Class ProteinRefSeqFileFormer

java.lang.Object
org.biojava.bio.seq.io.GenbankFileFormer
org.biojava.bio.seq.io.ProteinRefSeqFileFormer
All Implemented Interfaces:
SeqFileFormer, SeqIOListener

Deprecated.
Use org.biojavax.bio.seq.io framework instead
This class performs the detailed formatting of refseq protein entries. Functionality is essentially identical to GenbankFileFormer except that SimpleFeatures are created intead of StrandedFeatures
Author:
Greg Cox
  • Constructor Details

  • Method Details

    • addSymbols

      public void addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) 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
      Overrides:
      addSymbols in class GenbankFileFormer
      Parameters:
      theAlphabet - The alphabet of the symbol data
      theSymbols - An array containing symbols
      theStart - The start offset of valid data within the array
      theLength - 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
      Overrides:
      startFeature in class GenbankFileFormer
      Throws:
      ParseException
    • breakSymbolArray

      protected List breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) throws IllegalAlphabetException
      Deprecated.
      Converts the symbol list passed in into an array of strings. The strings will be blocks of ten, with six blocks on a line.
      Parameters:
      theAlphabet - The alphabet of the symbol data
      theSymbols - An array containing symbols
      theStart - The start offset of valid data within the array
      theLength - The number of valid symbols in the array
      Returns:
      The symbol list passed in broken into blocks of ten characters, six to a string.
      Throws:
      IllegalAlphabetException - if we can't cope with this alphabet.
    • 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.