@teselagen/ove 0.8.8 → 0.8.9

package/index.es.js

@@ -10749,7 +10749,7 @@ const _AbstractPointerSensor = class _AbstractPointerSensor {
 };
 __name(_AbstractPointerSensor, "AbstractPointerSensor");
 let AbstractPointerSensor = _AbstractPointerSensor;
-const events$1 = {
+const events = {
   move: {
     name: "pointermove"
   },
@@ -10763,7 +10763,7 @@ const _PointerSensor = class _PointerSensor extends AbstractPointerSensor {
       event
     } = props;
     const listenerTarget = getOwnerDocument(event.target);
-    super(props, events$1, listenerTarget);
+    super(props, events, listenerTarget);
   }
 };
 __name(_PointerSensor, "PointerSensor");
@@ -10786,7 +10786,7 @@ PointerSensor.activators = [{
     return true;
   }, "handler")
 }];
-const events$1$1 = {
+const events$1 = {
   move: {
     name: "mousemove"
   },
@@ -10800,7 +10800,7 @@ var MouseButton;
 })(MouseButton || (MouseButton = {}));
 const _MouseSensor = class _MouseSensor extends AbstractPointerSensor {
   constructor(props) {
-    super(props, events$1$1, getOwnerDocument(props.event.target));
+    super(props, events$1, getOwnerDocument(props.event.target));
   }
 };
 __name(_MouseSensor, "MouseSensor");
@@ -18200,7 +18200,7 @@ const __viteBrowserExternal$1 = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Ob
   __proto__: null,
   default: __viteBrowserExternal
 }, Symbol.toStringTag, { value: "Module" }));
-const require$$3$1 = /* @__PURE__ */ getAugmentedNamespace(__viteBrowserExternal$1);
+const require$$0 = /* @__PURE__ */ getAugmentedNamespace(__viteBrowserExternal$1);
 var objectInspect;
 var hasRequiredObjectInspect;
 function requireObjectInspect() {
@@ -18258,7 +18258,7 @@ function requireObjectInspect() {
     return $replace.call(str, sepRegex, "$&_");
   }
   __name(addNumericSeparator, "addNumericSeparator");
-  var utilInspect = require$$3$1;
+  var utilInspect = require$$0;
   var inspectCustom = utilInspect.custom;
   var inspectSymbol = isSymbol2(inspectCustom) ? inspectCustom : null;
   objectInspect = /* @__PURE__ */ __name(function inspect_(obj, options, depth, seen) {
@@ -90016,392 +90016,6 @@ function convertBasePosTraceToPerBpTrace(chromData) {
   }, chromData);
 }
 __name(convertBasePosTraceToPerBpTrace, "convertBasePosTraceToPerBpTrace");
-var events = { exports: {} };
-var hasRequiredEvents;
-function requireEvents() {
-  if (hasRequiredEvents) return events.exports;
-  hasRequiredEvents = 1;
-  var R2 = typeof Reflect === "object" ? Reflect : null;
-  var ReflectApply = R2 && typeof R2.apply === "function" ? R2.apply : /* @__PURE__ */ __name(function ReflectApply2(target, receiver, args) {
-    return Function.prototype.apply.call(target, receiver, args);
-  }, "ReflectApply");
-  var ReflectOwnKeys;
-  if (R2 && typeof R2.ownKeys === "function") {
-    ReflectOwnKeys = R2.ownKeys;
-  } else if (Object.getOwnPropertySymbols) {
-    ReflectOwnKeys = /* @__PURE__ */ __name(function ReflectOwnKeys2(target) {
-      return Object.getOwnPropertyNames(target).concat(Object.getOwnPropertySymbols(target));
-    }, "ReflectOwnKeys");
-  } else {
-    ReflectOwnKeys = /* @__PURE__ */ __name(function ReflectOwnKeys2(target) {
-      return Object.getOwnPropertyNames(target);
-    }, "ReflectOwnKeys");
-  }
-  function ProcessEmitWarning(warning) {
-    if (console && console.warn) console.warn(warning);
-  }
-  __name(ProcessEmitWarning, "ProcessEmitWarning");
-  var NumberIsNaN = Number.isNaN || /* @__PURE__ */ __name(function NumberIsNaN2(value) {
-    return value !== value;
-  }, "NumberIsNaN");
-  function EventEmitter() {
-    EventEmitter.init.call(this);
-  }
-  __name(EventEmitter, "EventEmitter");
-  events.exports = EventEmitter;
-  events.exports.once = once2;
-  EventEmitter.EventEmitter = EventEmitter;
-  EventEmitter.prototype._events = void 0;
-  EventEmitter.prototype._eventsCount = 0;
-  EventEmitter.prototype._maxListeners = void 0;
