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

..

fugue

trackster: Overview track, viz cloning, "Go-to" specific location, UI fixes

2010-08-26 12:12:32 -04:00

maf_icons

Scaling images. Changes to icons illustrating functionality of maf tools

2007-07-19 02:43:34 +00:00

qk

Add missing quickie icons, remove unused large icons

2010-01-05 16:49:56 -05:00

silk

Community: Display tool tarball contents on the view page and allow streaming contents directly from the tarball

2010-04-28 14:20:24 -04:00

tools/lda

Modify tools contributed by Chungoo Park (cxp440@psu.edu) for Linear Discriminant Analysis, and drawing Receiver Operating Characteristic plots; add a new tool to 'Generate A Matrix for using PC and LDA'; remove redundant 'Principal Component Analysis' tool.

2010-07-16 14:52:52 -04:00

tracks

Collapsed changeset: Trackster plugged into galaxy with behind-the-scenes indexing of Wiggle, coverage and interval datasets.

2009-03-11 00:29:01 +00:00

visualization

trackster: lighter intron colors

2010-01-26 16:43:58 -05:00

yui

1) Workflow changes

2007-10-30 05:44:08 +00:00

add_icon_dark.png

Image files for tagging UI

2009-08-27 16:27:10 -04:00

add_icon.png

Image files for tagging UI

2009-08-27 16:27:10 -04:00

aggregate_history1.png

score aggregate tool for .wig files

2007-01-22 20:28:36 +00:00

aggregate_history2.png

score aggregate tool for .wig files

2007-01-22 20:28:36 +00:00

Armitagep_manhattan.png

work around for composite objects without a base_name in grouping.py

2010-05-11 18:02:39 -04:00

Armitagep_qqplot.png

work around for composite objects without a base_name in grouping.py

2010-05-11 18:02:39 -04:00

bar_chart.png

Bar chart tool for use with taxonomy tools. Requires gnuplot and gnuplot.py. Still needs interface testing

2008-03-10 21:57:32 +00:00

bed_warn.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

blat_mapping_example.png

add images for short read tools.

2008-03-31 19:31:05 +00:00

brochure.pdf

More changes. Also should fix tests

2008-04-29 15:17:36 +00:00

closebox.png

A slightly better closing icon for screencast overlays

2010-02-10 15:13:46 -05:00

dat_points_table_brows_1.png

score aggregate tool for .wig files

2007-01-22 20:28:36 +00:00

ddarrowsplit.png

Fix various popup button issues. When there is no popup, button will be correctly sized (no extra space on right). When there is only a popup, entire button area is clickable. Combo buttons are mostly unchanged except that the popup click area is larger (anything to the right of the separator bar. An image is used so the arrow has a consistent shape and size across browsers.

2009-12-14 12:17:01 -05:00

delete_icon_dark.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

delete_icon.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

delete_tag_icon_gray.png

Image files for tagging UI

2009-08-27 16:27:10 -04:00

delete_tag_icon_white.png

Image files for tagging UI

2009-08-27 16:27:10 -04:00

delete.gif

Add a ratings framework so that users can rate shared items. All sharable items--histories, workflows, datasets, visualizations, and pages--can be rated. Main framework components are (1) database tables for storing ratings; (2) UsesItemRatings mixin that supports rating items and obtaining an item's average rating; (3) controller methods to handle rating asynchronously; and (4) jQuery star rating plugin and supporting code that enables interactive item rating. (2) and (4) can be reused in the community space.

2010-08-03 11:45:25 -04:00

draggable_horizontal.png

add image for trackster, use relative image url in css

2009-10-20 16:53:18 -04:00

dropdownarrow.png

Easier to see "new workflow" link in small window sizes. Proper dropdown arrow. Fixes #149

2009-09-24 19:58:35 -04:00

dualcolorcode.png

add images for short read tools.

2008-03-31 19:31:05 +00:00

dw.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

eye_icon_dark.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

eye_icon_grey.png

Fix bug reported by Gunnar Raetsch wherein a traceback is displayed if you view a file while it's uploading.

