Commit Graph
291 Commits
Author SHA1 Message Date
Kanwei Li 7fc83886e4 trackster: Fix error on saving when no chrom is currently viewed due to new saving of current viewport. Remove debug statements 2010-11-15 14:39:16 -05:00
Kanwei Li 48f582c3c4 trackster: Make navbar more compact; line things up properly. Fix ReferenceTrack adding extra space to top LabelTrack 2010-11-14 17:53:25 -05:00
James Taylor 87e426f400 Trackster: packed scripts, support LEN files that are space separated 2010-11-10 13:43:16 -05:00
James Taylor bb665f6b5e Trackster: save current viewport when saving viz 2010-11-07 17:31:07 -05:00
James Taylor 81b8472a87 Trackster UI tweaks, mainly moving the navigation to the top, still needs to be compressed and cleaned up. Also, getting borders and spacing a little more even. Some intial keyboard navigation 2010-11-07 15:56:53 -05:00
Ramkrishna Chakrabarty 45c6515b8b sample tracking
- new file browser for selecting datasets in the sequencer
2010-11-03 01:02:27 -04:00
Kanwei Li 6fd59bd382 No longer pre-generate menus on page load for popup-style menus. Instead, create menu dynamically when needed, greatly improving load time especially on data libraries with large number of potential menus.
Remove the creation of a background element that closes the active menu clicked. Instead, bind an event to close active menus to the document object of current and all other framesets. Tested in IE.

Update Tool Search/Recently Used code to reflect new changes.

Made some small tweaks to pass JSlint
2010-11-02 21:45:18 -04:00
Kanwei Li 6c79a5d8b4 trackster: Fix summary_tree data provider to reflect bottom level not being indexed anymore.
- Fix a bug causing no display modes to appear.
- Update "Visualize in Trackster" init code in root/history.mako

Fix small typo in root/tool_menu.mako
2010-11-02 21:35:35 -04:00
Dannon Baker 9e01737db3 Packing editor.
Tweak to reload.
2010-11-01 17:21:47 -04:00
Dannon Baker db8e1c8954 Cleanup of debug info. 2010-11-01 17:09:35 -04:00
Dannon Baker 5f3b33fff5 Shift management of the interaction between workflow outputs and HideDatasetActions to the front end editor.
This resolves the issue with multiple HideDatasetActions being created.
Existing workflows displaying multiple HideDatasetActions per step on the Run Workflow screen will persist.
These extra HideDatasetActions are harmless, but a simple edit workflow -> save will remove them.
2010-11-01 17:08:50 -04:00
Daniel Blankenberg ce7e2d3be9 Fix for refresh_on_change javascript. 2010-10-27 12:26:00 -04:00
Jeremy Goecks 235773f1d4 Fix condition used to check if tiles have been loaded/drawn in trackster. 2010-10-27 09:26:47 -04:00
Jeremy Goecks 30980f8f9b Fix path to closebox.png image; this will show the close button for screencasts. 2010-10-26 22:59:40 -04:00
Kanwei Li c9a510104b trackster: Fix LineTrack rendering bug when more than one tile on screen. Refactored to pass JSLint 2010-10-26 19:24:26 -04:00
Kanwei Li 31e4dd2867 trackster: Fix shared visualizations
- Add excanvas support for IE <9 to trackster, but performance is bad
- Refactor unused/duplicate init code for trackster

