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BioTreeContainer and its Features

Formal Definition


The BioTreeContainer consist of a list of nodes linked by unique node ids. Each node can have one or more features. A feature is a property of the node such as a sequence identifier, organism name or a color. Each feature has a unique identifying name within the tree and those feature names are specified in the tree's feature dictionary, fdict. Feature values are always strings. Some of the feature types have special meanings that can affect the tree’s layout or appearance. All features can be returned to the Treeviewer client in the JSON node descriptions.

Feature values with Special Meaning

Feature Value Meaning
$URL If the value of a feature contains the keyword ‘$URL’ then the specified link will be displayed in the tooltip for the node. The usage should follow the following example:


The feature value starts with $url=
The text between $url= and $text= is the link itself
Text after $text= is the display part of the link

Feature names with Special Meaning

Feature Name Meaning
label This feature holds the default label displayed for the node. Users can specify label formats based on other features if they don’t want to use ‘label’ as the default.
seq-id ID of the sequence associated with the node
seq-title Title of the sequence associated with the node
accession-nbr Sequence accession number
tax-id Taxonomic ID of the organism associated with the node
dist Distance from the node to its parent. This distance is used when formatting the tree for distance-based layouts.
cluster-id A cluster ID can be assigned to a group of nodes that have some common property.  All nodes with the same cluster ID are then drawn with a common color to show their association.
marker A marker attribute that changes the color and size at which a node is drawn.
$NODE_COLLAPSED When this feature set to 1, all nodes underneath this node are hidden (collapsed). When this feature is 0 or not present, child nodes appear normally.
$NODE_SIZE This feature is the size, expressed as a radius, at which the node is drawn. If this feature is not present for a node, the node is drawn with the default radius.
$NODE_BOUNDED This feature specifies a colored boundary to draw around the node and all its children.
$NODE_COLOR Color with which to draw the node. If $NODE_COLOR is not specified, the default color is used.
$LABEL_COLOR Color with which to draw the label text. If $LABEL_COLOR is not specified, the default color is used.
$LABEL_BG_COLOR Color with which to draw background of the label text. If $LABEL_BG_COLOR is not specified, no background is drawn.
$EDGE_COLOR Color of the edge from this node to its parent. If $EDGE_COLOR is not specified, the default color is used.
$EDGE_GRADIENT If this feature is set to “1” the color of the edge from this node to its parent will be interpolated between the $EDGE_COLOR of this node and the $EDGE_COLOR of the parent node.
$SEL_CLUSTERS This feature is similar to cluster-id except that it contains a list of clusters created via selection or macros. Each selection cluster has a unique name and color.
$PRIORITY The $PRIORITY feature is an integer value. When a node is collapsed and it does not already have a label assigned, we search all the nodes underneath it and if one or more have the $PRIORITY feature, than the label of the node with the highest $PRIORITY value is used as the label for the collapsed node.  If there is a tie for highest value, we pick the node closest to the center of the subtree.  Also, if any nodes have a priority > 1000, the node is not collapsed (if the user is using the collapse-to-viewport feature).
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Last updated: 2017-03-10T16:00:39-05:00