Package 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
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
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Constructor Summary
ConstructorsModifierConstructorDescriptionprotected
Deprecated.protected
ProteinRefSeqFileFormer
(PrintStream theStream) Deprecated. -
Method Summary
Modifier and TypeMethodDescriptionvoid
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.formatLocation
(StringBuffer sb, Location loc, StrandedFeature.Strand strand) formatLocation
creates an EMBL/Genbank style representation of aLocation
.formatLocation
(Feature theFeature) Formats the location of a feature.formatLocation
(Location loc, StrandedFeature.Strand strand) formatLocation
creates an EMBL/Genbank style representation of aLocation
.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
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Constructor Details
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ProteinRefSeqFileFormer
protected ProteinRefSeqFileFormer()Deprecated. -
ProteinRefSeqFileFormer
Deprecated.
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Method Details
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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 interfaceSeqIOListener
- Overrides:
addSymbols
in classGenbankFileFormer
- 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- Throws:
IllegalAlphabetException
- if we can't cope with this alphabet.
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startFeature
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 interfaceSeqIOListener
- Overrides:
startFeature
in classGenbankFileFormer
- Throws:
ParseException
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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 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.
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formatLocation
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
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formatLocation
formatLocation
creates an EMBL/Genbank style representation of aLocation
. This is a convenience method only. The version which has aStringBuffer
parameter (and returns theStringBuffer
) 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
- aLocation
to format.strand
- aStrandedFeature.Strand
indicating theLocation
's strand.- Returns:
- a
StringBuffer
.
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formatLocation
formatLocation
creates an EMBL/Genbank style representation of aLocation
. Supported location forms:123 invalid input: '<'123 or >123 (123.567) (123.567)..789 123..(567.789) (123.345)..(567.789) 123..456 invalid input: '<'123..567 or 123..>567 or invalid input: '<'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
- aStringBufferinvalid input: '<'/code to which the location will be appended.
loc
- aLocation
to format.strand
- aStrandedFeature.Strand
indicating theLocation
's strand.- Returns:
- a
StringBuffer
.
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