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## org.biojava.bio.seq
Class SequenceTools

    java.lang.Object
      org.biojava.bio.seq.SequenceTools

    public final class SequenceTools

extends Object

Methods for manipulating sequences.

Author:
  Matthew Pocock

Method Summary
`static void` | `addAllFeatures(Sequence seq, FeatureHolder fh)` Add features to a sequence that contain the same information as all those in a feature holder.
`static Sequence` | `createDummy(Alphabet alpha, int length, Symbol sym, String uri, String name)` Create a new Sequence that contains a single symbol repeated over and over.
`static Sequence` | `createDummy(String uri, String name)` Create a new Sequence that has no annotation, no features and a zero-length symbol list.
`static Sequence` | `createSequence(SymbolList syms, String uri, String name, Annotation ann)`
`static GappedSequence` | `gappedView(Sequence seq)` Create a new gapped sequence for a sequence.
`static Sequence` | `maskSequence(Sequence seq, RangeLocation loc)` Mask of a sequence.
`static Sequence` | `reverseComplement(Sequence seq)` Reverse-complement a sequence, and flip all of its features.
`static Sequence` | `subSequence(Sequence seq, int start, int end)` Extract a sub-sequence from a sequence.
`static Sequence` | `subSequence(Sequence seq, int start, int end, String name)` Extract a sub-sequence from a sequence.
`static Sequence` | `subSequence(Sequence seq, int start, int end, String name, StrandedFeature.Strand strand)` Extract a sub-sequence from a sequence.
`static ViewSequence` | `view(Sequence seq)` Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly.
`static ViewSequence` | `view(Sequence seq, FeatureRealizer fr)` Creates a new Sequence with the data of the old but with a different FeatureRealizer that will be applied to new Features.
`static ViewSequence` | `view(Sequence seq, String name)` Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Method Detail

### createSequence

    public static Sequence createSequence(SymbolList syms,
                                          String uri,
                                          String name,
                                          Annotation ann)

### subSequence

    public static Sequence subSequence(Sequence seq,
                                       int start,
                                       int end)
                                throws IndexOutOfBoundsException

  Extract a sub-sequence from a sequence.

  The sub-sequence will be indexed from 1 through to (end-start+1). An index of i in the sub-sequence corresponds to (i+start-1) in the original. All features from the original sequence will be projected down into this co-ordinate system. All features overlapping the edges will be given fuzzy locations.

  Parameters:
    `seq` - the sequence to sub-sequence
    `start` - the first index to include in the sub-sequence
    `end` - the last index to include in the sub-sequence
  Returns:
    a view Sequence for this region
  Throws:
    `IndexOutOfBoundsException` - if start or end are not in seq, or if end < start

### subSequence

    public static Sequence subSequence(Sequence seq,
                                       int start,
                                       int end,
                                       String name)
                                throws IndexOutOfBoundsException

  Extract a sub-sequence from a sequence.

  The sub-sequence will be indexed from 1 through to (end-start+1). An index of i in the sub-sequence corresponds to (i+start-1) in the original. All features from the original sequence will be projected down into this co-ordinate system. All features overlapping the edges will be given fuzzy locations.

  Parameters:
    `seq` - the sequence to sub-sequence
    `start` - the first index to include in the sub-sequence
    `end` - the last index to include in the sub-sequence
    `name` - a new name to give to this sub-sequence
  Returns:
    a view Sequence for this region
  Throws:
    `IndexOutOfBoundsException` - if start or end are not in seq, or if end < start

### subSequence

    public static Sequence subSequence(Sequence seq,
                                       int start,
                                       int end,
                                       String name,
                                       StrandedFeature.Strand strand)
                                throws IndexOutOfBoundsException,
                                       IllegalAlphabetException

  Extract a sub-sequence from a sequence.

  The sub-sequence will be indexed from 1 through to (end-start+1). If the strand is NEGATIVE, all features will be flipped in the same manner as the reverseComplement method. If it is UNKNOWN or POSITIVE, then this is identical to the other subSequence methods.

