org.biojava.bio.seq.io
Class ProteinRefSeqFileFormer
java.lang.Object
org.biojava.bio.seq.io.AbstractGenEmblFileFormer
org.biojava.bio.seq.io.GenbankFileFormer
org.biojava.bio.seq.io.ProteinRefSeqFileFormer
- All Implemented Interfaces:
- SeqFileFormer, SeqIOListener
- 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
Method Summary |
void |
addSymbols(Alphabet theAlphabet,
Symbol[] theSymbols,
int theStart,
int theLength)
Notify the listener of symbol data. |
protected java.util.List |
breakSymbolArray(Alphabet theAlphabet,
Symbol[] theSymbols,
int theStart,
int theLength)
Converts the symbol list passed in into an array of strings. |
void |
startFeature(Feature.Template templ)
Notify the listener that a new feature object is starting. |
Methods inherited from class org.biojava.bio.seq.io.GenbankFileFormer |
addFeatureProperty, addSequenceProperty, endFeature, endSequence, formatLocation, formatLocation, formatLocation, 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 |
ProteinRefSeqFileFormer
protected ProteinRefSeqFileFormer()
ProteinRefSeqFileFormer
protected ProteinRefSeqFileFormer(java.io.PrintStream theStream)
addSymbols
public void addSymbols(Alphabet theAlphabet,
Symbol[] theSymbols,
int theStart,
int theLength)
throws IllegalAlphabetException
- 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
- Throws:
IllegalAlphabetException
startFeature
public void startFeature(Feature.Template templ)
throws ParseException
- 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 java.util.List breakSymbolArray(Alphabet theAlphabet,
Symbol[] theSymbols,
int theStart,
int theLength)
throws IllegalAlphabetException
- 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 datatheSymbols
- An array containing symbolstheStart
- The start offset of valid data within the arraytheLength
- 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.