Details
-
Type:
Bug
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Fixed
-
Labels:None
Description
Windows v11940
The shortcuts with an 
may be unnecessary or are duplicated by something else. For example, we probably could get rid of Collapse and Expand and just keep toggle between the two.
When setting NEW shortcuts these are not working:
- All
- Change BG color
- Change FG color
- Change label color
- Clear script history
- Collapse
- Expand
- Export preferences
- Float
- General help
- Handle threads
- Help for current tab
- Hide
- Import preferences
- Join (Did we get rid of this option? I do not see it anywhere else.)
- Load all sequence
- Load sequence in view
- Next search span
- No tracks
- Remove data from selected tracks
- Repack all tracks
- Repack selected tracks
- Reset preferences to defaults
- Restore to Default
- Save selected annotations as file
- Set direction style arrow
- Set direction style color
- Set range of color by score
- Set threshold above
- Set threshold below
- Show
tiers - Show (+/-) tiers
- Show
tiers - Show 1 track (+/-)
- Show 2 tracks and
- Shrink wrap sequence
- Split (Did we get rid of this option? I do not see it anywhere else.)
- Toggle expand and collapse
- Toggle set threshold above and set threshold below
- Toggle show 1 track...
- Tracks*
- Unset direction style arrow
- Unset direction style color
- View alignment sequence in sequence viewer
- View genomic sequence in sequence viewer
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Description |
Windows v11940 The shortcuts with an (*) may be unnecessary or are duplicated by something else. We probably could get rid of Collapse and Expand and just keep toggle between the two. When setting NEW shortcuts these are not working: - All - Change BG color - Change FG color - Change label color - Clear script history - Collapse* - Expand* - Export preferences - Float - General help - Handle threads - Help for current tab - Hide - Import preferences - Join (Did we get rid of this option? I do not see it anywhere else.) - Load all sequence - Load sequence in view - Next search span - No tracks - Remove data from selected tracks - Repack all tracks - Repack selected tracks - Reset preferences to defaults - Restore to Default - Save selected annotations as file - Set direction style arrow* - Set direction style color* - Set range of color by score - Set threshold above - Set threshold below - Show (+) tiers - Show (+/-) tiers - Show (-) tiers - Show 1 track (+/-)* - Show 2 tracks (+) and (-)* - Shrink wrap sequence - Split (Did we get rid of this option? I do not see it anywhere else.) - Toggle expand and collapse* - Toggle set threshold above and set threshold below* - Toggle show 1 track...* - Tracks* - Unset direction style arrow* - Unset direction style color* - View alignment sequence in sequence viewer (Should we remove the '..." here?) - View genomic sequence in sequence viewer (Should we remove the '..." here?) |
Windows v11940 The shortcuts with an (*) may be unnecessary or are duplicated by something else. We probably could get rid of Collapse and Expand and just keep toggle between the two. When setting NEW shortcuts these are not working: - All - Change BG color - Change FG color - Change label color - Clear script history - Collapse(*) - Expand(*) - Export preferences - Float - General help - Handle threads - Help for current tab - Hide - Import preferences - Join (Did we get rid of this option? I do not see it anywhere else.) - Load all sequence - Load sequence in view - Next search span - No tracks - Remove data from selected tracks - Repack all tracks - Repack selected tracks - Reset preferences to defaults - Restore to Default - Save selected annotations as file - Set direction style arrow* - Set direction style color* - Set range of color by score - Set threshold above - Set threshold below - Show (+) tiers - Show (+/-) tiers - Show (-) tiers - Show 1 track (+/-)* - Show 2 tracks (+) and (-)* - Shrink wrap sequence - Split (Did we get rid of this option? I do not see it anywhere else.) - Toggle expand and collapse* - Toggle set threshold above and set threshold below* - Toggle show 1 track...* - Tracks* - Unset direction style arrow* - Unset direction style color* - View alignment sequence in sequence viewer (Should we remove the '..." here?) - View genomic sequence in sequence viewer (Should we remove the '..." here?) |
| Description |
