Editview alternative

James Bonfield jkb at arran.mrc-lmb.cam.ac.uk
Mon Sep 4 08:10:34 EST 2000


In <8ooomc$sai$1 at mercury.hgmp.mrc.ac.uk> Sven Klages <klages at molgen.mpg.de> writes:

> Since we were just testing the machine I just have a few files.
> But scf_dump gave me something like this ...

> [Header]
> 779314022       # magic_number
> 20001           # samples
> 7064            # samples_offset
> 578             # bases
> 0               # bases_left_clip
> 0               # bases_right_clip
> 128             # bases_offset
> 0               # comments_size
> 0               # comments_offset
> 3.00            # version
> 2               # sample_size
> 2               # code_set
> 171618          # private_size
> 167072          # private_offset
...

That looks _much_ better! The inclusion of bases and traces make it a "real"
scf trace in my opinion. There's still lots of private data, but that's OK -
that's what that block was designed for anyway.

> The significant difference seems to be the version (2.10 -> 3.00)
> and of course the "[bases]" block.
> Did I misunderstand the SCF definition in the Staden Manual ??
> It's possible to read those files with progs like 'chromas'.

Assuming that the base and trace information is correct then I can see no
reason why chromas (for example) wouldn't be able to read the files.

> Well, but that doesn't answer the original question, if there's
> a Mac Software which is able to read SCF file ...
> Sorry Perry, there's lots of software for win or Unix systems,
> I just don't know any other Mac software than SeqA3.x or EditView.

There's quite a few Java trace viewers, so I'd expect those to work (as well
as any Java app does).

We did manage to (just about) get our Trev viewer working on the Mac, but it
was a bit unstable and hideously slow compared to the Unix and PC version. (I
don't know why, but I'm guessing at some of the Tk X emulation we used).

James
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/


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