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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--org.biojava.bio.symbol.IntegerAlphabet
An efficient implementation of an Alphabet over the infinite set of integer values.
This class can be used to represent lists of integer numbers as a SymbolList with the alphabet IntegerAlphabet. These lists can then be annotated with features, or fed into dynamic-programming algorithms, or processed as per any other SymbolList object.
Object identity can not be used to decide if two IntegerResidue objects are the same. You must use the equals method, or compare intValue manualy.
Inner Class Summary | |
static class |
IntegerAlphabet.IntegerSymbol
A single int value. |
Inner classes inherited from class org.biojava.bio.symbol.Alphabet |
Alphabet.EmptyAlphabet |
Fields inherited from interface org.biojava.bio.symbol.Alphabet |
EMPTY_ALPHABET |
Constructor Summary | |
IntegerAlphabet()
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Method Summary | |
boolean |
contains(Symbol r)
Returns whether or not this Alphabet contains the symbol. |
static SymbolList |
fromArray(int[] iArray)
Retrieve a SymbolList view of an array of integers. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
static IntegerAlphabet |
getInstance()
Retrieve the single IntegerAlphabet instance. |
java.lang.String |
getName()
Get the name of the alphabet. |
SymbolParser |
getParser(java.lang.String name)
Get a parser by name. |
IntegerAlphabet.IntegerSymbol |
getSymbol(int val)
Retrieve the Symbol for an int. |
void |
validate(Symbol r)
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public IntegerAlphabet()
Method Detail |
public static SymbolList fromArray(int[] iArray)
The returned object is a view onto the underlying array, and does not copy it. Changes made to the original array will alter the resulting SymbolList.
iArray
- the array of integers to viewpublic static IntegerAlphabet getInstance()
public IntegerAlphabet.IntegerSymbol getSymbol(int val)
val
- the int to viewpublic Annotation getAnnotation()
public boolean contains(Symbol r)
An alphabet contains an ambiguity symbol iff the ambiguity symbol's getMemberAlphabet() returns an alphabe that is a propper sub-set of this alphabet. That means that every one of the symbols that could mach the ambiguity symbol is also a member of this alphabet.
r
- the Symbol to checkpublic void validate(Symbol r) throws IllegalSymbolException
This function is used all over the code to validate symbols as they enter a method. Also, the code is littered with catches for IllegalSymbolException. There is a preferred style of handling this, which should be covererd in the package documentation.
r
- the Symbol to validatepublic java.lang.String getName()
public SymbolParser getParser(java.lang.String name)
The parser returned is guaranteed to return Symbols and SymbolLists that conform to this alphabet.
Every alphabet should have a SymbolParser under the name 'token' that uses the symbol token characters to translate a string into a SymbolList. Likewise, there should be a SymbolParser under the name 'name' that uses symbol names to identify symbols. Any other names may also be defined, but the behaviour of that parser is not defined here.
name
- the name of the parser
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