[Biojava-l] Analysis output on sequences (calculating properties ofSymbolLists)

[Matthew Pocock]

Hi.

David Martin wrote:

> When you have other properties that relate to a sequence, such as AA
> composition calculated in a sliding window over the sequence then you run
> into problems. It is not a property of the whole sequence but a property
> of a subsequence, often much larger than a single position in the
> sequence.
>
> One would probably want a heavier weight object than just a single
> analysis. GC content for the whole sequence is a double and there isn't
> much else one can add.
> GC content ove a sliding window has a minimum of two parameters, one of
> which varies over the sequence length.

Currently, to perform a sliding-window analysis like this, you would do the
following:

WindowedSymbolList wrl = new WindowedSymbolList(seq, width);
TranslationTable ttab = new MyMetricCalculator();
TranslatedSymbolList metricView = new TranslatedSymbolList(wrl, ttab);

The type MyMetricCalculator returns the value of your metric for any given
tuple of 'window' symbols (i.e. it is a 'function'). metricView is now a
SymbolList of the results of your metric for each window of width 'width'
within seq.

If you want a sliding window, use 'new OrderNSymbolList(seq, width)' instead of
WindowedSymbolList. I guess we could add a third option which is a window of
fixed width with a specified 'step' between windows.

A gui can easily keep a collection of TranslationTable objects lying arround
and build apropreate TranslatedSymbolList objects when a user asks.

>
> ..d
>
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