[Bioperl-l] seqfeature.display_id

[Hilmar Lapp]

I implemented both Lincoln's suggestion and the seqname to seq_id 
change. I.e., on Bio::SeqFeatureI, the former seqname() is now 
seq_id(), and the former display_id() is now called display_name(). 
Also, display_name() is its own slot and not an alias any more in 
SeqFeature::Generic.

There are aliases for the former names in SeqFeature::Generic, which 
will print a deprecation message though.

I also suggested in an earlier email that we have consistency 
problems in certain areas, especially naming of array accessors. It 
occurred to me that get_XXXXs() appears to be newer naming 
convention since it is used in a number of more recent modules (e.g. 
RichSeq). So while I was at it I audaciously went ahead and changed 
all_tags() and each_tag_value to get_all_tags and get_tag_values, 
resp. There are aliases for the former names in SeqFeature::Generic, 
and those don't print warnings (yet). If me having done this causes 
an outrage and people think I went too far, I'll reverse it. To me, 
the inconsistency does suck however, and I do frequently find myself 
looking up the name of methods when the name should be obvious if it 
followed a convention.

I'm also happy to carry around aliases for the previous names for a 
while without even printing a warning, so the effect on existing 
code will be minimal, while people writing new code against the 
toolkit will hopefully be encouraged to follow the convention.

	-hilmar

On Wednesday, October 2, 2002, at 08:04 AM, Heikki Lehvaslaiho wrote:

>
> I am always confused bby dispaly_id/dispaly_name, so I welcome anything
> that could make the distinction clearer.
>
> On Tue, 2002-10-01 at 18:11, Hilmar Lapp wrote:
>> I agree with this. That's why I proposed to
>>
>> 1) make the meaning absolutely clear and rename display_id to
>> display_name (but keep an undocumented alias)
>>
>> 2) fix the implementation in SeqFeature::Generic to refer to its own
>> attribute instead of being an alias for seqname()
>
> I wonder how many ids there are in seqfeatures?
>
> I've used heavily seq_id(), which is defined in Bio::LocationI,
> in Bio::Coodinate modules.
>
> Hilmar, before changeing anything, could you have look if there is some
> overlap between Bio::LocationI and Bio::SeqFeatureI that could be 
> pruned
> out.
>
>
> 	-Heikki
>
>> Can I take your responses as agreement with me making these changes?
>>
>> Jason/Heikki, any comment or feeling on this?
>>
>> 	-hilmar
>>
>> On Tuesday, October 1, 2002, at 05:25 AM, Ewan Birney wrote:
>>
>>> On Tue, 1 Oct 2002, Lincoln Stein wrote:
>>>
>>>> Was there any further discussion on this?  I do use display_id()
>>>> in the
>>>> Bio::Graphics module, and am confused about the distinction between
>>>> display_id() and seqname().
>>>
>>> IMNSHO
>>>
>>> display_id() == thing to be displayed for this object to a user
>>>
>>> seqname() == name of sequence attached - possibly better called
>>> seq_id or
>>> seq_accession_number() or something more obviously "real id like".
>>>
>>>
>>>
>>>
>>>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
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>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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