[Biojava-dev] The future of BioJava

[Andy Yates]

> 
> Also could we make SymbolList implement List? The iterator() method
> would then do the cached conversion if required before returning an
> Iterator<Symbol> over the symbols. That would make it very pluggable.
> We'd need it to have a settable flag indicating whether the user wants
> 1-indexed or 0-indexed access (the default being 1-indexed as this is
> the most common biological use).

The important part of the 1.5 api is Iterable<T> which can be applied to 
any class. It just means it will return an iterator & can be used in the 
new foreach loop construct.

> 
> Only downside is that List uses generics and so SymbolList must too -
> meaning that SymbolList must always be declared as SymbolList<Symbol>
> (or some subclass of Symbol).
> 
> But that's also an upside - you could subclass Symbol into DNASymbol,
> RNASymbol, etc. etc. - meaning that an alphabet is tied directly to the
> symbol and need not be specified separately:
> 
>   SymbolList<DNASymbol> dna = new SymbolList<DNASymbol>();
>   dna.add(RNAAlphabet.Q); // Throws standard List exception!
> 
>   SymbolList<CompoundSymbol<DNASymbol,ScoreSymbol>> = new ....; // Cool!
> 
> Also cool is that you could do this:
> 
>   public SymbolList<RNASymbol> translate(SymbolList<DNASymbol> dna);
>       // Also cool!

Two problems with using generics that I've encountered:

1). getSomething(SymbolList<DNASymbol> list); & 
getSomething(SymbolList<RNASymbol> list); as far as the compiler is 
concerned are the same method. Both take in an instance of SymbolList 
(remember that generics are a list minute bolt-on to the JDK 1.5 API and 
it really shows).

2). It is impossible to infer the type of a generic i.e.

public <T> void doSomething(T genericObject) {
	if(T.equals(String.class)) {
		//Do something
	}
}

This T type is ... well magical. It exists but it doesn't.

Anyway just be careful with generics. They save a lot of time & effort 
but get too involved (or think they can solve everything like I did for 
a short period) they're going to burn you badly or drive you mad for 1/2 
a day wondering why javac claims something you've written is bogus.

Andy