[Biococoa-dev] Caching the NSArray of BCSymbol

[Charles Parnot]

On Jul 6, 2005, at 5:25 AM, John Timmer wrote:

>> I'm wondering to what extend we really need to cache the array of  
>> symbols, in fact when does one really need that array at all? Only  
>> if you ask a single position you get the symbol, in all other  
>> instances you don't want an array of symbols right, you want a  
>> BCSequence. So a subsequence -> a bcsequence is returned (again  
>> containing the char[]), the reverse of a BCSequence -> a  
>> bcsequence is returned etc... Want to display a sequence in a view  
>> -> the stringrepresentation of the bcsequence object is given.  
>> When would you like an array of symbols?
>> Alex
>>
> The symbols are the things that actually convey information.  Say  
> you want to generate all the information and statistics about a  
> sequence (complement, reverse complement, MW, melting point, etc.)  
> for display.  Without a cached version, the sequence array would  
> have to be recreated from data several times – doing so would  
> probably be the single largest time cost before the info could be  
> displayed.
>
> JT

Then, we should only cache it in one place: the accessor. Though for  
mutable sequences, we also need to remember to set the cached array  
to nil after modifications. Something like this:

- (NSArray *)symbolArray
{
     if ( cachedArray == nil ) {
         cachedArray = ...  //generate the array (and retain it)
     }
     return cachedArray;
}

- (void)emptyCache
{
     [cachedArray release];
     cachedArray = nil;
}

- (void)appendSequence:(BCSequence *)otherSequence
{
     //code to append the sequence
     ...
     //empty the cache: the array is not valid anymore!!
     [self emptyCache];
}


what do you think?

charles

--
Xgrid-at-Stanford
Help science move fast forward:
http://cmgm.stanford.edu/~cparnot/xgrid-stanford

Charles Parnot
charles.parnot at gmail.com