org.biojava.bio.seq.io

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

public class ProteinRefSeqFileFormer
extends GenbankFileFormer

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 Summary

Constructors

Modifier	Constructor and Description
protected	ProteinRefSeqFileFormer() Deprecated.
protected	ProteinRefSeqFileFormer(PrintStream theStream) Deprecated.

Method Summary

Modifier and Type	Method and Description
void	addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated. Notify the listener of symbol data.
protected List	breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) Deprecated. Converts the symbol list passed in into an array of strings.
String	formatLocation(Feature theFeature) Formats 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 sb, Location loc, StrandedFeature.Strand strand) formatLocation creates an EMBL/Genbank style representation of a Location.
void	startFeature(Feature.Template templ) Deprecated. Notify the listener that a new feature object is starting.

Methods inherited from class org.biojava.bio.seq.io.GenbankFileFormer

addFeatureProperty, addSequenceProperty, endFeature, endSequence, getPrintStream, getVectorNTISupport, setName, setPrintStream, setURI, setVectorNTISupport, startSequence

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.bio.seq.io.SeqFileFormer

formatLocation, formatLocation

Constructor Detail

ProteinRefSeqFileFormer

protected ProteinRefSeqFileFormer()

Deprecated.

ProteinRefSeqFileFormer

protected ProteinRefSeqFileFormer(PrintStream theStream)

Deprecated.

Method Detail

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
  <123 or >123
  (123.567)
  (123.567)..789
   123..(567.789)
  (123.345)..(567.789)
   123..456
  <123..567 or 123..>567 or <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 StringBuffer

loc - a Location to format.

strand - a StrandedFeature.Strand indicating the Location's strand.

Returns:

a StringBuffer.