Package org.biojava.bio.seq.io

Class SwissprotFileFormer

    • Constructor Detail

      • 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 Detail

      • 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

      • getPrintStream

        public PrintStream 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.

      • 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:
        theMaxIndex - Inner index of the fuzzy point
        theMinIndex - Outer 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.