Windows v11940 The shortcuts with an (*) may be unnecessary or are duplicated by something else. We probably could get rid of Collapse and Expand and just keep toggle between the two. When setting NEW shortcuts these are not working: - All - Change BG color - Change FG color - Change label color - Clear script history - Collapse(*) - Expand(*) - Export preferences - Float - General help - Handle threads - Help for current tab - Hide - Import preferences - Join (Did we get rid of this option? I do not see it anywhere else.) - Load all sequence - Load sequence in view - Next search span - No tracks - Remove data from selected tracks - Repack all tracks - Repack selected tracks - Reset preferences to defaults - Restore to Default - Save selected annotations as file - Set direction style arrow* - Set direction style color* - Set range of color by score - Set threshold above - Set threshold below - Show (+) tiers - Show (+/-) tiers - Show (-) tiers - Show 1 track (+/-)* - Show 2 tracks (+) and (-)* - Shrink wrap sequence - Split (Did we get rid of this option? I do not see it anywhere else.) - Toggle expand and collapse* - Toggle set threshold above and set threshold below* - Toggle show 1 track...* - Tracks* - Unset direction style arrow* - Unset direction style color* - View alignment sequence in sequence viewer (Should we remove the '..." here?) - View genomic sequence in sequence viewer (Should we remove the '..." here?) |
Windows v11940 The shortcuts with an (*) may be unnecessary or are duplicated by something else. We probably could get rid of Collapse and Expand and just keep toggle between the two. When setting NEW shortcuts these are not working: - All - Change BG color - Change FG color - Change label color - Clear script history - Collapse(*) - Expand(*) - Export preferences - Float - General help - Handle threads - Help for current tab - Hide - Import preferences - Join (Did we get rid of this option? I do not see it anywhere else.) - Load all sequence - Load sequence in view - Next search span - No tracks - Remove data from selected tracks - Repack all tracks - Repack selected tracks - Reset preferences to defaults - Restore to Default - Save selected annotations as file - Set direction style arrow(*) - Set direction style color(*) - Set range of color by score - Set threshold above - Set threshold below - Show (+) tiers - Show (+/-) tiers - Show (-) tiers - Show 1 track (+/-)(*) - Show 2 tracks (+) and (-)(*) - Shrink wrap sequence - Split (Did we get rid of this option? I do not see it anywhere else.) - Toggle expand and collapse(*) - Toggle set threshold above and set threshold below(*) - Toggle show 1 track...(*) - Tracks* - Unset direction style arrow(*) - Unset direction style color(*) - View alignment sequence in sequence viewer (Should we remove the '..." here?) - View genomic sequence in sequence viewer (Should we remove the '..." here?) |
| Description |
Windows v11940 The shortcuts with an (*) may be unnecessary or are duplicated by something else. We probably could get rid of Collapse and Expand and just keep toggle between the two. When setting NEW shortcuts these are not working: - All - Change BG color - Change FG color - Change label color - Clear script history - Collapse(*) - Expand(*) - Export preferences - Float - General help - Handle threads - Help for current tab - Hide - Import preferences - Join (Did we get rid of this option? I do not see it anywhere else.) - Load all sequence - Load sequence in view - Next search span - No tracks - Remove data from selected tracks - Repack all tracks - Repack selected tracks - Reset preferences to defaults - Restore to Default - Save selected annotations as file - Set direction style arrow(*) - Set direction style color(*) - Set range of color by score - Set threshold above - Set threshold below - Show (+) tiers - Show (+/-) tiers - Show (-) tiers - Show 1 track (+/-)(*) - Show 2 tracks (+) and (-)(*) - Shrink wrap sequence - Split (Did we get rid of this option? I do not see it anywhere else.) - Toggle expand and collapse(*) - Toggle set threshold above and set threshold below(*) - Toggle show 1 track...(*) - Tracks* - Unset direction style arrow(*) - Unset direction style color(*) - View alignment sequence in sequence viewer (Should we remove the '..." here?) - View genomic sequence in sequence viewer (Should we remove the '..." here?) |