-  var defaultMaxListeners = 10;
-  function checkListener(listener) {
-    if (typeof listener !== "function") {
-      throw new TypeError('The "listener" argument must be of type Function. Received type ' + typeof listener);
-    }
-  }
-  __name(checkListener, "checkListener");
-  Object.defineProperty(EventEmitter, "defaultMaxListeners", {
-    enumerable: true,
-    get: /* @__PURE__ */ __name(function() {
-      return defaultMaxListeners;
-    }, "get"),
-    set: /* @__PURE__ */ __name(function(arg) {
-      if (typeof arg !== "number" || arg < 0 || NumberIsNaN(arg)) {
-        throw new RangeError('The value of "defaultMaxListeners" is out of range. It must be a non-negative number. Received ' + arg + ".");
-      }
-      defaultMaxListeners = arg;
-    }, "set")
-  });
-  EventEmitter.init = function() {
-    if (this._events === void 0 || this._events === Object.getPrototypeOf(this)._events) {
-      this._events = /* @__PURE__ */ Object.create(null);
-      this._eventsCount = 0;
-    }
-    this._maxListeners = this._maxListeners || void 0;
-  };
-  EventEmitter.prototype.setMaxListeners = /* @__PURE__ */ __name(function setMaxListeners(n2) {
-    if (typeof n2 !== "number" || n2 < 0 || NumberIsNaN(n2)) {
-      throw new RangeError('The value of "n" is out of range. It must be a non-negative number. Received ' + n2 + ".");
-    }
-    this._maxListeners = n2;
-    return this;
-  }, "setMaxListeners");
-  function _getMaxListeners(that) {
-    if (that._maxListeners === void 0)
-      return EventEmitter.defaultMaxListeners;
-    return that._maxListeners;
-  }
-  __name(_getMaxListeners, "_getMaxListeners");
-  EventEmitter.prototype.getMaxListeners = /* @__PURE__ */ __name(function getMaxListeners() {
-    return _getMaxListeners(this);
-  }, "getMaxListeners");
-  EventEmitter.prototype.emit = /* @__PURE__ */ __name(function emit(type2) {
-    var args = [];
-    for (var i = 1; i < arguments.length; i++) args.push(arguments[i]);
-    var doError = type2 === "error";
-    var events2 = this._events;
-    if (events2 !== void 0)
-      doError = doError && events2.error === void 0;
-    else if (!doError)
-      return false;
-    if (doError) {
-      var er;
-      if (args.length > 0)
-        er = args[0];
-      if (er instanceof Error) {
-        throw er;
-      }
-      var err2 = new Error("Unhandled error." + (er ? " (" + er.message + ")" : ""));
-      err2.context = er;
-      throw err2;
-    }
-    var handler = events2[type2];
-    if (handler === void 0)
-      return false;
-    if (typeof handler === "function") {
-      ReflectApply(handler, this, args);
-    } else {
-      var len = handler.length;
-      var listeners = arrayClone(handler, len);
-      for (var i = 0; i < len; ++i)
-        ReflectApply(listeners[i], this, args);
-    }
-    return true;
-  }, "emit");
-  function _addListener(target, type2, listener, prepend) {
-    var m2;
-    var events2;
-    var existing;
-    checkListener(listener);
-    events2 = target._events;
-    if (events2 === void 0) {
-      events2 = target._events = /* @__PURE__ */ Object.create(null);
-      target._eventsCount = 0;
-    } else {
-      if (events2.newListener !== void 0) {
-        target.emit(
-          "newListener",
-          type2,
-          listener.listener ? listener.listener : listener
-        );
-        events2 = target._events;
-      }
-      existing = events2[type2];
-    }
-    if (existing === void 0) {
-      existing = events2[type2] = listener;
-      ++target._eventsCount;
-    } else {
-      if (typeof existing === "function") {
-        existing = events2[type2] = prepend ? [listener, existing] : [existing, listener];
-      } else if (prepend) {
-        existing.unshift(listener);
-      } else {
-        existing.push(listener);
-      }
-      m2 = _getMaxListeners(target);
-      if (m2 > 0 && existing.length > m2 && !existing.warned) {
