ed6ba595e20e8d55ba2d5441c5bc8cbd5d7937de kuhn Mon Nov 22 14:43:05 2021 -0800 tiny tweaks. refs #28551 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index e3902fb..3aaab77 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -737,44 +737,44 @@ 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. + 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. - <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> <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 like track selections, custom + 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. (At the moment, there is no visual indicator in such a Genome Browser window that changes are not saved, @@ -822,31 +822,31 @@ link</a> to select the checkbox for UCSC RefSeq subtrack in the refSeq composite track, allowing display alongside default tracks </li> </ul> <p> If a login and password is required to access data loaded through a URL (e.g., via https: protocol), this information can be included in the URL using the format protocol://user:password@server.com/somepath. Only Basic Authentication is supported for HTTP. Note that passwords included in URLs are not protected. If a password contains a non-alphanumeric character, such as $, the character must be replaced by the hexadecimal representation for that character. For example, in the password mypwd$wk, the $ character should be replaced by %24, resulting in the modified password mypwd%24wk.</p> <p> For integration into your own website e.g. in an html IFRAME, you can obtain the track image only, without the rest of the genome browser user interface, by replacing hgTracks in the URL with -hgRenderTracks, like in this example:</p> +hgRenderTracks, such as in this example:</p> <pre><code><a href="http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr9%3A136130563-136150630" target="_blank">http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr9%3A136130563-136150630</a></code></pre> <p> Combine the above pieces of information into a URL of the following format (the information specific to your annotation file is highlighted):</p> <pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?org=<font color="000099"><em><organismName></em></font>&position=<font color="000099"><em><chrPosition></em></font>&hgt.customText=<font color="000099"><em><url></em></font></code></pre> <p> <strong><em>Example #5:</em></strong><br> The following URL will open up the Genome Browser window to display chr22 of the latest human genome assembly and will show the annotation track pointed to by the URL http://genome.ucsc.edu/goldenPath/help/test.bed: <pre><code <a class="insideLink" href="../../cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed</a></code></pre> <p>