Package org.biojava.bio.seq.io

Class EmblFileFormer

  • All Implemented Interfaces:
    SeqFileFormer, SeqIOListener
    public class EmblFileFormer
extends Object
implements SeqFileFormer
    Deprecated.
    Use org.biojavax.bio.seq.io framework instead

    EmblFileFormer performs the detailed formatting of EMBL entries for writing to a PrintStream. Currently the formatting of the header is not correct. This really needs to be addressed in the parser which is merging fields which should remain separate.

    The event generator used to feed events to this class should enforce ordering of those events. This class will stream data directly to the PrintStream

    .

    This implementation requires that all the symbols be added in one block as is does not buffer the tokenized symbols between calls.

    Since:
    1.2
    Author:
    Keith James, Len Trigg (Taxon output), Lorna Morris

    • Constructor Detail

      • EmblFileFormer

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

      • EmblFileFormer

        protected EmblFileFormer​(PrintStream stream)
        Deprecated.
        Creates a new EmblFileFormer 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

      • 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.