Windows v11940 The shortcuts with an (*) may be unnecessary or are duplicated by something else. For example, we probably could get rid of Collapse and Expand and just keep toggle between the two. When setting NEW shortcuts these are not working: - All - Change BG color - Change FG color - Change label color - Clear script history - Collapse(*) - Expand(*) - Export preferences - Float - General help - Handle threads - Help for current tab - Hide - Import preferences - Join (Did we get rid of this option? I do not see it anywhere else.) - Load all sequence - Load sequence in view - Next search span - No tracks - Remove data from selected tracks - Repack all tracks - Repack selected tracks - Reset preferences to defaults - Restore to Default - Save selected annotations as file - Set direction style arrow(*) - Set direction style color(*) - Set range of color by score - Set threshold above - Set threshold below - Show (+) tiers - Show (+/-) tiers - Show (-) tiers - Show 1 track (+/-)(*) - Show 2 tracks (+) and (-)(*) - Shrink wrap sequence - Split (Did we get rid of this option? I do not see it anywhere else.) - Toggle expand and collapse(*) - Toggle set threshold above and set threshold below(*) - Toggle show 1 track...(*) - Tracks* - Unset direction style arrow(*) - Unset direction style color(*) - View alignment sequence in sequence viewer (Should we remove the '..." here?) - View genomic sequence in sequence viewer (Should we remove the '..." here?) |
| Assignee | Hiral Vora [ hiralv ] |
| Description |
Windows v11940 The shortcuts with an (*) may be unnecessary or are duplicated by something else. For example, we probably could get rid of Collapse and Expand and just keep toggle between the two. When setting NEW shortcuts these are not working: - All - Change BG color - Change FG color - Change label color - Clear script history - Collapse(*) - Expand(*) - Export preferences - Float - General help - Handle threads - Help for current tab - Hide - Import preferences - Join (Did we get rid of this option? I do not see it anywhere else.) - Load all sequence - Load sequence in view - Next search span - No tracks - Remove data from selected tracks - Repack all tracks - Repack selected tracks - Reset preferences to defaults - Restore to Default - Save selected annotations as file - Set direction style arrow(*) - Set direction style color(*) - Set range of color by score - Set threshold above - Set threshold below - Show (+) tiers - Show (+/-) tiers - Show (-) tiers - Show 1 track (+/-)(*) - Show 2 tracks (+) and (-)(*) - Shrink wrap sequence - Split (Did we get rid of this option? I do not see it anywhere else.) - Toggle expand and collapse(*) - Toggle set threshold above and set threshold below(*) - Toggle show 1 track...(*) - Tracks* - Unset direction style arrow(*) - Unset direction style color(*) - View alignment sequence in sequence viewer (Should we remove the '..." here?) - View genomic sequence in sequence viewer (Should we remove the '..." here?) |
Windows v11940 The shortcuts with an (*) may be unnecessary or are duplicated by something else. For example, we probably could get rid of Collapse and Expand and just keep toggle between the two. When setting NEW shortcuts these are not working: - All - Change BG color - Change FG color - Change label color - Clear script history - Collapse(*) - Expand(*) - Export preferences - Float - General help - Handle threads - Help for current tab - Hide - Import preferences - Join (Did we get rid of this option? I do not see it anywhere else.) - Load all sequence - Load sequence in view - Next search span - No tracks - Remove data from selected tracks - Repack all tracks - Repack selected tracks - Reset preferences to defaults - Restore to Default - Save selected annotations as file - Set direction style arrow(*) - Set direction style color(*) - Set range of color by score - Set threshold above - Set threshold below - Show (+) tiers - Show (+/-) tiers - Show (-) tiers - Show 1 track (+/-)(*) - Show 2 tracks (+) and (-)(*) - Shrink wrap sequence - Split (Did we get rid of this option? I do not see it anywhere else.) - Toggle expand and collapse(*) - Toggle set threshold above and set threshold below(*) - Toggle show 1 track...(*) - Tracks* - Unset direction style arrow(*) - Unset direction style color(*) - View alignment sequence in sequence viewer - View genomic sequence in sequence viewer |
| Assignee | Hiral Vora [ hiralv ] | Eric Blossom [ elb ] |
Fixed (revision 12074) the issue of some accelerators (shortcuts) not being set on the next start up. I also fixed it so that they are set right away, so you don't have to restart IGB. (Note that you still have to restart IGB to see tool bar changes.)
