persistence to biosql is offered by SimpleRichSequence

Author:

Matthew Pocock, Thomas Down, Mark Schreiber

See Also:

Serialized Form

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

Field Summary
- Fields inherited from interface org.biojava.bio.symbol.SymbolList
  EDIT, EMPTY_LIST
- Fields inherited from interface org.biojava.bio.Annotatable
  ANNOTATION
- Fields inherited from interface org.biojava.bio.seq.FeatureHolder
  EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Constructor Summary

Constructors
Constructor and Description
`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

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`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<Feature>`	`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
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
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

- Constructor Detail
  - SimpleSequence
```
public SimpleSequence(SymbolList sym,
                      String urn,
                      String name,
                      Annotation annotation)
```
    Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed.
    
    Parameters:
    
    sym - the SymbolList to wrap as a sequence
    
    urn - the URN
    
    name - the name - should be unique if practical
    
    annotation - the annotation object to use or null
  - SimpleSequence
```
public SimpleSequence(SymbolList sym,
                      String urn,
                      String name,
                      Annotation annotation,
                      FeatureRealizer realizer)
```
    Create a SimpleSequence using a specified FeatureRealizer.
    
    Parameters:
    
    sym - the SymbolList to wrap as a sequence
    
    urn - the URN
    
    name - the name - should be unique if practical
    
    annotation - the annotation object to use or null
    
    realizer - the FeatureRealizer implemetation to use when adding features
- Method Detail
  - 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
  - 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 template)
                      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
  - createFeature
```
public Feature createFeature(FeatureHolder fh,
                             Feature.Template template)
                      throws BioException,
                             ChangeVetoException
```
    Deprecated. Please use new 1-arg createFeature instead.
    
    Create a new feature in any FeatureHolder associated with this sequence.
    
    Throws:
    
    BioException
    
    ChangeVetoException
  - 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:
    - 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 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
  - featureHolderAllocated
```
protected boolean featureHolderAllocated()
```
  - features
```
public Iterator<Feature> 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 filter)
```
    Description copied from interface: FeatureHolder
    
    Query this set of features using a supplied FeatureFilter.
    
    Specified by:
    
    filter in interface FeatureHolder
    
    Parameters:
    
    filter - 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.
  - 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
  - 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
  - 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:
```
 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 
```
    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.
    Overrides:
    
    getChangeSupport in class AbstractChangeable
  - getFeatureHolder
```
protected SimpleFeatureHolder getFeatureHolder()
```
  - getName
```
public 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
  - 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
  - getURN
```
public 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
  - iterator
```
public 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
  - realizeFeature
```
public Feature realizeFeature(FeatureHolder parent,
                              Feature.Template template)
                       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
  - removeFeature
```
public void removeFeature(Feature f)
                   throws ChangeVetoException,
                          BioException
```
    Remove a feature attached to this sequence.
    
    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
  - seqString
```
public 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
  - setName
```
public void setName(String name)
```
    Assign a name to this sequence
  - setURN
```
public void setURN(String urn)
```
    Provide the URN for this sequence
  - 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
  - subStr
```
public 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
  - symbolAt
```
public Symbol symbolAt(int index)
```
    Description copied from interface: SymbolList
    
    Return the symbol at index, counting from 1.
    
    Specified by:
    
    symbolAt in interface SymbolList
    
    Parameters:
    
    index - the offset into this SymbolList
    
    Returns:
    
    the Symbol at that index
  - toList
```
public 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
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class SimpleSequence

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

Field Summary

Fields inherited from interface org.biojava.bio.symbol.SymbolList

Fields inherited from interface org.biojava.bio.Annotatable

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

Constructor Summary

Method Summary

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.utils.Changeable

Constructor Detail

SimpleSequence

SimpleSequence

Method Detail

containsFeature

countFeatures

createFeature

createFeature

edit

Description

Examples

featureHolderAllocated

features

filter

filter

getAlphabet

getAnnotation

getChangeSupport

getFeatureHolder

getName

getSchema

getURN

iterator

length

realizeFeature

removeFeature

seqString

setName

setURN

subList

subStr

symbolAt

toList

toString