5709a7858d5c197721be66d5218a79124abadb70
lrnassar
Tue Mar 17 08:46:31 2026 -0700
Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html
index db31eb32c9f..215a3fc17f9 100755
--- src/hg/htdocs/goldenPath/help/hgTracksHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html
@@ -178,31 +178,31 @@
immediately displaying the Genome Browser window. When this occurs, click on the item in which
you're interested and the Genome Browser will open to that location.
The search mechanism is not a site-wide search engine. Instead, it primarily searches GenBank mRNA
records whose text annotations can include gene names, gene symbols, journal title words, author
names, and RefSeq mRNAs. Searches on other selected identifiers, such as NP and NM accession
numbers, OMIM identifiers, and Entrez Gene IDs are supported. However, some types of queries will
return an error, e.g. post-assembly GenBank entries, withdrawn gene names, and abandoned synonyms.
If your initial query is unsuccessful, try entering a different related term that may produce the
same location. For example, if a query on a gene symbol produces no results, try entering an mRNA
accession, gene ID number, or descriptive words associated with the gene.
If you have genomic, mRNA, or protein sequence, but don't know the name or the location to which it
@@ -431,106 +431,106 @@
Hide: the track is not displayed at all. To hide all the annotation tracks, click
the hide all button. This mode is useful for restricting the display to only those tracks
in which you are interested. For example, someone who is not interested in SNPs or mouse synteny
may want to hide these tracks to reduce track clutter and improve speed. There are a few
annotation tracks that pertain only to one specific chromosome, e.g. Sanger22, Rosetta. In these
cases, the track and its associated controller will be hidden automatically when the track window
is not open to the relevant chromosome.
Dense: the track is displayed with all features collapsed into a single line.
This mode is useful for reducing the amount of space used by a track when you don't need
individual line item details or when you just want to get an overall view of an annotation. For
example, by opening an entire chromosome and setting the RefSeq Genes track to dense, you can get
a feel for the known gene density of the chromosome without displaying excessive detail.
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Full: the track is displayed with each annotation feature on a separate line. It
is recommended that you use this option sparingly, due to the large number of individual track
items that may potentially align at the selected position. For example, hundreds of ESTs might
align with a specified gene. When the number of lines within a requested track location exceeds
250, the track automatically defaults to a more tightly-packed display mode. In this situation,
you can restore the track display to full mode by narrowing the chromosomal range displayed or by
using a track filter to reduce the number of items displayed. On tracks that contain only hide,
dense, and full modes, you can toggle between full and dense display modes by clicking on the
track's center label.
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Squish: the track is displayed with each annotation feature shown separately, but
at 50% the height of full mode. Features are unlabeled, and more than one may be drawn on the same
line. This mode is useful for reducing the amount of space used by a track when you want to view a
large number of individual features and get an overall view of an annotation. It is particularly
good for displaying tracks in which a large number of features align to a particular section of a
chromosome, e.g. EST tracks.
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Pack: the track is displayed with each annotation feature shown separately and
labeled, but not necessarily displayed on a separate line. This mode is useful for reducing the
amount of space used by a track when you want to view the large number of individual features
allowed by squish mode, but need the labeling and display size provided by full mode. When the
number of lines within the requested track location exceeds 250, the track automatically defaults
to squish display mode. In this situation, you can restore the track display to pack mode by
narrowing the chromosomal range displayed or by using a track filter to reduce the number of items
displayed. To toggle between pack and full display modes, click on the track's center label.
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The track display controls are grouped into categories that reflect the type of data in the track,
e.g., Gene Prediction Tracks, mRNA and EST tracks, etc. To change the display mode for a track, find
the track's controller in the Track Controls section at the bottom of the Genome Browser page,
select the desired mode from the control's display menu, and then click the refresh button.
Alternatively, you can change the display mode by using the Genome Browser's
right-click navigation feature, or can toggle between dense and full
modes for a displayed track (or pack mode when available) by clicking on the optional center label
for the track.
Duplicating a track
Tracks that are not inside of composite or supertracks can be duplicated to allow for independent
track settings for a track. To duplicate a track, go to the track settings page for the track and
there will be a link, "Duplicate track", next to the Display mode setting:
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Clicking the link will take you to the new track
settings page for the duplicate track with the additional text, "(duplicate #1)". This number
will increment by one for each additional copy of the track. After creating the copy, a
"Remove duplicate" link will also appear on the track settings page for when you wish to
remove the duplicated track. As an example, duplicating the GENCODE track on hg38 allows users to
have two tracks, one in 'squish' mode and a second track in 'full' mode as a 'density graph'.
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Each copy of the track will have it's
own independent settings to allow for multiple display views without having to revert back to an
alternate view for the dataset.
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Changing the display mode for a group of tracks
Track display modes may be set individually or as a group on the Genome Browser Track Configuration
page. To access the configuration page, click the configure button on the annotation tracks
page or the configure tracks and display button on the Gateway page. Exercise caution when
using the show all buttons on track groups or assemblies that contain a large number
tracks; this may seriously impact the display performance of the Genome Browser or cause your
Internet browser to time out.
Hiding the track display controls
The entire set of track display controls at the bottom of the annotation tracks page may be hidden
@@ -557,31 +557,31 @@
information about the configuration options is available within the description text or through a
special help link located in the configuration section.
Filter and configuration settings are persistent from session to session on the same web browser.
To return the Genome Browser display to the default set of tracks (but retain custom tracks and
other configured Genome Browser settings), click the default tracks button on the Genome
Browser tracks page. To remove all user configuration settings and custom tracks, and completely
restore the defaults, click the "Reset All User Settings" under the top blue Genome
Browser menu.
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