Matthew
Thomas Down wrote:
Once upon a time, Benjamin Schuster-Boeckler wrote:
Benjamin Schuster-Boeckler wrote:
As I understood the principle, a FeatureFilter will be used to test one Feature after the other through it's accept(Feature f) method. Now my problem is that this is _far_ too slow. I need to check millions of Features of which only a few will be selected. So what I want to do is to get the "rule" that the FeatureFilter uses and translate it into a SQL query so I can get the right Features from the database straight away. Unfortunately, I don't see a way how this could be possible.Ah, toString() could do it, am I right? I think it returns a neat pattern that I could parse token for token...
You certainly could do this if you wanted to. However, I would generally advise against it. If you look at all the FeatureFilter implementations in BioJava, you'll find that they all have accessor methods for getting at their parameters. So while it's possible to convert a filter to text then parse it again, you'd do better by looking at filters as parse-trees, ready to analyse directly.
You'll find code which manipulates FeatureFilters in this way throughout the BioJava code base. One bit which might be particularly relevant to you is the (private) method sqlizeFilter in BioSQLSequenceDB. It's pretty simplistic, but might give you some ideas.
One thing to remember is that you don't have to translate every part of a complex filter to SQL -- just do the easy/ important bits, then use the FeatureFilter.accept methods to apply the parts of the filter your translater doesn't understand, and you should still get correct results with good performance.
In the past, David Huen has talked about some more general solutions for FeatureFilter -> SQL translation, so he might want to add something here,
Thomas. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
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