Package org.biojavax.bio.db.ncbi

Class GenbankRichSequenceDB

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojavax.bio.db.AbstractBioEntryDB
org.biojavax.bio.db.AbstractRichSequenceDB
org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
All Implemented Interfaces:
SequenceDB, SequenceDBLite, Changeable, BioEntryDB, BioEntryDBLite, RichSequenceDB, RichSequenceDBLite
public class GenbankRichSequenceDB extends AbstractRichSequenceDB implements RichSequenceDBLite
This class contains functions accessing DNA sequences in Genbank format. It adds methods to return RichSequences instead of plain Sequences.
Since:
1.5
Author:
Lei Lai, Matthew Pocock, Laurent Jourdren, Shuvankar Mukherjee, Mark Schreiber, Richard Holland

  • Field Details

  • Constructor Details

    • GenbankRichSequenceDB

      public GenbankRichSequenceDB()
      The default constructor delegates to the parent class. The constructor refers to RichObjectFactory.getDefaultNamespace() so make sure your factory is initialised before calling this constructor. Sets the default factory to THRESHOLD.

  • Method Details

    • getAddress

      protected URL getAddress(String id) throws MalformedURLException
      Get the URL object for locating sequence object using eutils. The default value of the return format of the sequence object is text.
      Throws:
      MalformedURLException

    • makeBatchRequest

      protected String makeBatchRequest(URL url, Set list)
      Create the Http Post Request to fetch (in batch mode) a list of sequence with Genbank.
      Parameters:
      url - URL of the request
      list - List of sequence identifier
      Returns:
      The Post request.

    • getRichSequence

      public RichSequence getRichSequence(String id) throws BioException, IllegalIDException
      Given the appropriate Genbank ID, return the matching RichSequence object.
      Specified by:
      getRichSequence in interface RichSequenceDBLite
      Parameters:
      id - the Genbank ID to retrieve.
      Returns:
      the matching RichSequence object, or null if not found.
      Throws:
      Exception - if the sequence could not be retrieved for reasons other than the identifier not being found.
      IllegalIDException - if the database doesn't know about the id
      BioException

    • getRichSequence

      public RichSequence getRichSequence(String id, Namespace nsp) throws BioException, IllegalIDException
      Given the appropriate Genbank ID, return the matching RichSequence object. Additionally define a new Namespace for the received RichSequence object.
      Parameters:
      id - the Genbank ID to retrieve.
      nsp - the Namespace to define.
      Returns:
      the matching RichSequence object, or null if not found.
      Throws:
      Exception - if the sequence could not be retrieved for reasons other than the identifier not being found.
      BioException
      IllegalIDException

    • getRichSequences

      public RichSequenceDB getRichSequences(Set list) throws BioException, IllegalIDException
      Retrieve rich sequences from a Genbank
      Specified by:
      getRichSequences in interface RichSequenceDBLite
      Parameters:
      list - List of NCBI sequence number (GI), accession, accession.version, fasta or seqid.
      Returns:
      The rich database object (HashSequenceDB) with downloaded rich sequences. You will need to cast the sequences you get from this database object into RichSequence objects if you want to access their full features.
      Throws:
      IllegalIDException - if the database doesn't know about the id
      BioException

    • getRichSequences

      public RichSequenceDB getRichSequences(Set list, RichSequenceDB database) throws BioException, IllegalIDException
      Retrieve rich sequences from a Genbank
      Specified by:
      getRichSequences in interface RichSequenceDBLite
      Parameters:
      list - List of NCBI sequence number (GI), accession, accession.version, fasta or seqid.
      database - Where to store rich sequences. If database is null, use an HashSequenceDB Object.
      Returns:
      The database object with downloaded rich sequences. You will need to cast the sequences you get from this database object into RichSequence objects if you want to access their full features.
      Throws:
      IllegalIDException - if the database doesn't know about the id
      BioException

    • getName

      public String getName()
      Description copied from interface: BioEntryDBLite
      Get the name of this sequence database.
      Specified by:
      getName in interface BioEntryDBLite
      Specified by:
      getName in interface SequenceDBLite
      Returns:
      the name of the sequence database, which may be null.

    • ids

      public Set ids()
      Description copied from interface: SequenceDB
      Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.
      Specified by:
      ids in interface BioEntryDB
      Specified by:
      ids in interface SequenceDB
      Returns:
      a Set of ids - at the moment, strings

    • getFactory

      public RichSequenceBuilderFactory getFactory()
      Getter for property factory.
      Returns:
      Value of property factory.

    • setFactory

      public void setFactory(RichSequenceBuilderFactory factory)
      Setter for property factory.
      Parameters:
      factory - New value of property factory.

    • getNamespace

      public Namespace getNamespace()
      Getter for property namespace.
      Returns:
      Value of property namespace.

    • setNamespace

      public void setNamespace(Namespace namespace)
      Setter for property namespace.
      Parameters:
      namespace - New value of property namespace.

    • setTool

      public void setTool(String tool)
      Set the tool identifier for Entrez. Defaults to 'biojavax'.
      Parameters:
      tool - the new identifier.

    • getTool

      public String getTool()
      Get the tool identifier for Entrez. Defaults to 'biojavax'.
      Returns:
      the identifier.

    • setEmail

      public void setEmail(String email)
      Set the email for Entrez. Defaults to 'anonymous@biojava.org'.
      Parameters:
      email - the new email.

    • getEmail

      public String getEmail()
      Get the email for Entrez. Defaults to 'anonymous@biojava.org'.
      Returns:
      the email.