[Gmod-ajax] right click menu: view mate location in iframe (BAM)

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[Gmod-ajax] right click menu: view mate location in iframe (BAM)

Keiran Raine
Hi,

It would be useful if the alignments2 tracks had a right-click menu option to display the location of the mate/next segment by default.  As it's not present I'd like to add it using the menu customisation.  This is very useful for looking at breakpoints due to rearrangements (kind of a half-way-house to the IGV split view).

I've created the following stub, however, I expect the base URL component can be done better.

"menuTemplate": [
    {
      "label": "View details",
      "title": "{type} {name}",
      "action": "contentDialog",
      "iconClass": "dijitIconTask"
    },
    {
      "iconClass": "dijitIconFilter"
    },
    {
      "iconClass": "dijitIconUndo",
      "url": "<a href="http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/?data=autoconf/t1012&amp;tracklist=0&amp;loc={next_segment_position}">http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/?data=autoconf/t1012&tracklist=0&loc={next_segment_position}",
      "action": "iframeDialog",
      "title": "QuickView mate location ({next_segment_position})",
      "label": "QvMate"
    },
    {
      "iconClass": "dijitIconUndo",
      "url": "<a href="http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/?data=autoconf/t1012&amp;tracklist=0&amp;loc={next_segment_position}">http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/?data=autoconf/t1012&tracklist=0&loc={next_segment_position}",
      "action": "newWindow",
      "title": "Open mate location ({next_segment_position})",
      "label": "OpenMate"
    }
  ],

Absence of the track list in the new windows makes it easier for the user to identify which window they started in.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: right click menu: view mate location in iframe (BAM)

Robert Buels-2
That's a great idea.  It's issue #406 now,
https://github.com/GMOD/jbrowse/issues/406.

I might not quite be able to get it into 1.11.1, there are a lot of
other things going on this week.  But it will probably at least be in
1.11.2.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/03/2014 07:29 PM, Keiran Raine wrote:

> Hi,
>
> It would be useful if the alignments2 tracks had a right-click menu
> option to display the location of the mate/next segment by default.  As
> it's not present I'd like to add it using the menu customisation.  This
> is very useful for looking at breakpoints due to rearrangements (kind of
> a half-way-house to the IGV split view).
>
> I've created the following stub, however, I expect the base URL
> component can be done better.
>
> "menuTemplate": [
>      {
>        "label": "View details",
>        "title": "{type} {name}",
>        "action": "contentDialog",
>        "iconClass": "dijitIconTask"
>      },
>      {
>        "iconClass": "dijitIconFilter"
>      },
>      {
>        "iconClass": "dijitIconUndo",
>        "url":
> "http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/?data=autoconf/t1012&tracklist=0&loc={next_segment_position}",
>        "action": "iframeDialog",
>        "title": "QuickView mate location ({next_segment_position})",
>        "label": "QvMate"
>      },
>      {
>        "iconClass": "dijitIconUndo",
>        "url":
> "http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/?data=autoconf/t1012&tracklist=0&loc={next_segment_position}",
>        "action": "newWindow",
>        "title": "Open mate location ({next_segment_position})",
>        "label": "OpenMate"
>      }
>    ],
>
> Absence of the track list in the new windows makes it easier for the
> user to identify which window they started in.
>
> Regards,
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> [hidden email] <mailto:[hidden email]>
> Tel:+44 (0)1223 834244 Ext: 7703
> Office: H104
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
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