Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, 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
Description
Situation: Currently, in IGB, the introns are represented by a line glyph connecting exons with multiple arrows showing the direction of the read, making it look like barbed wire.
Task: Create a glyph with a single arrow in the center, as shown in the image attached. Also, create the modified PointedGlyph as shown at the right end of the image (TAIR10 mRNA)
Develop a prototype using GenoViz SDK.
Attachments
Issue Links
- is blocked by
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- Closed
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- Closed
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- relates to
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BUG-120 Arrow on wrong end of bed feature - TopHat bed
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- Closed
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- Closed
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- Closed
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DB-117 Change barb wire to single arrow
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- Open
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IGBC-934 restore arrows to connector lines for "arrow" strand option
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- Closed
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Show 2 more links (2 relates to)
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-592 [ 15664 ] |
| Description | Currently, in IGB, the introns are represented by a line glyph connecting exons with multiple arrows showing the direction of the read, making it look like barbed wire. Create a glyph with a single arrow in the center, as shown in the image attached. Also, create the modified PointedGlyph as shown at the right end of the image. |
Situation: Currently, in IGB, the introns are represented by a line glyph connecting exons with multiple arrows showing the direction of the read, making it look like barbed wire.
Task: Create a glyph with a single arrow in the center, as shown in the image attached. Also, create the modified PointedGlyph as shown at the right end of the image. |
| Attachment | IGB Current representation.jpg [ 16353 ] |
| Description |
Situation: Currently, in IGB, the introns are represented by a line glyph connecting exons with multiple arrows showing the direction of the read, making it look like barbed wire.
Task: Create a glyph with a single arrow in the center, as shown in the image attached. Also, create the modified PointedGlyph as shown at the right end of the image. |
Situation: Currently, in IGB, the introns are represented by a line glyph connecting exons with multiple arrows showing the direction of the read, making it look like barbed wire.
Task: Create a glyph with a single arrow in the center, as shown in the image attached. Also, create the modified PointedGlyph as shown at the right end of the image (TAIR10 mRNA) . |
| Description |
Situation: Currently, in IGB, the introns are represented by a line glyph connecting exons with multiple arrows showing the direction of the read, making it look like barbed wire.
Task: Create a glyph with a single arrow in the center, as shown in the image attached. Also, create the modified PointedGlyph as shown at the right end of the image (TAIR10 mRNA) . |
Situation: Currently, in IGB, the introns are represented by a line glyph connecting exons with multiple arrows showing the direction of the read, making it look like barbed wire.
Task: Create a glyph with a single arrow in the center, as shown in the image attached. Also, create the modified PointedGlyph as shown at the right end of the image (TAIR10 mRNA) Develop a prototype using GenoViz SDK. |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | horizontal_LinkedArrowGlyph.jpg [ 16450 ] | |
| Attachment | vertical_LinkedArrowGlyph.jpg [ 16451 ] |
| Attachment | vertical_LinkedArrowGlyph.jpg [ 16451 ] |
| Attachment | horizontal_LinkedArrowGlyph.jpg [ 16450 ] |
| Attachment | Linked Arrows in Both orientation.jpg [ 16452 ] |
| Attachment | Linked Arrows in Both orientation.jpg [ 16452 ] |
| Attachment | BothOrientationMap.jpg [ 16453 ] |
| Attachment | BothOrientationMap2.jpg [ 16454 ] |
| Attachment | BothOrientationMap2.jpg [ 16454 ] |
| Attachment | BothOrientationMap2.jpg [ 16455 ] |
| Attachment | BothOrientationMap2.jpg [ 16455 ] |
| Attachment | BothOrientationMap.jpg [ 16453 ] |
| Attachment | BothOrientationMap.jpg [ 16459 ] | |
| Attachment | BothOrientationMap2.jpg [ 16460 ] |
| Sprint | Spring 5 2021 May 17 - May 28 [ 121 ] | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11 [ 121, 122 ] |
| Rank | Ranked higher |
| Attachment | TAIR10 mRNA.jpg [ 16352 ] |
| Attachment | TAIR10 mRNA.jpg [ 16550 ] |
| Attachment | Gene Model Progress v1.jpg [ 16556 ] |
| Sprint | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11 [ 121, 122 ] | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 121, 122, 123 ] |
| Rank | Ranked higher |
| Attachment | Bed File Zoomed In 2.jpg [ 16650 ] | |
| Attachment | Bed File Zoomed In.jpg [ 16651 ] | |
| Attachment | Bed File Zoomed Out.jpg [ 16652 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Karthik Raveendran [ karthik ] |
| Sprint | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 121, 122, 123 ] | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9 [ 121, 122, 123, 124 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | adaptive-direction-pointer-igb-6.7.3.png [ 16757 ] |
| Attachment | barbed-wire-pointer-igb-9.1.8.png [ 16758 ] |
| Comment | [ Please see comment on the commit for a concern about changing a class in the base library. ] |
| Comment |
[ Question: It looks like the small arrow in the middle of the connecting "intron" part is getting drawn even when there is no space for it. The older Glyph shown in the image above contained logic that calculated the available space for the arrow and only drew it if there was enough room for it.
Lastly, can you please locate the old code from previous incarnations of the IGB code base? I will also look into it. ] |
| Attachment | Current EfficientLabelledLineGlyph.jpg [ 16759 ] |
| Sprint | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9 [ 121, 122, 123, 124 ] | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23 [ 121, 122, 123, 124, 125 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] | Karthik Raveendran [ karthik ] |
| Attachment | ArrowHeadGlyph.jpg [ 16760 ] | |
| Attachment | ArrowHeadGlyph Zoomed In.jpg [ 16761 ] | |
| Attachment | ArrowHeadGlyph Zoomed Out.jpg [ 16762 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Summary | Create Connector Glyph with single directional arrow | Investigate glyphs representing introns in older versions of IGB |
| Sprint | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23 [ 121, 122, 123, 124, 125 ] | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13 [ 121, 122, 123, 124, 125, 126 ] |
| Rank | Ranked higher |
| Sprint | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13 [ 121, 122, 123, 124, 125, 126 ] | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27 [ 121, 122, 123, 124, 125, 126, 127 ] |
| Rank | Ranked higher |
| Sprint | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27 [ 121, 122, 123, 124, 125, 126, 127 ] | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, 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 [ 121, 122, 123, 124, 125, 126, 127, 128 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |