Fix 258 (#301)

* started converting * started converting rest * finished empress.js * convert node menu * fixed tests/style * fixed node select * Update empress/support_files/js/empress.js Co-authored-by: Marcus Fedarko <[email protected]> * Update tests/python/test_core.py Co-authored-by: Marcus Fedarko <[email protected]> * addressed comments * changed to camel case * fixed barplot error * Update empress/support_files/js/empress.js Co-authored-by: Marcus Fedarko <[email protected]> * Update empress/support_files/js/empress.js Co-authored-by: Marcus Fedarko <[email protected]> * Update empress/support_files/js/empress.js Co-authored-by: Marcus Fedarko <[email protected]> * removed appending attributes * Update empress/support_files/js/empress.js Co-authored-by: Marcus Fedarko <[email protected]> * tojson Co-authored-by: Marcus Fedarko <[email protected]>
biocore · Aug 6, 2020 · 29d4563 · 29d4563
1 parent 776910e
commit 29d4563
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Showing 10 changed files with 673 additions and 621 deletions.
diff --git a/empress/core.py b/empress/core.py
@@ -266,38 +266,76 @@ def _to_dict(self):
             4020, 4020
         )
 
-        tree_data = {}
+        # store node data in a postorder fashion.
+        # Note: currently, bp-tree uses 1-based index so the first element will
+        #       start at 1. Thus, the 0th index is null. This will be fixed in
+        #       #223
+        tree_data = [0]
+        td_to_ind = {
+            # note: color, isColored, visible, and inSample with be appended in
+            # empress constructor. They are not added here because all nodes
+            # will be initialized with the same value.
+            #
+            # all nodes
+            "name": 0,
+            "x2": 1,
+            "y2": 2,
+            "xr": 3,
+            "yr": 4,
+            "xc1": 5,
+            "yc1": 6,
+            "xc0": 7,
+            "yc0": 8,
+            "angle": 9,
+            # all internal nodes
+            "highestchildyr": 10,
+            "lowestchildyr": 11,
+            # non-root internal nodes
+            "arcx0": 12,
+            "arcy0": 13,
+            "arcstartangle": 14,
+            "arcendangle": 15
+        }
         names_to_keys = {}
         # Note: tree_data starts with index 1 because the bp tree uses 1 based
         # indexing
         for i, node in enumerate(self.tree.postorder(include_self=True), 1):
-            tree_data[i] = {
-                'name': node.name,
-            }
+            if node.is_tip():
+                # add one to account for 0-based index
+                tree_data.append([0] * (td_to_ind["angle"] + 1))
+            elif node.is_root():
+                # add 2 to account for highestchildyr and lowestchildyr
+                tree_data.append([0] * (td_to_ind["angle"] + 2 + 1))
+            else:
+                tree_data.append([0] * len(td_to_ind))
+            tree_data[i][td_to_ind["name"]] = node.name
             # Add coordinate data from all layouts for this node
             for layoutsuffix in layout_to_coordsuffix.values():
                 xcoord = "x" + layoutsuffix
                 ycoord = "y" + layoutsuffix
-                tree_data[i][xcoord] = getattr(node, xcoord)
-                tree_data[i][ycoord] = getattr(node, ycoord)
+                tree_data[i][td_to_ind[xcoord]] = getattr(node, xcoord)
+                tree_data[i][td_to_ind[ycoord]] = getattr(node, ycoord)
             # Hack: it isn't mentioned above, but we need start pos info for
             # circular layout. The start pos for the other layouts is the
             # parent xy coordinates so we need only need to specify the start
             # for circular layout.
-            tree_data[i]["xc0"] = node.xc0
-            tree_data[i]["yc0"] = node.yc0
-            tree_data[i]["angle"] = node.clangle
+            tree_data[i][td_to_ind["xc0"]] = node.xc0
+            tree_data[i][td_to_ind["yc0"]] = node.yc0
+            tree_data[i][td_to_ind["angle"]] = node.clangle
 
             # Also add vertical bar coordinate info for the rectangular layout,
             # and start point & arc coordinate info for the circular layout
             if not node.is_tip():
-                tree_data[i]["highestchildyr"] = node.highest_child_yr
-                tree_data[i]["lowestchildyr"] = node.lowest_child_yr
+                tree_data[i][td_to_ind["highestchildyr"]] = \
+                    node.highest_child_yr
+                tree_data[i][td_to_ind["lowestchildyr"]] = node.lowest_child_yr
                 if not node.is_root():
-                    tree_data[i]["arcx0"] = node.arcx0
-                    tree_data[i]["arcy0"] = node.arcy0
-                    tree_data[i]["arcstartangle"] = node.highest_child_clangle
-                    tree_data[i]["arcendangle"] = node.lowest_child_clangle
+                    tree_data[i][td_to_ind["arcx0"]] = node.arcx0
+                    tree_data[i][td_to_ind["arcy0"]] = node.arcy0
+                    tree_data[i][td_to_ind["arcstartangle"]] = \
+                        node.highest_child_clangle
+                    tree_data[i][td_to_ind["arcendangle"]] = \
+                        node.lowest_child_clangle
 
             if node.name in names_to_keys:
                 names_to_keys[node.name].append(i)
@@ -326,6 +364,7 @@ def _to_dict(self):
             'tree': shifting(self._bp_tree),
             'lengths': lengths,
             'tree_data': tree_data,
+            'td_to_ind': td_to_ind,
             'names': names,
             'names_to_keys': names_to_keys,
             # feature table

diff --git a/empress/support_files/js/canvas-events.js b/empress/support_files/js/canvas-events.js
@@ -156,14 +156,14 @@ define(["glMatrix", "SelectedNodeMenu"], function (gl, SelectedNodeMenu) {
                 // margin of error for mouse click to still register a node sel
                 var epsilon = 10;
                 var closestDist = Infinity;
-                var closestNode = null;
+                var closeNode = null;
                 var xDist, yDist, closeNodeKey;
 
                 // Go through all the nodes in the tree and find the node
                 // closest to the (x, y) point that was clicked
                 for (var i = 1; i <= empress._tree.size; i++) {
                     var node = empress._treeData[i];
-                    if (!node.visible) continue;
+                    if (!empress.getNodeInfo(node, "visible")) continue;
                     var nodeX = empress.getX(node);
                     var nodeY = empress.getY(node);
                     xDist = x - nodeX;