[Biojava-dev] Why is the Residue Number a String?

[James Carman]

I assumed that.  My point was that the field name should match the
getter/setter name. :)

On Fri, Mar 27, 2009 at 12:31 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
> Hi James,
>
> Just to clarify, the names for the methods currently used in BJ are:
>
> group.getPDBCode() gives you the number + insertion code
> group.getPDBName() gives you the 3-letter name of the group, e.g. "ALA"
>
> If people think that these names are not clear, we can of course
> deprecate them and come up with more descriptive ones...
>
> Andreas
>
>
>
> On Fri, Mar 27, 2009 at 9:05 AM, James Carman
> <james at carmanconsulting.com> wrote:
>> Why would residueName's getter/setter be named getResidueNumber() and
>> setResidueNumber()?  Wouldn't it be better to have the getter/setter
>> as getResidueName() and setResidueName() or change the field to
>> residueNumber?
>>
>> On Fri, Mar 27, 2009 at 11:52 AM,  <tallpaulinjax at yahoo.com> wrote:
>>>
>>> Hi,
>>>
>>> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
>>> String residueNumber = line.substring(22,27).trim();
>>> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>>>
>>> Thanks!
>>>
>>> Paul
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>>
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>