e76728e08e3fc0a1095b4961bb3dabeb0a8cb364 kuhn Mon Nov 22 17:10:22 2021 -0800 rephrasing a bit diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index 762be37..9706731 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -733,61 +733,65 @@ <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hideTracks=1" target="_blank">example link</a> to show no tracks at all</li> <li> <code>hideTracks=1&<trackName>=full|dense|pack|hide</code> - hide all tracks and show other tracks - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hideTracks=1&cytoBand=pack" target="_blank">example link</a> to show only the Chromosome Bands track and nothing else</li> <li> <code>highlight=<db>.<chrom>:<chromStart>-<chromEnd>#<color>|...</code> - highlight one or more regions in a given color on the image. Note that the arguments have to be URL-encoded for Internet browsers, so ":" becomes "%3A", "#" becomes "%23" and "|" becomes "%7"C. - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136136597-136139844&highlight=hg19.chr9%3A136138630-136139650%23AA0000%7Chg19.chr9%3A136136630-136137650%230000FF" target="_blank">example link</a> to highlight two parts of the ABO locus in red and blue.</li> <li> + <code>ignoreCookie=1</code> - do not load the user's existing settings saved in the internet browser's UCSC Genome Browser cookie. This means that the link will show the Genome Browser default settings such as track selections, custom tracks, and track hubs. Any changes you make in this new session will, however, affect the user's settings. E.g., if you add a track in this new window, and come back to the genome browser - later, this track will appear there. This setting is useful if a website - wants to link to the Genome Browser, wants to start with a "clean slate" but - the user will most likely come back to the Genome Browser and expect the - changes that they made still to be there. + later, the track will still be there. This setting is useful if a website + wants to link to the Genome Browser, starting with a "clean slate" but + believes the user will come back to the Genome Browser expecting the + changes to still be there. + Compare this behavior to the setting <code>incognito=1</code> described below. - <a href="../../cgi-bin/hgTracks?db=hg19&ignoreCookie=1" target="_blank">example link</a> to show the default tracks and positions for hg19, - in a new, clean session</li> + in a new, clean session.</li> <li> + <code>incognito=1</code> - do not load the user's existing settings saved in the internet browser's UCSC Genome Browser cookie and also never save them to the cookie. This means that that link will show the Genome Browser default settings such as track selections, custom tracks, and track hubs. Also: Any changes made by the user or other URL arguments will not affect the user's Genome Browser settings. E.g., if you add a track in this new window, and come back to the genome browser later, this track will appear NOT in the new window. This setting is useful if a website wants to link to the Genome Browser, wants to start with a "clean slate" but does not want any changes to affect other Genome Browser windows that are open or that the user may open later. - <a href="../../cgi-bin/hgTracks?db=hg19&incognito=1" target="_blank">example link</a> to show the default tracks and positions for hg19, in a new, clean session, that is completely independent from all other Genome Browser windows that the user has open or will open later. Any changes made to this window won't be saved and are lost as soon as the window is closed. + Compare this behavior to the setting <code>ignoreCookie=1</code> described above. (At the moment, there is no visual indicator in such a Genome Browser window that changes are not saved, but we could add one in the future, please contact us if you think this could be useful for you.) This variable is probably useful for most websites using our tool hgRenderTracks to show only the Browser's main image from a Javascript-driven website. </li> <li> <code>oligoMatch=pack&hgt.oligoMatch=<dnaSeq></code> - switch on the Short Match track and highlight a matching sequence - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&oligoMatch=pack&hgt.oligoMatch=TATAWAR" target="_blank">example link</a> to highlight the TATAWAR motif in the ABO locus</li> <li> <code>pix=<number></code> - set the width of the image in pixels -