Re: Measuring Substring with Hash

[Edward Wijaya]

Hi John and David,
Thanks so much for your reply.
I forgot to mentioned another variances of scoring apart from
this two
.......    .......   ......
GATTACGAGTGGCGCTCGTGTAACGGCA    #Score 21
GATTACG    GCGCTCG   AACGGCA
CASE B:
           ..            ..      #Score 4
GATTACGAGTGGCGCTCGTGTAACGGCA
           GG            GG
They are cases where they overlap:
CASE C:
.........       .......           #score 16
GATTACGAGTGGCGCTCGTGTAACGGCA
GATTACG
  TTACGAG       CGTGTAA
CASE D:
             GCTCGTG             #score 17
  ..................
GATTACGAGTGGCGCTCGTGTAACGGCA
   TACGAGT
        GTGGCGC
my @ar2 =  ('GATTACG','TTACGAG','CGTGTAA');  #16
my @ar3 =  ('TACGAGT','GTGGCGC','GCTCGTG');  #17
And Dave's modification below (that includes $offset) works just fine for  
it.

__BEGIN__
#!/usr/bin/perl -w

   my %position_score;
     my $offset = 0;
[snip]
     	   my $idx = index($str, $frag, $offset) + 1;
[snip]
        $offset = $idx;
Don't mean to nitpick.
Just wondering if it's possible to modify Krahn's snippet to accomodate
the overlapping cases?
yet another fans request ;-)
--
Edward WIJAYA
Singapore
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