- Fix IE workflow bug with Input Datasets
- Fix IE search button displaying twice
2010-10-25 18:49:26 -04:00
Kanwei Li 7e72dec4be Workflows now work in Internet Explorer again. IE does not implement Array.indexOf so we define it in galaxy.base. Update excanvas 2010-10-22 18:23:47 -04:00
Jeremy Goecks dc0075bf9a Fix setting of minimum and maximum values for tracker slider filters. 2010-10-20 00:42:45 -04:00
Kanwei Li 43028dbcc0 trackster: Add proper CIGAR support to BAM display (properly displays matches, deletions, skipped bases, and clipping. Padding and insertions are skipped as of now as there is no good way to insert new space into the view.)
- Don't re-add new datasets when refreshing after using "Add into current viz" link
- To prevent browser lockup, only display up to 50 lines of features by default (user-editable in future). TODO: add warning message when this occurs
2010-10-19 18:58:57 -04:00
Jeremy Goecks 3caf212cab Add dynamic attribute filtering framework for trackster and enable dynamic filtering of VCF quality values and BED score values. Framework enables users to interactively filter a visualized dataset within trackster; for example, a BED file of peaks can be filtering so that only peaks with a score greater than 100 are shown.
Individual changes include: (a) improvements to datatypes and data providers to support BED score filtering and VCF quality filtering; (b) addition of jQueryUI theme for slider; (c) modifications to trackster to show, update, and apply filters.
2010-10-19 16:25:51 -04:00
Kanwei Li 22525a5fe4 trackster:
- New histogram mode for LineTrack that's used by default.
- Refactored LineTrack drawing code
- Can change draw color of LineTrack
- summary_tree now shows maximum y-axis value
- When editing track config, "Enter" and "Esc" keys submit and cancel the changes, respectively
2010-10-15 14:24:35 -04:00
Kanwei Li fbae6b5f6a trackster: Fix ReferenceTrack not drawing, summary_tree display is now histogram and more fine grained. Small overview fix, UI tweaks 2010-10-13 17:59:56 -04:00
Kanwei Li 51da44adf9 trackster: Fix refactor breaking bam tracks. Only show draggable handle in editor mode. Update jQuery UI to 1.8.5 and add slider widget 2010-10-12 15:24:41 -04:00
Kanwei Li 2de6b5e055 trackster:
- Fix LineTrack axis labels not aligning consistently
- New image for draggable elements
- New slider that is rounded, easier to see and will go off-screen if smaller than the minimum width
- Added "Close overview" link when overview is showing
- Fix array_tree from recent refactoring
2010-10-08 16:56:45 -04:00
Jeremy Goecks abea9f8f76 Make VCF a first-class type in trackster. Added VCF data provider and VCF tracks type to trackster; new functionality is used to show reference base and alternate base for SNPs in VCF tracks. Also refactored data providers so that they inherit from a base provider. 2010-10-07 21:26:21 -04:00
Kanwei Li a889f76076 trackster: Can now reorder tracks inline. Put cancel button in modal dialogs to the left instead of right 2010-10-06 13:07:45 -04:00
Kanwei Li 6ba7f2811f New style for search boxes in grids. Grid items will no longer show outline when hovered upon if there are no actions to be performed. 2010-10-05 18:21:31 -04:00
Kanwei Li 06b9b59b96 Make links in split menubuttons take the link instead of popping up the menu options. Use new menubutton style in data libraries and sharing_base. 2010-10-03 19:12:40 -04:00
Kanwei Li 52459bceb0 Refactored refresh_on_change javascript code to run in galaxy.base when the page is loaded. Fixed bug with autocomplete_select: when switching from a value within refresh_on_change_values to a value outside of it, the page did not refresh. Removed duplicate code from templates. 2010-10-01 16:20:34 -04:00
Kanwei Li 65a474b9a0 trackster: Move "Add Tracks" button to main pane, UI tweaks for overview 2010-09-29 13:56:09 -04:00
Kanwei Li 0fbab45d14 trackster: Inline editing of configuration and removing of tracks, obsoleting the right editing panel. Improved appearance of overview box by adding a background for the scroll bar, and having a sliding window to indicate region shown. Added id numbers in front of API results for upcoming interactive script. 2010-09-23 20:00:58 -04:00
