## org.biojava.bio.program.das
Class DASSequence

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.program.das.DASSequence

All Implemented Interfaces:
  Changeable

    public class DASSequence

extends AbstractChangeable

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/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
`FeatureHolder.EmptyFeatureHolder`

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
`protected ChangeForwarder` `annotationForwarder`
`static ChangeType` `ANNOTATIONS` Change type which indicates that the set of annotation servers used by this DASSequence has been changed.
`static String` `PROPERTY_ANNOTATIONSERVER`
`static String` `PROPERTY_FEATUREID`
`static String` `PROPERTY_FEATURELABEL`
`static String` `PROPERTY_LINKS`
`static 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`

Fields inherited from interface org.biojava.bio.seq.FeatureHolder
`EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA`

Method Summary
`void` `addAnnotationSource(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.
`Set` `dataSourceURLs()`
`void` `edit(Edit e)` Apply an edit to the SymbolList as specified by the edit object.
`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.
`String` `getName()` The name of this sequence.
`DASSequenceDB` `getParentDB()`
`FeatureFilter` `getSchema()` Return a schema-filter for this `FeatureHolder`.
`protected SymbolList` `getSymbols()`
`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 dest, Feature.Template temp)` Realize a feature template.
`void` `removeAnnotationSource(URL dataSourceURL)`
`void` `removeFeature(Feature f)` Remove a feature from this FeatureHolder.
`String` `seqString()` Stringify this symbol list.
`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 pos)` Return the symbol at index, counting from 1.
`List` `toList()` Returns a List of symbols.

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, toString, wait, wait, wait`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

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 String PROPERTY_ANNOTATIONSERVER

See Also:
  Constant Field Values

### PROPERTY_FEATUREID

    public static final String PROPERTY_FEATUREID

See Also:
  Constant Field Values

### PROPERTY_FEATURELABEL

    public static final String PROPERTY_FEATURELABEL

See Also:
  Constant Field Values

### PROPERTY_LINKS

    public static final String PROPERTY_LINKS

See Also:
  Constant Field Values

### PROPERTY_SEQUENCEVERSION

    public static final String PROPERTY_SEQUENCEVERSION

See Also:
  Constant Field Values

### SIZE_THRESHOLD

    public static final int SIZE_THRESHOLD

See Also:
  Constant Field Values

### annotationForwarder

    protected transient ChangeForwarder annotationForwarder

Method Detail

### getParentDB

    public DASSequenceDB getParentDB()

### dataSourceURLs

    public Set dataSourceURLs()

### addAnnotationSource

    public void addAnnotationSource(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.

  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`

### removeAnnotationSource

    public void removeAnnotationSource(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.

  Returns:
    the alphabet

### 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.

  Returns:
    an iterator

### length

    public int length()

  Description copied from interface: `SymbolList`
  The number of symbols in this SymbolList.

  Returns:
    the length

### 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.

  Returns:
    a string representation of the symbol list

### 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.

  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.

  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.

  Parameters:
    `pos` - 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.

  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:

  - 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());

  `

  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 String getName()

  Description copied from interface: `Sequence`
  The name of this sequence.

  The name may contain spaces or odd characters.

  Returns:
    the name as a String

### 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

  Returns:
    the URI as a String

### features

    public Iterator features()

  Description copied from interface: `FeatureHolder`
  Iterate over the features in no well defined order.

  Returns:
    an Iterator

### containsFeature

    public boolean containsFeature(Feature f)

  Description copied from interface: `FeatureHolder`
  Check if the feature is present in this holder.

  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`.

  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.

  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 `Feature`s 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))`.

  Returns:
    the schema filter

### countFeatures

    public int countFeatures()

  Description copied from interface: `FeatureHolder`
  Count how many features are contained.

  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.

  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.

  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.

  Throws:
    `BioException`

### getAnnotation

    public Annotation getAnnotation()

  Description copied from interface: `Annotatable`
  Should return the associated annotation object.

  Returns:
    an Annotation object, never null