schrodinger.ui.sequencealignment.tree_node module¶

Implementation of multiple sequence viewer TreeNode class.

class schrodinger.ui.sequencealignment.tree_node.TreeNode(level)[source]¶

Bases: object

The TreeNode class is a simple implementation of tree structure used to represent and display phylogenetic trees in the sequence viewer.

__init__(level)[source]¶

original_node¶: Corresponding node in the original tree.

maxLevel(level=0)[source]¶

Returns a maximum tree depth.

Parameters: level (int (optional)) – optional initial level
Return type: int
Returns: Maximum tree depth level.

findNode(x, y, radius)[source]¶

Finds a tree node at a specified position within a specified radius.

Parameters

x (int) – x coordinate
y (int) – y coordinate
radius (int) – node search radius (used as a Manhattan distance)

Return type

TreeNode

Returns

Tree node at (x, y) or None if node was not found there.

selectSequences()[source]¶: Recursively select all sequences within self.

hideSequences()[source]¶: Recursively hide all sequences within self.

sequencesVisible()[source]¶

Return True if any sequence within self is visible.

Returns: True if any sequence is visible
Return type: boolean

swap()[source]¶: Swaps tree branches.

getSequenceList(sequence_list)[source]¶

Builds a list of sequences by traversing the tree starting from self and appending the sequences to the sequence list.

Parameters: sequence_list (list of Sequence) – list of sequences to be extended
Return type: list of Sequence
Returns: built list of sequences

getVisibleTree()[source]¶

Return a subset of the tree that includes only the visible sequences. This method is used to actually draw the tree with branches that are partially hidden.

Return type: TreeNode
Returns: visible tree

buildSequenceList(sequence_group)[source]¶

Build a list of sequences using a given sequence group as a source.

Initially, the tree has no sequences associated with it. Every node has a name corresposing to a particular sequence index in the sequence group. This method finds these correspoding sequences in the sequence group and adds them to the node’s sequence list.

This method expects the sequence names to be in format used by fileio.load_clustal_file function, i.e. in format SEQxxxx where xxxx corresponds to a sequence index in the sequence group.

Parameters: sequence_group (SequenceGroup) – source sequence group