org.biojava.bio.seq.io

Class SwissprotFileFormer

java.lang.Object

org.biojava.bio.seq.io.SwissprotFileFormer

All Implemented Interfaces:

SeqFileFormer, SeqIOListener

Deprecated.

Use org.biojavax.bio.seq.io framework instead

public class SwissprotFileFormer
extends Object
implements SeqFileFormer

Formats a sequence into Swissprot/TrEMBL format. Modeled after EmblFileFormer.

Since:

1.2

Author:

Greg Cox

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SwissprotFileFormer() Deprecated. Creates a new SwissprotFileFormer using System.out stream.
protected	SwissprotFileFormer(PrintStream theStream) Deprecated. Creates a new SwissprotFileFormer using the specified stream.

Method Summary

Methods

Modifier and Type	Method and Description
void	addFeatureProperty(Object key, Object value) Deprecated. Null implementation
void	addSequenceProperty(Object key, Object value) Deprecated. Notify the listener of a sequence-wide property.
void	addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated. Prints out the sequences properties in order.
protected List	breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated. Converts the symbol list passed in into an array of strings.
void	endFeature() Deprecated. Null implementation.
void	endSequence() Deprecated. Notify the listener that processing of the sequence is complete.
protected void	fillBuffer(StringBuffer theBuffer, int theLength) Deprecated. Simple method that adds spaces onto the buffer passed in.
String	formatLocation(Feature theFeature) Deprecated. Creates a string representation of the location of a feature
String	formatLocation(Location loc, StrandedFeature.Strand strand) formatLocation creates an EMBL/Genbank style representation of a Location.
StringBuffer	formatLocation(StringBuffer theBuffer, Location theLocation) Deprecated. formatLocation creates a String representation of a Location.
StringBuffer	formatLocation(StringBuffer theBuffer, Location theLocation, StrandedFeature.Strand theStrand) Deprecated. formatLocation creates a String representation of a Location.
protected StringBuffer	formatPoint(int theMinIndex, int theMaxIndex, boolean isFuzzy) Deprecated. Formats the points from fuzzy locations.
PrintStream	getPrintStream() Deprecated. getPrintStream returns the PrintStream to which an instance of SwissprotFileFormer will write the formatted data.
protected void	printOutSequenceHeaderLine(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated. Prints out sequence header with only length data.
void	setName(String theName) Deprecated. The name is printed out as part of the identifier line.
void	setPrintStream(PrintStream theStream) Deprecated. setPrintStream informs an instance which PrintStream to use.
void	setURI(String theURI) Deprecated. Null implementation.
void	startFeature(Feature.Template templ) Deprecated. Null implementation.
void	startSequence() Deprecated. Start the processing of a sequence.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

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

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.

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:

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.