Shear UI

empress/support_files/js/emperor-callbacks.js

@@ -64,15 +64,12 @@ plotView.on("click", function (name, object) {
 });
 
 plotView.on("select", function (samples, view) {
+    // remove any strangling observers
+    shearer.unregisterObserver("emperor-select");
+
     // cancel any ongoing timers
     clearTimeout(empress.timer);
 
-    // if there's any coloring setup remove it, and re-enable the update button
-    sPanel.sUpdateBtn.classList.remove("hidden");
-    sPanel.fUpdateBtn.classList.remove("hidden");
-    empress.clearLegend();
-    empress.resetTree();
-
     // fetch a mapping of colors to plottable objects
     var groups = view.groupByColor(samples);
     var namesOnly = {};
@@ -83,9 +80,23 @@ plotView.on("select", function (samples, view) {
             return item.name;
         });
     }
-    empress.colorSampleGroups(namesOnly);
+
+    var colorEmpress = () => {
+        // if there's any coloring setup remove it, and re-enable the update button
+        sPanel.sUpdateBtn.classList.remove("hidden");
+        sPanel.fUpdateBtn.classList.remove("hidden");
+        empress.clearLegend();
+        empress.resetTree();
+        empress.colorSampleGroups(namesOnly);
+    };
+    colorEmpress();
 
     // 4 seconds before resetting
+    var shearObs = {
+        shearerObserverName: "emperor-select",
+        shearUpdate: colorEmpress,
+    };
+    shearer.registerObserver(shearObs);
     empress.timer = setTimeout(function () {
         empress.resetTree();
         empress.drawTree();
@@ -95,6 +106,7 @@ plotView.on("select", function (samples, view) {
         }
 
         plotView.needsUpdate = true;
+        shearer.unregisterObserver("emperor-select");
     }, 4000);
 });
 
@@ -164,6 +176,9 @@ ec.controllers.animations.addEventListener("animation-ended", function (
 ec.controllers.color.addEventListener("value-double-clicked", function (
     payload
 ) {
+    // remove any strangling observers
+    shearer.unregisterObserver("emperor-value-double-clicked");
+
     // when dealing with a biplot ignore arrow-emitted events
     if (payload.target.decompositionName() !== "scatter") {
         return;
@@ -177,24 +192,33 @@ ec.controllers.color.addEventListener("value-double-clicked", function (
     ec.decViews.scatter.setEmissive(0x000000);
     plotView.needsUpdate = true;
 
-    // if there's any coloring setup remove it, and re-enable the update button
-    sPanel.sUpdateBtn.classList.remove("hidden");
-    sPanel.fUpdateBtn.classList.remove("hidden");
-    empress.clearLegend();
-    empress.resetTree();
-
     var names = _.map(payload.message.group, function (item) {
         return item.name;
     });
     var container = {};
     container[payload.message.attribute] = names;
-    empress.colorSampleGroups(container);
+
+    var colorEmpress = () => {
+        // if there's any coloring setup remove it, and re-enable the update button
+        sPanel.sUpdateBtn.classList.remove("hidden");
+        sPanel.fUpdateBtn.classList.remove("hidden");
+        empress.clearLegend();
+        empress.resetTree();
+        empress.colorSampleGroups(container);
+    };
+    colorEmpress();
 
     // 4 seconds before resetting
+    var shearObs = {
+        shearerObserverName: "emperor-value-double-clicked",
+        shearUpdate: colorEmpress,
+    };
+    shearer.registerObserver(shearObs);
     empress.timer = setTimeout(function () {
         empress.resetTree();
         empress.drawTree();
 
         plotView.needsUpdate = true;
+        shearer.unregisterObserver("emperor-value-double-clicked");
     }, 4000);
 });

empress/support_files/js/empress.js

@@ -2656,19 +2656,13 @@ define([
             this.setNodeInfo(node, "isColored", false);
             this.setNodeInfo(node, "visible", true);
         }
+        this._collapsedClades = {};
         this._dontCollapse = new Set();
         this._collapsedCladeBuffer = [];
         this._drawer.loadThickNodeBuff([]);
         this._drawer.loadCladeBuff([]);
         this._group = new Array(this._tree.size + 1).fill(-1);
-
-        // if _collapsedClades is empty then there is no need to call
-        // getTreeCoords which can save a fair amount of time depending on the
-        // size of the tree
-        if (Object.keys(this._collapsedClades).length > 0) {
-            this._drawer.loadTreeCoordsBuff(this.getTreeCoords());
-        }
-        this._collapsedClades = {};
+        this._drawer.loadTreeCoordsBuff(this.getTreeCoords());
     };
 
