Class EmblFileFormer

java.lang.Object
org.biojava.bio.seq.io.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 Details

    • 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 Details

    • 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.
    • setPrintStream

      public void setPrintStream(PrintStream stream)
      Deprecated.
      Description copied from interface: SeqFileFormer
      setPrintStream informs an instance which PrintStream to use.
      Specified by:
      setPrintStream in interface SeqFileFormer
      Parameters:
      stream - a PrintStream to write 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
    • startSequence

      public void startSequence() throws ParseException
      Deprecated.
      Description copied from interface: SeqIOListener
      Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.
      Specified by:
      startSequence in interface SeqIOListener
      Throws:
      ParseException
    • endSequence

      public void endSequence() throws ParseException
      Deprecated.
      Description copied from interface: SeqIOListener
      Notify the listener that processing of the sequence is complete.
      Specified by:
      endSequence in interface SeqIOListener
      Throws:
      ParseException
    • setURI

      public void setURI(String uri) throws ParseException
      Deprecated.
      Description copied from interface: SeqIOListener
      Notify the listener of a URI identifying the current sequence.
      Specified by:
      setURI in interface SeqIOListener
      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.
    • addSequenceProperty

      public void addSequenceProperty(Object key, Object value) throws ParseException
      Deprecated.
      Description copied from interface: SeqIOListener
      Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.
      Specified by:
      addSequenceProperty in interface SeqIOListener
      Throws:
      ParseException
    • 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
    • endFeature

      public void endFeature() throws ParseException
      Deprecated.
      Description copied from interface: SeqIOListener
      Mark the end of data associated with one specific feature.
      Specified by:
      endFeature in interface SeqIOListener
      Throws:
      ParseException
    • addFeatureProperty

      public void addFeatureProperty(Object key, Object value)
      Deprecated.
      Description copied from interface: SeqIOListener
      Notify the listener of a feature property.
      Specified by:
      addFeatureProperty in interface SeqIOListener
    • 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
        invalid input: '<'123 or >123
        (123.567)
        (123.567)..789
         123..(567.789)
        (123.345)..(567.789)
         123..456
        invalid input: '<'123..567 or 123..>567 or invalid input: '<'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 StringBufferinvalid input: '<'/code to which the location will be appended.
      loc - a Location to format.
      strand - a StrandedFeature.Strand indicating the Location's strand.
      Returns:
      a StringBuffer.