[Biococoa-dev] BCSymbolMapping

Philipp Seibel biococoa at bioworxx.com
Sun Mar 13 17:18:53 EST 2005

ok you won ;-). I just want to finish one version ;-)


Am 13.03.2005 um 23:11 schrieb Alexander Griekspoor:

>> Am 13.03.2005 um 22:41 schrieb Alexander Griekspoor:
>>> Hmmm, somehow I totally miss the reason the remapping. Why would it 
>>> be leaner/faster?
>> It would not be faster, but more flexible, because we map the symbols 
>> to the minimal set of ints.
> An int is 4 times the size of a char so there goes part of the 
> optimization. And why it would be more flexible I don't see, a basic 
> 128x128 array features all the ascii characters that you want.
>> Not only for perfomance or memory optimization.
> All the trouble to save from using 16kb (a 128x128 char matrix)?! And 
> it's only allocated once!
> As far as a 500 nucleotide char array goes, it will be just as big in 
> memory if it is: 'ACGT' as '0x00 0x01 0x02 0x03'. And what code is 
> easier to read? Also the remapping will come with cost (not much but 
> hey, more code is more time and more errors).
>> The next problem is the handling only through the char method, 
>> because we need to check for uppercase or other semantic things, 
>> where the algorithm is not really responsible for.
> No we do not have to, because we know what char each symbol will 
> return. The symbol templates dictate that (currently uppercase)!
> The proposed -charArrayRepresentation (or something alike) method in 
> the BCSequence superclass will simply itterate over the symbols and 
> ask each one for it's symbol via the  - (unichar) symbol; method. For 
> the otherway around we should just add an initFromCharArray or 
> somthing to BCSequence.
>> These things should be handled by the BCSymbol stuff. For example a 
>> 'a' and 'A' should be mapped to the same int int the dna symbol 
>> class.
> Well, you can store 4 variants of a char in the space of one int ;-) 
> But again that's not an issue, see above.
>>> What's the difference between:
>>> char c = ('a' == 'a') ? 'I' : 'X';
>>> and:
>>> char c = ('0x00' == '0x00') ? 'I' : 'X';
>>> So in the example I lend from the sample code I used previously 
>>> already, the substitution matrix is a simple 128x128 char array and 
>>> the characters are placed at their own spot.
>>>> 	    match = 1;
>>>> 	    mismh = -1;
>>>> 	    /* set match and mismatch weights */
>>>> 	    for ( i = 0; i < 128 ; i++ )
>>>> 	      for ( j = 0; j < 128 ; j++ )
>>>> 	         if (i == j ) v[i][j] = match;
>>>> 	         else v[i][j] = mismh;
>>>> 	    v['N']['N'] = mismh;
>>>>        	v['n']['n'] = mismh;
>>>>         v['A']['a'] = v['a']['A'] = match;
>>>>        	v['C']['c'] = v['c']['C'] = match;
>>>>        	v['G']['g'] = v['g']['G'] = match;
>>>>         v['T']['t'] = v['t']['T'] = match;
>>>> So, you simply build a 128x128 char matrix using the fact that 
>>>> chars are ints
>>>> Next to calculate the score:
>>>>  char *a = A[++i];	// character i in sequence A
>>>>  char *b = B[++j];	// character j in sequence B
>>>>  char *c++ = (*a == *b || isdna && v[*a][*b] == MATCHSC ) ? '|' : ' 
>>>> ';
>>> So again, if we convert the sequences to char arrays why the remap? 
>>> In the sample code above this 128x128 matrix is instantiated only 
>>> once, takes up hardly any memory and prevents the time needed for 
>>> the remap! So why the hassle for the few unused spots in the matrix? 
>>> It it really worth all the trouble going from a 128x128 array (we're 
>>> talking about 16Kb of RAM!) to a 16x16 array or so?
>>> I understand the conversion from BCSequence to char-array, but that 
>>> can still be done with the normal chars right? Or is the idea that 
>>> when we do the conversion we can do the remap along? I'm just 
>>> worried that the code won't be easier to understand and much more 
>>> error prone if we're have to remap everything all the time.
>>> And Koen has a point, can we just add the method charRepresentation 
>>> in BCSequence for instance, which does the translation job (and 
>>> sequenceFromCharArray) or something. No need for a translation 
>>> object right?
>>> Again, perhaps I'm taking to many steps in the wrong direction at 
>>> once...
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