01975a2c494b690fb94245a35ec2c016a3aa93ed kuhn Thu Sep 9 16:26:57 2021 -0700 changed level of browser lines and track lines sections to make them subsections. displayed by include in hgTracksHelp.html and customTrack.html diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index d5da05f..7641737 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -399,31 +399,31 @@ data is not displayed. Because of this, the data cannot be incrementally edited through this interface, but instead must be fully replaced using one of the data entry methods described in <a href="#ADD_CT">Loading a Custom Track into the Genome Browser</a>. If description text has been uploaded for the track, it will be displayed in the track documentation edit box, where it may be edited or completely replaced. Once you have completed your updates, click the Submit button to upload the new data into the Genome Browser.</p> <p> If the data or description text for your custom track was originally loaded from a file on your hard disk or server, you should first edit the file, then reload it from the Update Custom Track page using the "Choose File" button. Note that edits made on this page to description text uploaded from a file will not be saved to the original file on your computer or server. Because of this, we recommend that you use the documentation edit box only for changes made to text that was typed or pasted in.</p> <a name="lines"></a> -<h2>Browser lines</h2> +<h3>Browser lines</h3> <p> Browser lines configure the overall display of the Genome Browser window when your annotation file is uploaded. Each line defines one display attribute. Browser lines consist of the format:</p> <p> <pre><code>browser attribute_name attribute_value(s)</code></pre> <p> For example, if the browser line <code>browser position chr22:1-20000</code> is included in the annotation file, the Genome Browser window will initially display the first 20000 bases of chr 22.</p> <p> The following browser line attribute name/value options are available. The value <em>track_primary_table_name</em> must be set to the name of the primary table on which the track is based. To identify this table, open up the <A HREF="../../cgi-bin/hgTables" TARGET=_blank>Table Browser</A>, @@ -485,31 +485,31 @@ <li> <strong>full all</strong> - Displays all tracks in full mode. See NOTE for "dense all".</li> <li> <strong>full <<em>track_primary_table_name(s)</em>></strong> - Displays the specified tracks in full mode. Symbolic names must be used. Multiple track names should be space-separated.</li> </ul> <p> Note that the Genome Browser will open to the range defined in the Gateway page <em>search term</em> box or the position saved as the default unless the browser line position attribute is defined in the annotation file. Although this attribute is optional, it's recommended that you set this value in your annotation file to ensure that the track will appear in the display range when it is uploaded into the Genome Browser.</p> <a name="TRACK"></a> -<h2>Track lines</h2> +<h3>Track lines</h3> <p> Track lines define the display attributes for all lines in an annotation data set. If more than one data set is included in the annotation file, each group of data must be preceded by a track line that describes the display characteristics for that set of data. A track line begins with the word <code>track</code>, followed by one or more <code>attribute=value</code> pairs. Unlike browser lines - in which each attribute is defined on a separate line - all of the track attributes for a given set of data are listed on one line <em>with no line breaks</em>. The inadvertent insertion of a line break into a track line will generate an error when you attempt to upload the annotation track into the Genome Browser.</p> <p> The following track line attribute=value pairs are defined in the Genome Browser:</p> <ul> <li> <strong>name=<<em>track_label</em>></strong> - Defines the track label that will be displayed to the left of the track in the Genome Browser window, and also the label of the track control at the