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.</p> <p> 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 However, some types of queries will return an error, e.g. post-assembly GenBank entries, withdrawn gene names, and abandoned synonyms.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.</p> <p> <!--#if expr="${SERVER_NAME} = /-china/" --> <a href='../../../videos/5zc9sqd4SD4.mp4'> - <img src=../../images/videoIcon.png></a> + <img alt="" src=../../images/videoIcon.png></a> Visit our <a href="/videos/" target="_blank">Video Page</a>. <!--#else --> <iframe width="560" height="350" src="https://www.youtube.com/embed/5zc9sqd4SD4?rel=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> </p> <p> Visit our <a href="https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" target="_blank">YouTube channel</a> for more videos. <!--#endif --> </p> <h6>Finding a genome location using BLAT</h6> <p> If you have genomic, mRNA, or protein sequence, but don't know the name or the location to which it @@ -431,106 +431,106 @@ <ul class="gbsNoBullet"> <li> <strong>Hide:</strong> the track is not displayed at all. To hide all the annotation tracks, click the <em>hide all</em> 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.</li> <li> <strong>Dense:</strong> 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. <br> - <img src="../../images/dense14_800_gc29.png" width="800px"> + <img alt="GENCODE gene tracks in dense display mode collapsed into a single line per track" src="../../images/dense14_800_gc29.png" width="800px"> </li> <li> <strong>Full:</strong> 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.<br> - <img src="../../images/full14_800_gc29-1.png" width="800px"> + <img alt="GENCODE gene tracks in full display mode showing each transcript individually" src="../../images/full14_800_gc29-1.png" width="800px"> </li> <li> <strong>Squish:</strong> 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.<br> - <img src="../../images/squish14_800_gc29-1.png" width="800px"> + <img alt="GENCODE gene tracks in squish display mode with compressed transcript labels" src="../../images/squish14_800_gc29-1.png" width="800px"> </li> <li> <strong>Pack:</strong> 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.<br> - <img src="../../images/pack14_800_gc29-1.png" width="800px" > + <img alt="GENCODE gene tracks in pack display mode with labeled transcripts at reduced height" src="../../images/pack14_800_gc29-1.png" width="800px" > </li> </ul> <p> 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 <em>refresh</em> button. Alternatively, you can change the display mode by using the Genome Browser's <a href="#RIGHT_CLICK_NAV">right-click navigation</a> 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.</p> <a name="duplicate"></a> <h3>Duplicating a track</h3> <p> 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:</p> -<p class="text-center"><img src="/images/duplicateDisplay.png"></p> +<p class="text-center"><img alt="Track settings showing the Duplicate track link next to the Display mode dropdown" src="/images/duplicateDisplay.png"></p> <p> 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'.</p> <div class="row"> <div class="col-md-6"> - <p class="text-center"><img src="/images/duplicateTrackUi_GENCODEV43.png" width="550px"></p> + <p class="text-center"><img alt="Track settings for a duplicated GENCODE V43 track with independent configuration" src="/images/duplicateTrackUi_GENCODEV43.png" width="550px"></p> </div> <div class="col-md-6"> - <p class="text-center"><img src="/images/removeDuplicateTrackUi_GENCODEV43.png" width="550px"></p> + <p class="text-center"><img alt="Track settings showing the option to remove a duplicated GENCODE V43 track" src="/images/removeDuplicateTrackUi_GENCODEV43.png" width="550px"></p> </div> </div> <p> 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.</p> <p class="text-center"> -<img src="/images/duplicationHgTracks_GENCODEV43.png" width="800px"> +<img alt="Browser view showing two copies of the GENCODE V43 track with different display settings" src="/images/duplicationHgTracks_GENCODEV43.png" width="800px"> </p> <h3>Changing the display mode for a group of tracks</h3> <p> 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 <em>configure</em> button on the annotation tracks page or the <em>configure tracks and display</em> button on the Gateway page. Exercise caution when using the <em>show all</em> 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.</p> <h3>Hiding the track display controls</h3> <p> 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.</p> <p> 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 <em>default tracks</em> 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.</p> <h3> Video tutorial on changing track display modes</h3> <p> <!--#if expr="${SERVER_NAME} = /-china/" --> <a href='../../../videos/jKix2B3hwnw.mp4'> - <img src=../../images/videoIcon.png></a> + <img alt="" src=../../images/videoIcon.png></a> Visit our <a href="/videos/" target="_blank">Video Page</a>. <!--#else --> <iframe width="560" height="350" src="https://www.youtube.com/embed/jKix2B3hwnw?rel=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> </p> <p> Visit our <a href="https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" target="_blank">YouTube channel</a> for more videos. <!--#endif --> </p> <a name="NAV"></a> <h3>Zooming and scrolling the tracks display</h3> <p>