Re: [Gmod-ajax] creating links

[Colin <col...@gm...>]

Hi there,
There are several options for how the action can occur

1. Configuring left-click
2. Configuring right-click menu
3. Customizing the View details popup

These are all documented in the jbrowse docs
https://jbrowse.org/docs/mouse_configs.html

The callback can contain such things like this

function(feature) { return 'http://google.com/?q='+feature.get('Dbxref') }

That will generate a google link for a Dbxref. Note the Dbxref in full is
*TIGRFAM*:TIGR00756 not just the bolded part

It will just take a little javascript if you want to add conditional
statements or parse the string or something like this

-Colin



On Thu, Aug 8, 2019 at 10:50 PM Michał T. Lorenc <m.t...@gm...>
wrote:

> Hi,
> I have below a subset of a GFF3 file which contains different DbXrefs,
> InterProScan accession numbers and GO terms. However, some lines of the
> GFF3 are missing InterProScan accession numbers and GO terms. However, all
> lines contain DbXrefs. Here (https://www.uniprot.org/docs/dbxref) is a
> list of all possible dbxrefs.
>
> How is possible to allow the user to click in JBrowse on a feature and get
> options to be redirected to DbXrefs, InterProScan and ontogy?
>
>    - NbV1Ch09 interpo domain 71124892 71125030 . . . Name=RNase_HI_RT_Ty1;
>    *Dbxref=CDD*:cd09272;Note=CDD
>    - NbV1Ch14 interpo domain 93274595 93274797 . . . Name=Ribonuclease H
>    superfamily;*Dbxref=Gene3D*:G3DSA:3.30.420.10;Note=Gene3D;_Accession=
>    *IPR036397*;Ontology_term=*GO:0003676*
>    - NbV1Ch16 interpo domain 66731787 66732421 . . .
>    Name=Deoxyxylulose-5-phosphate synthase;*Dbxref=Hamap*
>    :MF_00315;Note=Hamap;_Accession=*IPR005477*;Ontology_term=
>    *GO:0008661,GO:0016114*
>    - NbV1Ch09 interpo domain 71124160 71124256 . . . Name=consensus
>    disorder prediction;*Dbxref=MobiDBLite*:mobidb-lite;Note=MobiDBLite
>    - NbV1Ch01 interpo domain 175378467 175379194 . . . Name=AP-1/2/4
>    complex subunit beta;*Dbxref=PIRSF*:PIRSF002291;Note=PIRSF;_Accession=
>    *IPR016342*;Ontology_term=*GO:0015031,GO:0030276*
>    - NbV1Ch07 interpo domain 107909842 107909860 . . . Name=Recoverin
>    family signature;*Dbxref=PRINTS*:PR00450;Note=PRINTS
>    - NbV1Ch09 interpo domain 71123771 71123905 . . . Name=gag-polypeptide
>    of LTR copia-type;*Dbxref=Pfam*:PF14223;Note=Pfam
>    - NbV1Ch03 interpo domain 33983707 33983721 . . . Name=Trp-Asp (WD)
>    repeats signature.;*Dbxref=ProSitePatterns*
>    :PS00678;Note=ProSitePatterns;_Accession=*IPR019775*
>    - NbV1Ch09 interpo domain 71124317 71124413 . . . Name=Integrase,
>    catalytic core;*Dbxref=ProSiteProfiles*
>    :PS50994;Note=ProSiteProfiles;_Accession=*IPR001584*;Ontology_term=
>    *GO:0015074*
>    - NbV1Ch17 interpo domain 30522620 30522886 . . . Name=C1.5: HAD,
>    Beta-PGM, Phosphatase Like;*Dbxref=SFLD*:SFLDG01129;Note=SFLD
>    - NbV1Ch03 interpo domain 33983723 33983761 . . . Name=WD40 repeat;
>    *Dbxref=SMART*:SM00320;Note=SMART;_Accession=*IPR001680*;Ontology_term=
>    *GO:0005515*
>    - NbV1Ch09 interpo domain 71124311 71124414 . . . Name=Ribonuclease
>    H-like superfamily;*Dbxref=SUPERFAMILY*
>    :SSF53098;Note=SUPERFAMILY;_Accession=*IPR012337*
>    - NbV1Ch01 interpo domain 157928056 157928088 . . . Name=PPR:
>    pentatricopeptide repeat domain;*Dbxref=TIGRFAM*
>    :TIGR00756;Note=TIGRFAM;_Accession=*IPR002885*
>
> Thank you in advance,
>
> Michal
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