2009-05-05 17:06:11 -04:00

eye_icon.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

fetchTax.png

Changes to taxonomy fetches and two new datatypes: taxonomy and newick

2008-03-04 20:30:26 +00:00

galaxy.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

galaxyIcon_noText.png

Tool description cleanup. Next tool_conf. New logo

2007-07-13 18:36:44 +00:00

galaxyLogo_small.png

Made logo smaller

2007-07-12 19:04:15 +00:00

gsummary_out_groups.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

gsummary_out.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

hatch-023858.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

hatch-fade-023858.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

histogram2.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

histogram.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

history_down_arrow.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

history_up_arrow.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

history.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

icon_error_lrg.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

icon_error_sml.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

icon_info_lrg.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

icon_info_sml.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

icon_success_lrg.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

icon_success_sml.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

icon_warning_lrg.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

icon_warning_sml.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

kendall.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

light_gray_grid.gif

1) Workflow changes

2007-10-30 05:44:08 +00:00

loading_large_white_bg.gif

Workflow editor updates. Many UI improvements.

2007-10-19 02:55:45 +00:00

loading_small_white_bg.gif

Workflow editor updates. Many UI improvements.

2007-10-19 02:55:45 +00:00

lock.jpg

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

mag_glass.png

Tweaks to grid filter UI: (1) added search image/submit button for initiating search and (2) styled text filter criteria.

2009-11-18 11:51:09 -05:00

mutation_visualization_example.png

Mutation visualization tool

2010-08-12 14:21:59 -04:00

noodles.png

Genetic welcome page

2010-01-07 10:01:34 -05:00

overview_arrows.png

Overview improvements:

2009-08-06 14:43:51 -04:00

pearson.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

pencil_icon_dark.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

pencil_icon_grey.png

Fix bug reported by Gunnar Raetsch wherein a traceback is displayed if you view a file while it's uploading.

2009-05-05 17:06:11 -04:00

pencil_icon.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

pileup_parser_help1.png

Modifications to pileup_parser

2010-03-02 16:35:21 -05:00

pileup_parser_help2.png

Modifications to pileup_parser

2010-03-02 16:35:21 -05:00

pileup_parser_help3.png

Modifications to pileup_parser

2010-03-02 16:35:21 -05:00

pileup_parser_help4.png

Modifications to pileup_parser

2010-03-02 16:35:21 -05:00

poisson2test_eqn1.png

add figures for poisson2test tool.

2008-04-09 17:30:40 +00:00

poisson2test_eqn2.png

add figures for poisson2test tool.

2008-04-09 17:30:40 +00:00

resizable.png

Overview improvements:

2009-08-06 14:43:51 -04:00

scatter.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

scatterplot.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

screencast.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

SetAttr.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

SetGenome.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

short_reads_boxplot.png

Test fixes and first attampt to clean up short read tools

2008-03-21 20:27:24 +00:00

solid_qual.png

Second pass of help and interface updates. Not done yet...

2009-09-22 08:59:36 -04:00

spearman.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

square_empty.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

square_error.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

square_ok.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

square_queued.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

square_running.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

star.gif

Add a ratings framework so that users can rate shared items. All sharable items--histories, workflows, datasets, visualizations, and pages--can be rated. Main framework components are (1) database tables for storing ratings; (2) UsesItemRatings mixin that supports rating items and obtaining an item's average rating; (3) controller methods to handle rating asynchronously; and (4) jQuery star rating plugin and supporting code that enables interactive item rating. (2) and (4) can be reused in the community space.

2010-08-03 11:45:25 -04:00

t2ps_autoscale_tree.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2ps_autoscale.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2ps_heatmap.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2ps_ideal_ssp.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2ps_ideal.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2ps_missing_nodes.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2ps_node_label.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2t_dropdown.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2t_exclude.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2t_include.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2t_tree_exclude.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

t2t_tree_include.png

All taxonomy analysis tools are now in place

2008-03-13 14:45:10 +00:00

thumbtack_icon_dark.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

thumbtack_icon.png

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

tipsy.gif

Update tooltips using a modified version of tipsy, these can be used on any page if you include the tipsy script. Also, updating some styles and icons for tags.

2010-02-09 04:16:26 -05:00

tool_menu_down_arrow.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

tools.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

toolsExpandingMenu.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

up.gif

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

welcomePhoto.jpg

New welcome per james style but with images instead. Everything is now .flv

2009-04-20 14:28:08 -04:00

xy_example.jpg

Updating help for extract_GFF_features, get_flanks, xy_plot and Build_ucsc_custom_track tools.

2007-07-16 15:27:26 +00:00