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  1. IGB
  2. IGBF-2900

Create an intron glyph for genoviz-sdk (ArrowHeadGlyph)

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24, Fall 4 2021 Sep 27 - Oct 8, Fall 5 2021 Oct 11 - Oct 22, Fall 6 2021 Oct 25 - Nov 5

          Description

          Create an intron glyph class for genoviz-sdk. Based on the findings of IGBF-2865, the class should have the dynamic arrowhead properties of ArrowHeadGlyph class from igb_6_7 branch

          Note: Remove all IGB references from the class (comments, method names etc.) to make it production-ready.

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-2865 Investigate glyphs representing introns in older versions of IGB

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-2992 Test: Create an intron glyph for genoviz-sdk (ArrowHeadGlyph)

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                karthik Karthik Raveendran created issue -
                karthik Karthik Raveendran made changes -
                Field Original Value New Value
                Epic Link IGBF-592 [ 15664 ]
                karthik Karthik Raveendran made changes -
                Link This issue blocks IGBF-2865 [ IGBF-2865 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                aloraine Ann Loraine made changes -
                Sprint Summer 3 2021 Jul 12 - Jul 23 [ 125 ] Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13 [ 125, 126 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
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                karthik Karthik Raveendran added a comment -

                Added a new class called IntronGlyph and ArrowHeadGlyph based on the IGB version 6.7.1 to implement the arrow glyph. Improved the BedSequenceDemo to respond well to zooming. Commit Link

                Show
                karthik Karthik Raveendran added a comment - Added a new class called IntronGlyph and ArrowHeadGlyph based on the IGB version 6.7.1 to implement the arrow glyph. Improved the BedSequenceDemo to respond well to zooming. Commit Link
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ] Ann Loraine [ aloraine ]
                aloraine Ann Loraine made changes -
                Sprint Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13 [ 125, 126 ] Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27 [ 125, 126, 127 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                aloraine Ann Loraine made changes -
                Sprint Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27 [ 125, 126, 127 ] Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Aug 10 [ 125, 126, 127, 128 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                aloraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Hide
                Permalink
                aloraine Ann Loraine added a comment -

                Please submit PR.

                Show
                aloraine Ann Loraine added a comment - Please submit PR.
                aloraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                aloraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Karthik Raveendran [ karthik ]
                aloraine Ann Loraine made changes -
                Sprint Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10 [ 125, 126, 127, 128 ] Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021Sep 13 - Sep 24 [ 125, 126, 127, 128, 129 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                aloraine Ann Loraine made changes -
                Sprint Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24 [ 125, 126, 127, 128, 129 ] Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24, Fall 4 2021 Sep 27 - Oct 8 [ 125, 126, 127, 128, 129, 130 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                karthik Karthik Raveendran made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                Hide
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                karthik Karthik Raveendran added a comment -

                Submitted PR

                Show
                karthik Karthik Raveendran added a comment - Submitted PR
                Hide
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                aloraine Ann Loraine added a comment -

                Sorry, the PR can not be merged as-is.

                The “bed” file added to the repository is very large. Is there some reason you need to include the entire file?

                Also, to confirm: Did you get the file from here?

                Unless there is a compelling reason to include the entire file, can you reduce it to a smaller size?

                Lastly, the file itself should include the file extension in the name. The file added does not appear to include the extension. The file name of the bed file should terminate with the file extension suffix “.bed”.

                Show
                aloraine Ann Loraine added a comment - Sorry, the PR can not be merged as-is. The “bed” file added to the repository is very large. Is there some reason you need to include the entire file? Also, to confirm: Did you get the file from here? http://igbquickload.org/quickload/A_thaliana_Jun_2009/Araport11.bed.gz Unless there is a compelling reason to include the entire file, can you reduce it to a smaller size? Lastly, the file itself should include the file extension in the name. The file added does not appear to include the extension. The file name of the bed file should terminate with the file extension suffix “.bed”.
                aloraine Ann Loraine made changes -
                Assignee Karthik Raveendran [ karthik ]
                aloraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                aloraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] To-Do [ 10305 ]
                aloraine Ann Loraine made changes -
                Sprint Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24, Fall 4 2021 Sep 27 - Oct 8 [ 125, 126, 127, 128, 129, 130 ] Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24, Fall 4 2021 Sep 27 - Oct 8, Fall 5 2021 Oct 11 - Oct 22 [ 125, 126, 127, 128, 129, 130, 131 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
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                karthik Karthik Raveendran added a comment -

                Pushed commits to repo.
                Commit in branch IGBF-2900
                Changed the file to a bed file and deleted all data except for Chromosome 5 to reduce size.
                Commit in branch IGBF-2900
                Changed absolute path to relative path.
                I did download the file from http://igbquickload.org/quickload/A_thaliana_Jun_2009/Araport11.bed.gz

                Show
                karthik Karthik Raveendran added a comment - Pushed commits to repo. Commit in branch IGBF-2900 Changed the file to a bed file and deleted all data except for Chromosome 5 to reduce size. Commit in branch IGBF-2900 Changed absolute path to relative path. I did download the file from http://igbquickload.org/quickload/A_thaliana_Jun_2009/Araport11.bed.gz
                aloraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                aloraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                aloraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                aloraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                aloraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                Hide
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                aloraine Ann Loraine added a comment -

                To test: Run the demonstration application and "open" the added bed file. Confirm that gene models are being shown, and take a screen capture showing the demo display.

                (See commits associated with the above PR to identify relevant classes.)

                Request for Karthik Raveendran: can you provide instructions on how to run the demo?

                Show
                aloraine Ann Loraine added a comment - To test: Run the demonstration application and "open" the added bed file. Confirm that gene models are being shown, and take a screen capture showing the demo display. (See commits associated with the above PR to identify relevant classes.) Request for Karthik Raveendran : can you provide instructions on how to run the demo?
                Hide
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                aloraine Ann Loraine added a comment - - edited

                Creating new issue for testing, as this could be very involved due to the documentation requirement. Moving this to closed.

                Show
                aloraine Ann Loraine added a comment - - edited Creating new issue for testing, as this could be very involved due to the documentation requirement. Moving this to closed.
                aloraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                aloraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                aloraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                aloraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] To-Do [ 10305 ]
                aloraine Ann Loraine made changes -
                Sprint Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24, Fall 4 2021 Sep 27 - Oct 8, Fall 5 2021 Oct 11 - Oct 22 [ 125, 126, 127, 128, 129, 130, 131 ] Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24, Fall 4 2021 Sep 27 - Oct 8, Fall 5 2021 Oct 11 - Oct 22, Fall 6 2021 Oct 25 - Nov 5 [ 125, 126, 127, 128, 129, 130, 131, 132 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                aloraine Ann Loraine made changes -
                Link This issue relates to IGBF-2992 [ IGBF-2992 ]
                aloraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Hide
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                aloraine Ann Loraine added a comment -

                New ticket created:

                • IGBF-2992 Test: Create an intron glyph for genoviz-sdk (ArrowHeadGlyph)
                Show
                aloraine Ann Loraine added a comment - New ticket created: IGBF-2992 Test: Create an intron glyph for genoviz-sdk (ArrowHeadGlyph)
                Hide
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                aloraine Ann Loraine added a comment -

                New ticket for testing is created. Moving this to Done.

                Show
                aloraine Ann Loraine added a comment - New ticket for testing is created. Moving this to Done.
                aloraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                aloraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                aloraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                aloraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                aloraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                aloraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                aloraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                aloraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                aloraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    karthik Karthik Raveendran
                  • Votes:
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                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: