Re: substring implementation (long string)

Joe,

Thanks--that looks like exactly what I need. Here's a related question:
when I do the alter table, is there a way I can make it "retroactive".
That is, I ran the alter table, and nothing happened. I expected the
storage space for the database to jump, and for it to take a while to do
it, but it did not. So I am guessing that the alter table only applies
to new data put in. Is there a way to make it apply to all the data
already in the column, short of dropping the table and reloading it.
Dropping and reloading is unattractive because of several foreign key
constraints on this table.

Thanks,
Scott

On Wed, 2003-07-30 at 00:46, Joe Conway wrote:
> Scott Cain wrote:
> > I am wondering about the implementation of substring for very large
> > strings. I've got strings that are several million characters long and
> > frequently need to extract relatively small substrings (5000-40000
> > characters) (that's right, it's DNA). Before I cared much about
> > performance, I retrieved the whole string and and substr'ed it in perl.
> > I realized recently it is better to do the substring in postgres
> > (performance increase by an order of magnitude). So here is what I am
> > wondering: does postgres read the whole string into memory before it
> > does the substring, or does it have some sort of smart way of reading
> > just the substring from disk?
>
> I believe that if you store the text uncompressed (which is not the
> default) then the substring function can just grab the section of
> interest. Normally text columns this large are compressed though, which
> requires them to be read completely from disk before they are sliced.
>
> See:
> http://www.postgresql.org/docs/view.php?version=7.3&idoc=0&file=sql-altertable.html
>
> In particular:
> ALTER TABLE [ ONLY ] table [ * ] ALTER [ COLUMN ] column
> SET STORAGE { PLAIN | EXTERNAL | EXTENDED | MAIN }
>
> SET STORAGE
>
> This form sets the storage mode for a column. This controls whether
> this column is held inline or in a supplementary table, and whether the
> data should be compressed or not. PLAIN must be used for fixed-length
> values such as INTEGER and is inline, uncompressed. MAIN is for inline,
> compressible data. EXTERNAL is for external, uncompressed data and
> EXTENDED is for external, compressed data. EXTENDED is the default for
> all data types that support it. The use of EXTERNAL will make substring
> operations on a TEXT column faster, at the penalty of increased storage
> space.
>
>
> I think you'll want
> ALTER TABLE mytable ALTER COLUMN bigtextcol SET STORAGE EXTERNAL;
>
> As far as I know, there is no way to create a table with STORAGE
> EXTERNAL; you have to create the table and then alter it with the above
> statement.
>
>
> HTH,
>
> Joe
>
>
>
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Scott Cain, Ph. D. cain(at)cshl(dot)org
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory