[Jalview-discuss] Re: linkUrl and regexp

Tue Sep 9 11:43:38 BST 2008

Sebastien MORETTI a écrit :
> Sebastien MORETTI a écrit :
>>>>> The easiest way to do generate these links without changing the 
>>>>> existing
>>>>> URL link behaviour would be to create a features file with URL links
>>>>> embedded in the description line - these will be shown in the link 
>>>>> menu
>>>>> when the user right clicks on the sequence ID.
>>>> I think I will try this.
>>>> Should I use this kind of syntax:
>>>> http://...    seq_ID
>>>>
>>>> With URL as description, a tab, sequence identifier ?
>>> not quite...
>>>
>>> Here's an example from 
>>> http://www.jalview.org/examples/exampleFeatures.txt :
>>>
>>> <html>Fer2 Status: True Positive <a
>>> href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam
>>> 8_8</a></html>    FER_CAPAA    -1    8    83    Pfam
>>> Ferredoxin_fold Status: True Positive     FER_CAPAA    -1    3    
>>> 93    Cath
>>>
>>> Specify start and end as -1 in order to add a non-positional feature
>>> Jalview will recognise the anchors embedded in the description and parse
>>> them as  URL links where the link text is used for the menu name.
>>>
>>> I see that this process is not described in the features file
>>> documentation (
>>> http://www.jalview.org/help/html/features/featuresFormat.html ) -
>>> that'll have to be fixed !
>>>
>>> Jim
>>>
>>> ps. With regard to 'magic FeatureTypes' - Jalview does not do anything
>>> intelligent with feature types, currently (with the exception of the
>>> disulphide_bond type), which is a big limitation. It is easy to imagine
>>> that features like 'DBRef' or 'Reference' might be translated into
>>> database accession links and citation lists, and may actually be
>>> implemented in the future.
>>
>> I have tried this syntax but it fails with an error in the java console:
>> Sequence not found: <html><a 
>> href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl</a></html> 
>> ENPL_HUMAN    -1    -1    -1    DBRef
>>
>> Feature lines look like this:
>> <html><a 
>> href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl</a></html> 
>> ENPL_HUMAN    -1    -1    -1    DBRef
>> <html><a 
>> href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSPTRG00000005372'>ensembl</a></html> 
>> HSP90B1_PANTR    -1    -1    -1    DBRef
>>
>>
>> And sequence headers look like this:
>>  >ENPL_HUMAN     ID=ENST00000299767.4 GENEID=ENSG00000166598
>>  >HSP90B1_PANTR     ID=ENSPTRT00000009873.3 GENEID=ENSPTRG00000005372
>>
>> So, it seems the features cannot be allocated to the proper sequences.
>> What should be the right sequence name in this case ?
>>
>> Thanks
> 
> "Sequence not found" message came from a forgotten tab. It is resolved 
> now, sorry.
> 
> But I do not have links yet.
> 
> Now, feature file looks like this:
> ensembl    red
> <html><a 
> href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl</a></html> 
> ENPL_HUMAN    -1    -1    -1    ensembl
> <html><a 
> href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSPTRG00000005372'>ensembl</a></html> 
> HSP90B1_PANTR    -1    -1    -1    ensembl
> ...
> 
> And sequence headers look like this:
>  >ENPL_HUMAN ID=ENST00000299767.4 GENEID=ENSG00000166598
>  >HSP90B1_PANTR ID=ENSPTRT00000009873.3 GENEID=ENSPTRG00000005372
> 
> 
> 
> I have nothing but SRS link in the links menu.

Another point !
With reel start and end positions, links appear on sequences but not in 
link menu of the sequence name.

And href MUST have URL between double quotes because it does not work 
with simple quotes.

So now, how to have links in link menu of the sequence name ?
And / or how to get links on sequences without changing amino acid 
colours with the feature colour ?

Best regards
Sébastien

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4056