You can set accelerators for toggles and their clients separately. e.g. for Collapse, Expand, and Toggle Collapse and Expand with three different accelerators if you like.
The popup menu must be visible for the accelerators for those actions to work. Similarly, the Preferences dialog must be up for it's actions to be available through accelerator key strokes.
So everything is working according to the Swing True Way. However, it is still a bit subtle to the user why the shortcuts to the popup menu items don't "work" when the popup is not visible.
It's all good now. Shortcuts work even for pop up menu items and toolbar buttons.
svn revision 12116.
| Assignee | Eric Blossom [ elb ] | Alyssa Gulledge [ alyssa ] |
The short cuts shows "None", the list about shows "No tracks"...
None is in reference to removing the transformation on an annotation track? What does No tracks come from? Is it a mistake, or has it been removed? Also using this shortcut seems to do nothing
Set threshold above/below are not in shortcuts list. Have they been removed?
"Float" does not toggle to an UNfloated state! This should self toggle.
Set arrow and set direction color have separate 'unsets' - can't we just have one option that toggles? *BUG* Current the unset arrow clicks off the arrow box, but does NOT remove the arrows from the glyphs. Same for color.
Activating 'Show 2 track' via shortcut does NOT properly check the '2 track' box in Data management. Also - why is there a short cut to show 1 track, a short cut to show 2 tracks AND a short cut to toggle between??? Just keep the toggle short cut!!
| Assignee | Alyssa Gulledge [ alyssa ] | Eric Blossom [ elb ] |
"All" and "None" refer to track selection. If you pull down "Edit" and click on "Select Tracks" you will see those as items in the pull right list. We can change them to "Select All Tracks" and "Deselect All Tracks" respectively.
Yes, set threshold above/below have been removed.
I'll work on a toggle for "Float" and its inverse.
I'll look into new toggles for the directional arrows and colors. This a new (and a good) request and deserving of a new Jira issue.
I'll look into the the coordination of "show 2 track" between the shortcut action and the data management table.
There are a few instances of toggles that switch state. (Unfortunately, we overload this term a bit and also use it to refer to boolean menu items (checkbox menu items)). The confusion you are seeing with the 1 and 2 track actions is that there is one to show 1 track and another to show 2. The toggle in the tool bar uses those two as clients. It is reasonable to have a shortcut for all three. One might also prefer to have any of those three in the tool bar. Note that toggles use their clients' icons. Toggles start with the verb "Toggle".
I would like this to be resolved.
I have opened new Jira issues (385 and 386)for the new toggles.
I have also opened a new issue for the bug in coordination with the data management table (387)
| Assignee | Eric Blossom [ elb ] | Alyssa Gulledge [ alyssa ] |
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
There seem to be several things going on here.
The troublesome (non working) actions are those that do not appear in the main menu system. The way Swing works these actions are not available for accelerator keys (the technical term for the shortcuts). Another problem is that the accelerators are not even set for these actions when IGB starts up.
There are also several bugs in the editor for accelerator keys in the "shortcuts" panel. There are tool bar buttons to toggle between two client actions. e.g. Expand and Collapse. The client actions still appear in the menu system and, hence, should be able to have accelerators. We could do one of the following:
IGB uses a GenericActionHolder instead of Swing's InputMap and ActionMap objects. Not sure if this helps or hurts.