|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava.bio.seq.io.GenbankFileFormer
org.biojava.bio.seq.io.ProteinRefSeqFileFormer
public class ProteinRefSeqFileFormer
This class performs the detailed formatting of refseq protein entries. Functionality is essentially identical to GenbankFileFormer except that SimpleFeatures are created intead of StrandedFeatures
Constructor Summary | |
---|---|
protected |
ProteinRefSeqFileFormer()
Deprecated. |
protected |
ProteinRefSeqFileFormer(PrintStream theStream)
Deprecated. |
Method Summary | |
---|---|
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 |
---|
protected ProteinRefSeqFileFormer()
protected ProteinRefSeqFileFormer(PrintStream theStream)
Method Detail |
---|
public void addSymbols(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) throws IllegalAlphabetException
SeqIOListener
addSymbols
in interface SeqIOListener
addSymbols
in class GenbankFileFormer
theAlphabet
- The alphabet of the symbol datatheSymbols
- An array containing symbolstheStart
- The start offset of valid data within the arraytheLength
- The number of valid symbols in the array
IllegalAlphabetException
- if we can't cope with this
alphabet.public void startFeature(Feature.Template templ) throws ParseException
SeqIOListener
startFeature
in interface SeqIOListener
startFeature
in class GenbankFileFormer
ParseException
protected List breakSymbolArray(Alphabet theAlphabet, Symbol[] theSymbols, int theStart, int theLength) throws IllegalAlphabetException
theAlphabet
- The alphabet of the symbol datatheSymbols
- An array containing symbolstheStart
- The start offset of valid data within the arraytheLength
- The number of valid symbols in the array
IllegalAlphabetException
- if we can't cope with this
alphabet.public String formatLocation(Feature theFeature)
theFeature
- The feature with the location to format
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.
loc
- a Location
to format.strand
- a StrandedFeature.Strand
indicating the Location
's strand.
StringBuffer
.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.
sb
- a StringBuffer
loc
- a Location
to format.strand
- a StrandedFeature.Strand
indicating the Location
's strand.
StringBuffer
.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |