Class GenbankFileFormer

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

    • 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 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) throws ParseException
      Deprecated.
      Description copied from interface: SeqIOListener
      Notify the listener of a feature property.
      Specified by:
      addFeatureProperty 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
        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.