org.biojava.bridge.Biocorba.Seqcore
Class SeqImpl

java.lang.Object
  |
  +--org.biojava.bridge.GNOME.UnknownImpl
        |
        +--org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl
              |
              +--org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl
                    |
                    +--org.biojava.bridge.Biocorba.Seqcore.SeqImpl

public class SeqImpl
extends PrimarySeqImpl
implements _Seq_Operations


Constructor Summary
SeqImpl(Sequence sequence)
           
SeqImpl(Sequence sequence, java.lang.String id)
           
SeqImpl(Sequence sequence, java.lang.String displayID, java.lang.String primaryID, java.lang.String accessionNumber)
           
 
Method Summary
 SeqFeatureIterator all_features_iterator(org.omg.CORBA.portable.ObjectImpl seq)
           
 SeqFeature[] all_features(org.omg.CORBA.portable.ObjectImpl seq)
           
 SeqFeatureIterator features_region_iterator(org.omg.CORBA.portable.ObjectImpl seq, int start, int end)
           
 SeqFeature[] features_region(org.omg.CORBA.portable.ObjectImpl seq, int start, int end)
           
 PrimarySeq get_PrimarySeq(org.omg.CORBA.portable.ObjectImpl seq)
           
 Sequence getSequence()
           
 int max_feature_request(org.omg.CORBA.portable.ObjectImpl seq)
           
 
Methods inherited from class org.biojava.bridge.Biocorba.Seqcore.PrimarySeqImpl
accession_number, display_id, primary_id, version
 
Methods inherited from class org.biojava.bridge.Biocorba.Seqcore.AnonymousSeqImpl
get_seq, get_subseq, getSymbolList, length, max_request_length, type
 
Methods inherited from class org.biojava.bridge.GNOME.UnknownImpl
query_interface, ref, unref
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SeqImpl

public SeqImpl(Sequence sequence)
        throws IllegalAlphabetException

SeqImpl

public SeqImpl(Sequence sequence,
               java.lang.String id)
        throws IllegalAlphabetException

SeqImpl

public SeqImpl(Sequence sequence,
               java.lang.String displayID,
               java.lang.String primaryID,
               java.lang.String accessionNumber)
        throws IllegalAlphabetException
Method Detail

getSequence

public Sequence getSequence()

all_features

public SeqFeature[] all_features(org.omg.CORBA.portable.ObjectImpl seq)
                          throws RequestTooLarge
Specified by:
all_features in interface _Seq_Operations

all_features_iterator

public SeqFeatureIterator all_features_iterator(org.omg.CORBA.portable.ObjectImpl seq)
Specified by:
all_features_iterator in interface _Seq_Operations

features_region

public SeqFeature[] features_region(org.omg.CORBA.portable.ObjectImpl seq,
                                    int start,
                                    int end)
                             throws OutOfRange,
                                    UnableToProcess,
                                    RequestTooLarge
Specified by:
features_region in interface _Seq_Operations

features_region_iterator

public SeqFeatureIterator features_region_iterator(org.omg.CORBA.portable.ObjectImpl seq,
                                                   int start,
                                                   int end)
                                            throws OutOfRange,
                                                   UnableToProcess
Specified by:
features_region_iterator in interface _Seq_Operations

max_feature_request

public int max_feature_request(org.omg.CORBA.portable.ObjectImpl seq)
Specified by:
max_feature_request in interface _Seq_Operations

get_PrimarySeq

public PrimarySeq get_PrimarySeq(org.omg.CORBA.portable.ObjectImpl seq)
Specified by:
get_PrimarySeq in interface _Seq_Operations