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java.lang.Objectorg.biojava.utils.Unchangeable
org.biojava.bio.seq.io.AlternateTokenization
public class AlternateTokenization
Implementation of SymbolTokenization which binds symbols to strings of characters. These tokenizations are intented to provide alternate way of writing sequences into Strings. Therefore they cannot be used for parsing files.
As this release, alternate tokenizations are available for the built-in DNA alphabet (write symbols as capital letter) and PROTEIN-TERM alphabet (write symbol as triplets of characters with the first one being a capital letter as in "Glu".
By convention, instances of AlternateTokenization should have an associated token starting by the word 'alternate'.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.io.SymbolTokenization |
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SymbolTokenization.TokenType |
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
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Annotatable.AnnotationForwarder |
Field Summary |
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Fields inherited from interface org.biojava.bio.seq.io.SymbolTokenization |
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CHARACTER, FIXEDWIDTH, SEPARATED, UNKNOWN |
Fields inherited from interface org.biojava.bio.Annotatable |
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ANNOTATION |
Constructor Summary | |
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AlternateTokenization(Alphabet alpha,
boolean caseSensitive)
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Method Summary | |
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void |
bindSymbol(Symbol s,
String str)
Bind a Symbol to a string. |
Alphabet |
getAlphabet()
The alphabet to which this tokenization applies. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
SymbolTokenization.TokenType |
getTokenType()
Tokens have fixed size. |
int |
getWidth()
Get the width of the tokens. |
StreamParser |
parseStream(SeqIOListener listener)
Will throw an exception. |
Symbol |
parseToken(String token)
Will throw an exception. |
String |
tokenizeSymbol(Symbol s)
Return a token representing a single symbol. |
String |
tokenizeSymbolList(SymbolList sl)
Return a string representation of a list of symbols. |
Methods inherited from class org.biojava.utils.Unchangeable |
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addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Constructor Detail |
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public AlternateTokenization(Alphabet alpha, boolean caseSensitive)
Method Detail |
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public Alphabet getAlphabet()
SymbolTokenization
getAlphabet
in interface SymbolTokenization
public SymbolTokenization.TokenType getTokenType()
getTokenType
in interface SymbolTokenization
public Annotation getAnnotation()
Annotatable
getAnnotation
in interface Annotatable
public int getWidth()
public void bindSymbol(Symbol s, String str)
s
- the Symbol to bindstr
- the string to bind it topublic Symbol parseToken(String token) throws IllegalSymbolException
parseToken
in interface SymbolTokenization
token
- the token to retrieve a Symbol for
IllegalSymbolException
- if there is no Symbol for the tokenpublic String tokenizeSymbol(Symbol s) throws IllegalSymbolException
SymbolTokenization
tokenizeSymbol
in interface SymbolTokenization
s
- The symbol
IllegalSymbolException
- if the symbol isn't recognized.public String tokenizeSymbolList(SymbolList sl) throws IllegalAlphabetException
SymbolTokenization
tokenizeSymbolList
in interface SymbolTokenization
sl
- A SymbolList
IllegalAlphabetException
- if alphabets don't matchpublic StreamParser parseStream(SeqIOListener listener)
parseStream
in interface SymbolTokenization
listener
- The listener which gets notified of parsed symbols.
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