org.biojava.bridge.Biocorba.Seqcore
Class SequenceAdapter

java.lang.Object
  |
  +--org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
        |
        +--org.biojava.bridge.Biocorba.Seqcore.SequenceAdapter

public class SequenceAdapter
extends SymbolListAdapter
implements Sequence


Inner classes inherited from class org.biojava.bio.symbol.SymbolList
SymbolList.EmptySymbolList
 
Inner classes inherited from class org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
 
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EMPTY_LIST
 
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER
 
Constructor Summary
SequenceAdapter(PrimarySeq primarySeq)
           
 
Method Summary
 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)
           
 java.util.Iterator features()
          Iterate over the features in no well defined order.
 FeatureHolder filter(FeatureFilter fc, boolean recurse)
          Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
 Annotation getAnnotation()
          Should return the associated annotation object.
 java.lang.String getName()
          The name of this sequence.
 PrimarySeq getPrimarySeq()
           
 Seq getSeq()
           
 java.lang.String getURN()
          The URN for this sequence.
 void removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 
Methods inherited from class org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
getAlphabet, getAnonymousSeq, iterator, length, seqString, subList, subStr, symbolAt, toList
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SequenceAdapter

public SequenceAdapter(PrimarySeq primarySeq)
                throws IllegalAlphabetException,
                       IllegalSymbolException,
                       BioException
Method Detail

getPrimarySeq

public PrimarySeq getPrimarySeq()

getSeq

public Seq getSeq()

createFeature

public Feature createFeature(FeatureHolder fh,
                             Feature.Template template)
                      throws java.lang.UnsupportedOperationException

createFeature

public Feature createFeature(Feature.Template template)
                      throws java.lang.UnsupportedOperationException
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.
Tags copied from interface: FeatureHolder
Throws:
java.lang.UnsupportedOperationException - if this FeatureHolder does not support addition of new features.

removeFeature

public void removeFeature(Feature f)
Description copied from interface: FeatureHolder
Remove a feature from this FeatureHolder.
Tags copied from interface: FeatureHolder
Throws:
java.lang.UnsupportedOperationException - if this FeatureHolder does not support feature removal.

getName

public java.lang.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
Tags copied from interface: Sequence
Returns:
the name as a String

getURN

public java.lang.String getURN()
Description copied from interface: Sequence
The URN for this sequence. This will be something like urn:sequence/embl:U32766 or urn:sequence/fasta:sequences.fasta|hox3.
Specified by:
getURN in interface Sequence
Tags copied from interface: Sequence
Returns:
the urn as a String

countFeatures

public int countFeatures()
Description copied from interface: FeatureHolder
Count how many features are contained.
Tags copied from interface: FeatureHolder
Returns:
a positive integer or zero, equal to the number of features contained

features

public java.util.Iterator features()
Description copied from interface: FeatureHolder
Iterate over the features in no well defined order.
Tags copied from interface: FeatureHolder
Returns:
an Iterator

filter

public FeatureHolder filter(FeatureFilter fc,
                            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.
Tags copied from interface: FeatureHolder
Parameters:
fc - 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.

getAnnotation

public Annotation getAnnotation()
Description copied from interface: Annotatable
Should return the associated annotation object.
Tags copied from interface: Annotatable
Returns:
an Annotation object, never null