  Parameters:
    `seq` - the sequence to sub-sequence
    `start` - the first index to include in the sub-sequence
    `end` - the last index to include in the sub-sequence
    `name` - a new name to give to this sub-sequence
    `strand` - a StrandedFeature.Strand indicating which strand the sub-sequence should be on
  Returns:
    a view Sequence for this region
  Throws:
    `IndexOutOfBoundsException` - if start or end are not in seq, or if end < start
    `IllegalAlphabetException`

### reverseComplement

    public static Sequence reverseComplement(Sequence seq)
                                      throws IllegalAlphabetException

  Reverse-complement a sequence, and flip all of its features.

  Parameters:
    `seq` - the Sequence to reverse-complement
  Returns:
    the flipped Sequence
  Throws:
    `IllegalAlphabetException` - if the symbols in the sequence can not be complemented

### view

    public static ViewSequence view(Sequence seq)

  Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly. Use this as a scratch-space.

  Parameters:
    `seq` - the Sequence to view
  Returns:
    a new ViewSequence

### view

    public static ViewSequence view(Sequence seq,
                                    String name)

  Create a new sequence that has all of the data in the original, but allows new features and top-level annotations to be added independantly. Use this as a scratch-space.

  Parameters:
    `seq` - the Sequence to view
    `name` - a new name for the sequence
  Returns:
    a new ViewSequence with the new name

### view

    public static ViewSequence view(Sequence seq,
                                    FeatureRealizer fr)

  Creates a new Sequence with the data of the old but with a different FeatureRealizer that will be applied to new Features.

  Parameters:
    `seq` - the Sequence to wrap
    `fr` - the new FeatureRealizer
  Returns:
    the new ViewSequence

### gappedView

    public static GappedSequence gappedView(Sequence seq)

  Create a new gapped sequence for a sequence.

  The gapped sequence can be used to insert gaps. The features on the underlying sequence will be projected onto the view taking the gaps into account.

  Parameters:
    `seq` -
  Returns:
    a GappedSequence view of seq

### maskSequence

    public static Sequence maskSequence(Sequence seq,
                                        RangeLocation loc)
                                 throws IndexOutOfBoundsException,
                                        IllegalArgumentException

  Mask of a sequence.

  This will return a view of a sequence where everything outside loc is dropped. This includes all symbols, which become gaps, and all features, which behave in a similar manner to those produced by subSequence().

  Parameters:
    `seq` - the Sequence to mask
    `loc` - the region to retain
  Returns:
    a Sequence viewing just the retained portion of seq
  Throws:
    `IndexOutOfBoundsException` - if loc is not totaly within seq
    `IllegalArgumentException` - fixme: not sure where this comes from

### createDummy

    public static Sequence createDummy(String uri,
                                       String name)

  Create a new Sequence that has no annotation, no features and a zero-length symbol list. Instantiate this if an API requres a sequence, but you can't be bothered or are not able to provide full sequence information. It is sometimes usefull to create a dummy sequence and then wrap this in a view.

  Parameters:
    `uri` - the URI to give the dummy sequence
    `name` - the name of the dummy sequence
  Returns:
    a dummy Sequence

### createDummy

    public static Sequence createDummy(Alphabet alpha,
                                       int length,
                                       Symbol sym,
                                       String uri,
                                       String name)
                                throws IllegalSymbolException

  Create a new Sequence that contains a single symbol repeated over and over.

  Parameters:
    `alpha` - the Alphabet this sequence is over
    `length` - the length of the sequence
    `sym` - the symbol returned by every call to symbolAt
    `uri` - the URI of the sequence
    `name` - the name of the sequence
  Returns:
    a new sequence of the right length
  Throws:
    `IllegalSymbolException` - if sym is not in alpha
  Since:
    1.4

### addAllFeatures

    public static void addAllFeatures(Sequence seq,
                                      FeatureHolder fh)
                               throws ChangeVetoException,
                                      BioException

  Add features to a sequence that contain the same information as all those in a feature holder.

  Parameters:
    `seq` - the Sequence to add features to
    `fh` - the features to add
  Throws:
    `ChangeVetoException` - if the sequence could not be modified
    `BioException` - if there was an error creating the features

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