BioTreeContainer and its Features
Formal Definition
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/asn_spec/BioTreeContainer.html
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: $url=https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/String/substring$text=substring 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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