Package org.biojava.bio.seq.impl

Class SimpleSequence

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:

  • Constructor Details

    • 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 Details

    • 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