Class SwissprotFileFormer

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

public class SwissprotFileFormer extends Object implements SeqFileFormer
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Formats a sequence into Swissprot/TrEMBL format. Modeled after EmblFileFormer.
Since:
1.2
Author:
Greg Cox
  • Constructor Details

    • SwissprotFileFormer

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

      protected SwissprotFileFormer(PrintStream theStream)
      Deprecated.
      Creates a new SwissprotFileFormer using the specified stream.
      Parameters:
      theStream - a PrintStream object.
  • Method Details

    • startSequence

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

      public void setName(String theName) throws ParseException
      Deprecated.
      The name is printed out as part of the identifier line. It will be replaced if an ID keyword exists in the annotations.
      Specified by:
      setName in interface SeqIOListener
      Parameters:
      theName - the String that should be returned by getName for the sequence being parsed
      Throws:
      ParseException
    • setURI

      public void setURI(String theURI) throws ParseException
      Deprecated.
      Null implementation. This object formats and prints a sequence. The URI alone cannot be printed in Swissprot format. Therefore, it's easiest to ignore it.
      Specified by:
      setURI in interface SeqIOListener
      Parameters:
      theURI - the new URI of the sequence
      Throws:
      ParseException
    • addSymbols

      public void addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) throws IllegalAlphabetException
      Deprecated.
      Prints out the sequences properties in order. Prints out the symbol array passed in in lines of 60, blocks of 10
      Specified by:
      addSymbols in interface SeqIOListener
      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.
    • addSequenceProperty

      public void addSequenceProperty(Object key, Object value) throws ParseException
      Deprecated.
      Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle. Checks for possible known properties to be shown in the file.
      Specified by:
      addSequenceProperty in interface SeqIOListener
      Parameters:
      key - Key the property will be stored under
      value - Value stored under the key
      Throws:
      ParseException
    • startFeature

      public void startFeature(Feature.Template templ) throws ParseException
      Deprecated.
      Null implementation.
      Specified by:
      startFeature in interface SeqIOListener
      Parameters:
      templ - The template for this new feature object
      Throws:
      ParseException
    • endFeature

      public void endFeature() throws ParseException
      Deprecated.
      Null implementation.
      Specified by:
      endFeature in interface SeqIOListener
      Throws:
      ParseException
    • addFeatureProperty

      public void addFeatureProperty(Object key, Object value) throws ParseException
      Deprecated.
      Null implementation
      Specified by:
      addFeatureProperty in interface SeqIOListener
      Parameters:
      key - Key the property will be stored under
      value - Value stored under the key
      Throws:
      ParseException
    • getPrintStream

      Deprecated.
      getPrintStream returns the PrintStream to which an instance of SwissprotFileFormer will write the formatted data. The default is System.out
      Specified by:
      getPrintStream in interface SeqFileFormer
      Returns:
      the PrintStream which will be written to.
    • setPrintStream

      public void setPrintStream(PrintStream theStream)
      Deprecated.
      setPrintStream informs an instance which PrintStream to use.
      Specified by:
      setPrintStream in interface SeqFileFormer
      Parameters:
      theStream - a PrintStream to write to.
    • formatLocation

      public StringBuffer formatLocation(StringBuffer theBuffer, Location theLocation, StrandedFeature.Strand theStrand)
      Deprecated.
      formatLocation creates a String representation of a Location. Strand information is ignored, as Swissprot files represent proteins. An alternative form of this function does not take a Strand; that form is available only on SwissprotFileFormer; it is not part of the SeqFileFormer interface.
      Specified by:
      formatLocation in interface SeqFileFormer
      Parameters:
      theBuffer - a StringBuffer to append the location to.
      theLocation - a Location to format.
      theStrand - a StrandedFeature.Strand indicating nothing of relevance
      Returns:
      a StringBuffer with the location appended.
    • formatLocation

      public String formatLocation(Feature theFeature)
      Deprecated.
      Creates a string representation of the location of a feature
      Specified by:
      formatLocation in interface SeqFileFormer
      Parameters:
      theFeature - The feature with the location to format
      Returns:
      String The formatted location
    • formatLocation

      public StringBuffer formatLocation(StringBuffer theBuffer, Location theLocation)
      Deprecated.
      formatLocation creates a String representation of a Location. The stringbuffer returned represents columns 15-27 of the Swissprot feature table entry. An alternative form of this function takes a Strand; that form is part of the SeqFileFormer interface.
      Parameters:
      theBuffer - a StringBuffer to append the location to.
      theLocation - a Location to format.
      Returns:
      a StringBuffer with the location appended.
    • printOutSequenceHeaderLine

      protected void printOutSequenceHeaderLine(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) throws IllegalAlphabetException
      Deprecated.
      Prints out sequence header with only length data.
      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.
    • 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.
    • fillBuffer

      protected void fillBuffer(StringBuffer theBuffer, int theLength)
      Deprecated.
      Simple method that adds spaces onto the buffer passed in. This method exists to refactor some code used in location formatting. It isn't intended to be generally used.
      Parameters:
      theBuffer - Buffer to append whitespace to.
      theLength - Ammount of whitespace to append.
    • formatPoint

      protected StringBuffer formatPoint(int theMinIndex, int theMaxIndex, boolean isFuzzy)
      Deprecated.
      Formats the points from fuzzy locations. This is called easily with this.formatPoint(FuzzyLocation.getInnerMax(), FuzzyLocation.getOuterMax(), FuzzyLocation.isFuzzyMax())
      Parameters:
      theMinIndex - Outer index of the fuzzy point
      theMaxIndex - Inner index of the fuzzy point
      isFuzzy - Indicates if this point is fuzzy
    • 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.