     /**

empress/support_files/js/shearer.js

@@ -241,12 +241,34 @@ define(["underscore", "util", "TreeController"], function (
      * the model is updated. Note this object must implement a shearUpdate()
      * method.
      *
-     * @param{Object} obs The object to register.
+     * @param{Object} obs The object to register. A '.shearerObserverName'
+     *                    property must be provided if this observer will at
+     *                    some point be unregistered.
      */
     ShearModel.prototype.registerObserver = function (obs) {
         this.observers.push(obs);
     };
 
+    /**
+     * Unregisters an observer to the model. The method will remove all
+     * observers with a '.shearerObserverName' === to removeObsName.
+     *
+     * @param{String} removeObsName The name of the observer to unregister.
+     */
+    ShearModel.prototype.unregisterObserver = function (removeObsName) {
+        var removeIndx;
+        var tempObs = [];
+        _.each(this.observers, function (obs, indx) {
+            if (
+                !obs.hasOwnProperty("shearerObserverName") ||
+                obs.shearerObserverName !== removeObsName
+            ) {
+                tempObs.push(obs);
+            }
+        });
+        this.observers = tempObs;
+    };
+
     /**
      * Removes a shear layer from a ShearModel
      * @param{ShearModel} model The ShearModel to use
@@ -354,12 +376,24 @@ define(["underscore", "util", "TreeController"], function (
     /**
      * Registers an observer to the model.
      *
-     * @param{Object} obs The object to register to the model
+     * @param{Object} obs The object to register to the model. A
+     *                    '.shearerObserverName' property must be provided if
+     *                    this observer will at some point be unregistered.
      */
     ShearController.prototype.registerObserver = function (obs) {
         this.model.registerObserver(obs);
     };
 
+    /**
+     * Unregisters an observer to the model. The method will remove all
+     * observers with a '.shearerObserverName' === to removeObsName.
+     *
+     * @param{String} removeObsName The name of the observer to unregister.
+     */
+    ShearController.prototype.unregisterObserver = function (removeObsName) {
+        this.model.unregisterObserver(removeObsName);
+    };
+
     /**
      * @class Shearer
      *
@@ -421,11 +455,23 @@ define(["underscore", "util", "TreeController"], function (
     /**
      * Registers an observer to the model.
      *
-     * @param{Object} obs The object to register to the model
+     * @param{Object} obs The object to register to the model. A
+     *                    '.shearerObserverName' property must be provided if
+     *                    this observer will at some point be unregistered.
      */
     Shearer.prototype.registerObserver = function (obs) {
         this.controller.registerObserver(obs);
     };
 
+    /**
+     * Unregisters an observer to the model. The method will remove all
+     * observers with a '.shearerObserverName' === to removeObsName.
+     *
+     * @param{String} removeObsName The name of the observer to unregister.
+     */
+    Shearer.prototype.unregisterObserver = function (removeObsName) {
+        this.controller.unregisterObserver(removeObsName);
+    };
+
     return Shearer;
 });

empress/support_files/js/util.js

@@ -276,10 +276,12 @@ define(["underscore"], function (_) {
     }
 
     /**
-     * Removes all keys from a if that same key is found in b and contains an
-     * empty array.
+     * Given two Objects that map keys to arrays, removes all keys from object
+     * "a" that are present in object "b" and point to a zero-length array in
+     * "b".
      *
-     * @param{Object} obj The object to remove keys from
+     * @param {Object} a The object from which keys will be removed.
+     * @param {Object} b The object used as a guide to remove keys from a.
      */
     function removeEmptyArrayKeys(a, b) {
         for (var key in b) {

empress/support_files/templates/side-panel.html

@@ -300,6 +300,10 @@
     (specified by the trajectory) at different timepoints throughout a
     gradient.
   </p>
+  <p class="side-panel-notes">
+    <b>Warning:</b> Do not shear the tree while an animation is running. Please
+    stop and restart if the tree was sheared during an animation.
+  </p>
   <p>
     <label for="animate-color-select">Color Map</label>
     <label class="select-container">
@@ -428,7 +432,9 @@
   </p>
   <p class="needs-feature-metadata side-panel-notes">
     These statistics will be automatically updated as the tree is sheared
-    using the "Shear Tree" functionality.
+    using the "Shear Tree" functionality. Note that, in the rare case when
+    the tree is sheared to only contain the root node, the root node will
+    be counted as a tip instead of an internal node.
   </p>
   <p class="needs-metadata side-panel-notes">
     Note that these statistics only pertain to the tree shown here,
@@ -465,6 +471,10 @@
   </p>
   <p class="side-panel-notes indented">
     Controls behavior of when to draw circles at nodes' positions.
+    Note that, in the rare case when the tree is sheared to only
+    contain the root node, a circle will nonetheless always be
+    drawn for it to serve as a visual marker (unless "Hide all node
+    circles" is selected).
   </p>
   <hr />
   <p class="side-panel-inner-header">