Ramkrishna Chakrabarty b8d1b02a55 interactivity bug fixed in mutation viz tool 2010-09-20 14:58:59 -04:00
Ramkrishna Chakrabarty 1bac740073 mutation viz tool
- now the tool requires the user to enter the specific columns indicating ref base, position, and start of a sample
- added an interactive zoom option. when this option is selected, the image can be zoomed in or out using the mouse wheel.
- fixed the firefox & opera problems in displaying the svg image
2010-09-20 12:07:09 -04:00
Kanwei Li a5ef9b53e2 - Refactored tagging/autocomplete JS, fixing bugs regarding leaving the tagging box
- Better packing for trackster when zoomed in as packing will be done on a w_scale basis instead of rounding to levels
- Move folder icon in data libraries to next to the text, rephrase suggestion on compression schemes
2010-09-17 17:51:11 -04:00
Dannon Baker 5a28632683 Tweak to prevent workflow output indicator icon from getting out of sync. And repack. 2010-09-10 12:14:30 -04:00
Dannon Baker e629c020d2 Packed scripts. 2010-09-10 12:05:30 -04:00
Dannon Baker 74f9454636 Workflow changes-
Output flagging now has a third faded icon, and tooltip, and aligns properly on multiline outputs.
    ToolForm width now properly calculated, taking into account the length of input and output rows.
        -Max width is 250px, min is 150px.
    Output extensions are now properly separated by ', ' (including space) instead of just slammed together.
    Fixed a bug where a newly created node had no outputs array.
2010-09-10 11:59:38 -04:00
Jeremy Goecks 9e44caf592 UI improvements for annotating items: more descriptive messages and larger targets. 2010-09-08 17:52:01 -04:00
Dannon Baker 85e7c42ba8 Flagging of workflow outputs from within the workflow editor itself.
Hover over any output, click the asterisk to flag/unflag an output as a workflow-wide output.
2010-09-08 15:24:15 -04:00
Kanwei Li a541704a4a trackster: Fix drawing of features being cut off at bottom, added dropdown to track name for setting overview, and preferences in the future 2010-09-02 18:46:23 -04:00
Kanwei Li 4ea8dd779b trackster: Changing display mode from "Auto" now fetches additional detail data and displays features. Displays error messages in canvas elements if present. Limit number of features displayed in one tile due to above feature. Fix bugs in visualization creation from form 2010-09-01 18:20:42 -04:00
Dannon Baker 894e1a43c3 Repacked workflow editor. 2010-08-31 11:58:59 -04:00
Dannon Baker a7aab68bbc Constrain connection to correct outputs when using ChangeDatatypeAction in workflow editor. 2010-08-30 18:48:08 -04:00
Dannon Baker 1d7a117da0 Workflow Fix- Enabled connection of nodes using ChangeDatatypeAction in the editor pane. 2010-08-30 18:38:35 -04:00
Kanwei Li ab8217d1e9 trackster: fix use of an old variable 2010-08-27 15:43:11 -04:00
Kanwei Li d8ad672ecf trackster: make "go-to" navigation inline, activated when chrom position is clicked. Drag-zoom overlay should now cover entire viewport (was missing a bit at bottom) 2010-08-26 19:04:55 -04:00
Kanwei Li 2b1d895ecf Repack js 2010-08-26 12:14:04 -04:00
Kanwei Li 4f291405f6 trackster: Overview track, viz cloning, "Go-to" specific location, UI fixes
- Each track now has an Overview checkbox that will set the initial chromosome-wide view of that track to become the overview
- Visualizations that users own or are shared with can now be cloned
- Go-to feature lets users go directly to a certain chrom (eg "chr1"), or chrom and position ("chr1:1-100,000,000")
- Fix double flushing when creating converter
- Line tracks display mode is now inline
- Use smaller font for tracks
- Fix web-kit bug where using scrollbar would also trigger viewport dragging
- Fix Line tracks jumping around when changing position
- Made default Line track height 80px from 100px
- Fix drag-zoom overlay appearing at top of header instead of Label track

- Minor grid refactoring
2010-08-26 12:12:32 -04:00
Dannon Baker 1d6896a316 Fix for the issue where multiple of the same action on separate outputs of a single tool were being overwritten as one. 2010-08-26 08:10:12 -04:00
Kanwei Li 4bd9e909b7 Use image_path for workflows and show_modal instead of relative paths 2010-08-20 15:00:52 -04:00