[Biopython-dev] [Bug 2711] GenomeDiagram.py: write() and write_to_string() are inefficient and don't check inputs

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http://bugzilla.open-bio.org/show_bug.cgi?id=2711





------- Comment #12 from biopython-bugzilla at maubp.freeserve.co.uk  2008-12-15 06:17 EST -------
(In reply to comment #9)
> (In reply to comment #3)
> > As an aside, I'd like write_to_string() to support a DPI argument like
> > write() does.
> 
> The way I originally intended write_to_string() to be used - sending graphics
> to a browser - the DPI has no influence at all.  DPI is only of any importance
> for printing graphics ...

OK, so its less useful than I had expected.  Rending bitmaps to strings so they
can be inserted into a database as blobs is one potential use-case.  Also for a
web-service where you expect the user to save and print the naked image
(unusual, and probably software dependent on how the DPI is treated).

> In that case, I think that an appropriate merging of the write() and
> write_to_string() methods could be:
> 
> def write(self, filename=None, output=default_output, dpi=default_dpi,
> encoding=default_encoding):
> 
> encoding could then be either 'binary' (default), or 'string' - which would
> emulate write_to_string()'s function.
> 
> Where handle is not None, the resulting output would be sent to the passed
> handle - which could potentially include sys.stdout.  Where handle is None,
> the method could return the encoded image directly, as write_to_string()
> does, now.
> 
> Other than the obvious problem with ReportLab's drawToFile requiring a
> filename, rather than a handle - does this seem like a reasonable plan to
> others?

On the plus side, this would be backwards compatible (and we could deprecate
the draw_to_string function).

However, I'm not so keen on this style personally - the return value is
radically different depending on the arguments (nothing, or a string of data).

If we were designing this from scratch, I would have suggested one write
function which wrote to a handle - which would let you then write to a file or
a string (using StringIO).  On the other hand, this is perhaps a little low
level.  We're had similar discussions regarding Bio.SeqIO in the past.


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