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## org.biojava.bio.seq.impl
Class SubSequence

    java.lang.Object
      org.biojava.bio.seq.impl.SubSequence

All Implemented Interfaces:
  Serializable, Annotatable, FeatureHolder, Sequence, SymbolList, Changeable

    public class SubSequence

extends Object
implements Sequence, 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, 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.
`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()`
`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()`
`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.
`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.
`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 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,
                       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:
    `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:
    `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 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 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 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 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:

  - 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

### 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 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 `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))`.

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

### getFeatures

    protected ProjectedFeatureHolder getFeatures()

### 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

### 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

### 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

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