Package org.biojava.bio.seq.io

Class GenbankFileFormer

  • All Implemented Interfaces:
    SeqFileFormer, SeqIOListener
    Direct Known Subclasses:
    ProteinRefSeqFileFormer
    public class GenbankFileFormer
extends Object
implements SeqFileFormer
    Deprecated.
    Use org.biojavax.bio.seq.io framework instead
    GenbankFileFormer performs the detailed formatting of Genbank entries for writing to a PrintStream. There is some code dupication with EmblFileFormer which could be factored out.
    Since:
    1.2
    Author:
    Keith James

    • Constructor Detail

      • GenbankFileFormer

        protected GenbankFileFormer()
        Deprecated.
        Creates a new GenbankFileFormer using System.out stream.

      • GenbankFileFormer

        protected GenbankFileFormer​(PrintStream stream)
        Deprecated.
        Creates a new GenbankFileFormer using the specified stream.
        Parameters:
        stream - a PrintStream.

    • Method Detail

      • getPrintStream

        public PrintStream getPrintStream()
        Deprecated.
        Description copied from interface: SeqFileFormer
        getPrintStream returns the PrintStream to which an instance will write the formatted data. If this has not been set, an implementation should default to System.out.
        Specified by:
        getPrintStream in interface SeqFileFormer
        Returns:
        the PrintStream which will be written to.

      • setName

        public void setName​(String id)
             throws ParseException
        Deprecated.
        Description copied from interface: SeqIOListener
        Notify the listener that the current sequence is generally known by a particular name.
        Specified by:
        setName in interface SeqIOListener
        Parameters:
        id - the String that should be returned by getName for the sequence being parsed
        Throws:
        ParseException

      • addSymbols

        public void addSymbols​(Alphabet alpha,
                       Symbol[] syms,
                       int start,
                       int length)
                throws IllegalAlphabetException
        Deprecated.
        Description copied from interface: SeqIOListener
        Notify the listener of symbol data. All symbols passed to this method are guarenteed to be contained within the specified alphabet. Generally all calls to a given Listener should have the same alphabet -- if not, the listener implementation is likely to throw an exception
        Specified by:
        addSymbols in interface SeqIOListener
        Parameters:
        alpha - The alphabet of the symbol data
        syms - An array containing symbols
        start - The start offset of valid data within the array
        length - The number of valid symbols in the array
        Throws:
        IllegalAlphabetException - if we can't cope with this alphabet.

      • startFeature

        public void startFeature​(Feature.Template templ)
                  throws ParseException
        Deprecated.
        Description copied from interface: SeqIOListener
        Notify the listener that a new feature object is starting. Every call to startFeature should have a corresponding call to endFeature. If the listener is concerned with a hierarchy of features, it should maintain a stack of `open' features.
        Specified by:
        startFeature in interface SeqIOListener
        Throws:
        ParseException

      • setVectorNTISupport

        public void setVectorNTISupport​(boolean b)
        Deprecated.
        VectorNTI requires GenBank format to be a little more specific than required by the GenBank definition. By setting this to true the produced output should be parsable by VectorNTI. By default this is false.
        Parameters:
        b - to support or not to support.

      • getVectorNTISupport

        public boolean getVectorNTISupport()
        Deprecated.
        Is VectorNTI compatable output being produced?
        Returns:
        false by default.

      • formatLocation

        public String formatLocation​(Feature theFeature)
        Formats the location of a feature. This version is required when formatting remote locations, since the location field of a remote feature is the projection of that feature on the sequence. When a distinction is made between 'order' and 'join' this method will likely be extended for that also.
        Parameters:
        theFeature - The feature with the location to format
        Returns:
        String The formatted location

      • formatLocation

        public String formatLocation​(Location loc,
                             StrandedFeature.Strand strand)
        formatLocation creates an EMBL/Genbank style representation of a Location. This is a convenience method only. The version which has a StringBuffer parameter (and returns the StringBuffer) is preferred. If a compound location is formatted using this method, it is returned as a join-type location rather than an order-type.
        Parameters:
        loc - a Location to format.
        strand - a StrandedFeature.Strand indicating the Location's strand.
        Returns:
        a StringBuffer.

      • formatLocation

        public StringBuffer formatLocation​(StringBuffer sb,
                                   Location loc,
                                   StrandedFeature.Strand strand)
        formatLocation creates an EMBL/Genbank style representation of a Location. Supported location forms: 
           123
  <123 or >123
  (123.567)
  (123.567)..789
   123..(567.789)
  (123.345)..(567.789)
   123..456
  <123..567 or 123..>567 or <123..>567
   123^567
   AL123465:(123..567)
        If a compound location is formatted using this method, it is returned as a join-type location rather than an order-type. To preserve the join/order distinction; and to format locations like AL123465:(123..567), use the formatLocation(Feature) method.
        Parameters:
        sb - a StringBuffer
        loc - a Location to format.
        strand - a StrandedFeature.Strand indicating the Location's strand.
        Returns:
        a StringBuffer.