GBrowse Links

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GBrowse Links

kkarra@stanford.edu
Hi,

What do I need to do include the GBrowse image link on the gene report page and to link it to an external GBrowse?

Thanks,
-Kalpana


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Re: GBrowse Links

Vallejos, Andrew
You need to create your own locatedSequenceFeatureImage.jsp file.  The
file should be put in

yourMine/webapp/resources/webapp/model

directory.

I've attached the JSP that RatMine currently uses as a reference.  The
one that I have attached is compatible with InterMine versions 0.94.1.
I've also attached the old JSP, marked old, that works with Intermine
versions previous to 0.94.

You also have to update your webconfig-model.xml file to tell InterMine
which class objects the JSP should be rendered.  Here is an excerpt from
RatMine's webconfig for QTLs.

<class className="org.intermine.model.bio.QTL">
   <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"></displayer>
      <displayer
src="/model/locatedSequenceFeatureImage.jsp"></displayer> <!--This is
the line you need to add -->
   </longdisplayers>
   <fields>
      <fieldconfig fieldExpr="primaryIdentifier"></fieldconfig>
      <fieldconfig fieldExpr="symbol"></fieldconfig>
      <fieldconfig fieldExpr="name"></fieldconfig>
      <fieldconfig showInResults="false"
displayer="/model/chromosomeLocDisplayer.jsp"
fieldExpr="chromosomeLocation"></fieldconfig>
      <fieldconfig fieldExpr="lod"></fieldconfig>
      <fieldconfig fieldExpr="pValue"></fieldconfig>
   </fields>
</class>

-Andrew
-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Kalpana Karra
Sent: Thursday, December 09, 2010 10:46 AM
To: Intermine
Subject: [InterMine Dev] GBrowse Links

Hi,

What do I need to do include the GBrowse image link on the gene report
page and to link it to an external GBrowse?

Thanks,
-Kalpana


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
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[hidden email]
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locatedSequenceFeatureImage.jsp.old (4K) Download Attachment
locatedSequenceFeatureImage.jsp (3K) Download Attachment
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Re: GBrowse Links

Vallejos, Andrew
In reply to this post by kkarra@stanford.edu
Oh...those JSP's that I sent you originally came from FlyMine, hence
there are FlyMine classes that are irrelevant to RatMine.  I have yet to
go back and clean those out, but it's on my TODO list.

-Andrew

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Kalpana Karra
Sent: Thursday, December 09, 2010 10:46 AM
To: Intermine
Subject: [InterMine Dev] GBrowse Links

Hi,

What do I need to do include the GBrowse image link on the gene report
page and to link it to an external GBrowse?

Thanks,
-Kalpana


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev