Re: Serializing a large object

[BrowserUk]

To store the data in a more compact form, it's necessary to understand the data so you can look for more compact representations of the information it represents. And for now, that isn't clear (to me).

I set up a small set of input ranges--of both the normal--$start <= $end type; and the inverted $end < $start type; and then tried to make sense of the numbers returned by num_ranges_containing(). And I cannot.

I input these ranges:

my @ranges = (
    [ 0, 5 ], [ 1, 6 ], [ 2, 7 ], [ 3, 8 ], [ 4, 9 ], [ 5, 10 ],
    [ 5, 0 ], [ 6, 1 ], [ 7, 2 ], [ 8, 3 ], [ 9, 4 ], [ 10, 5 ],
);

And then asked for the counts containing the ranges: [0,3], [1,4], ...., [7,10], and as the returns didn't add up, I did a simple plot:

c:\test>861961
------                0.. 5
 ------               1.. 6
  ------              2.. 7
   ------             3.. 8
    ------            4.. 9
     ------           5..10
      -----           5.. 0
-      ----           6.. 1
--      ---           7.. 2
---      --           8.. 3
----      -           9.. 4
-----                10.. 5

----                  0.. 3     range: 0 .. 3 is contained by 1 ranges
 ----                 1.. 4     range: 1 .. 4 is contained by 4 ranges
  ----                2.. 5     range: 2 .. 5 is contained by 4 ranges
   ----               3.. 6     range: 3 .. 6 is contained by 3 ranges
    ----              4.. 7     range: 4 .. 7 is contained by 3 ranges
     ----             5.. 8     range: 5 .. 8 is contained by 3 ranges
      ----            6.. 9     range: 6 .. 9 is contained by 2 ranges
       ----           7..10     range: 7 .. 10 is contained by 1 range
+s

Looking at just a couple:

• [0,3] returns 1;

  But to my eyes, it appears to be contained by at least: the first, and last two input ranges?

• [1,4] returns 4;

  But only appears to be contained by the first two, and last input ranges?

How am I misinterpreting the data?

[daverave]

The ranges are given in biological coordinates, meaning the first coordinate is 1 (0 is illegal) and max_length is a legal coordinate. So, if max_length=10 then our coordinates are in 1..10 (both inclusive). Also note that a range like [2,4] expands to2,3,4 since both start and end are inclusive.

This convention always causes some trouble, and most of the time I use to convert the coordinates at the beginning and at the end so I can work with 0-based coordinates. In this case I didn't since it's quite simple, so I'm working with biological coordinates.

Anyway, if we now take your example and arbitrarily replace all 0's with 1's we get:

my @ranges = ([ 1, 5 ], [ 1, 6 ], [ 2, 7 ], [ 3, 8 ], [ 4, 9 ], [ 5,  
+10 ],[ 5, 1 ], [ 6, 1 ], [ 7, 2 ], [ 8, 3 ], [ 9, 4 ], [ 10, 5 ],);
my $rm = RangeMap->new( 10, \@ranges );

Now, [1,3] returns 5; since only the first two and last three ranges contain it.

[1,4] returns 4; since only the first two and last two ranges contain it.

I hope it makes sense now

[BrowserUk]

So, an inverted range like [9, 4] includes: 1,2,3,4 & 9,10?

[daverave]

Exactly.