-        existing.warned = true;
-        var w2 = new Error("Possible EventEmitter memory leak detected. " + existing.length + " " + String(type2) + " listeners added. Use emitter.setMaxListeners() to increase limit");
-        w2.name = "MaxListenersExceededWarning";
-        w2.emitter = target;
-        w2.type = type2;
-        w2.count = existing.length;
-        ProcessEmitWarning(w2);
-      }
-    }
-    return target;
-  }
-  __name(_addListener, "_addListener");
-  EventEmitter.prototype.addListener = /* @__PURE__ */ __name(function addListener(type2, listener) {
-    return _addListener(this, type2, listener, false);
-  }, "addListener");
-  EventEmitter.prototype.on = EventEmitter.prototype.addListener;
-  EventEmitter.prototype.prependListener = /* @__PURE__ */ __name(function prependListener(type2, listener) {
-    return _addListener(this, type2, listener, true);
-  }, "prependListener");
-  function onceWrapper() {
-    if (!this.fired) {
-      this.target.removeListener(this.type, this.wrapFn);
-      this.fired = true;
-      if (arguments.length === 0)
-        return this.listener.call(this.target);
-      return this.listener.apply(this.target, arguments);
-    }
-  }
-  __name(onceWrapper, "onceWrapper");
-  function _onceWrap(target, type2, listener) {
-    var state2 = { fired: false, wrapFn: void 0, target, type: type2, listener };
-    var wrapped = onceWrapper.bind(state2);
-    wrapped.listener = listener;
-    state2.wrapFn = wrapped;
-    return wrapped;
-  }
-  __name(_onceWrap, "_onceWrap");
-  EventEmitter.prototype.once = /* @__PURE__ */ __name(function once3(type2, listener) {
-    checkListener(listener);
-    this.on(type2, _onceWrap(this, type2, listener));
-    return this;
-  }, "once");
-  EventEmitter.prototype.prependOnceListener = /* @__PURE__ */ __name(function prependOnceListener(type2, listener) {
-    checkListener(listener);
-    this.prependListener(type2, _onceWrap(this, type2, listener));
-    return this;
-  }, "prependOnceListener");
-  EventEmitter.prototype.removeListener = /* @__PURE__ */ __name(function removeListener(type2, listener) {
-    var list2, events2, position2, i, originalListener;
-    checkListener(listener);
-    events2 = this._events;
-    if (events2 === void 0)
-      return this;
-    list2 = events2[type2];
-    if (list2 === void 0)
-      return this;
-    if (list2 === listener || list2.listener === listener) {
-      if (--this._eventsCount === 0)
-        this._events = /* @__PURE__ */ Object.create(null);
-      else {
-        delete events2[type2];
-        if (events2.removeListener)
-          this.emit("removeListener", type2, list2.listener || listener);
-      }
-    } else if (typeof list2 !== "function") {
-      position2 = -1;
-      for (i = list2.length - 1; i >= 0; i--) {
-        if (list2[i] === listener || list2[i].listener === listener) {
-          originalListener = list2[i].listener;
-          position2 = i;
-          break;
-        }
-      }
-      if (position2 < 0)
-        return this;
-      if (position2 === 0)
-        list2.shift();
-      else {
-        spliceOne2(list2, position2);
-      }
-      if (list2.length === 1)
-        events2[type2] = list2[0];
-      if (events2.removeListener !== void 0)
-        this.emit("removeListener", type2, originalListener || listener);
-    }
-    return this;
-  }, "removeListener");
-  EventEmitter.prototype.off = EventEmitter.prototype.removeListener;
-  EventEmitter.prototype.removeAllListeners = /* @__PURE__ */ __name(function removeAllListeners(type2) {
-    var listeners, events2, i;
-    events2 = this._events;
-    if (events2 === void 0)
-      return this;
-    if (events2.removeListener === void 0) {
-      if (arguments.length === 0) {
-        this._events = /* @__PURE__ */ Object.create(null);
-        this._eventsCount = 0;
-      } else if (events2[type2] !== void 0) {
-        if (--this._eventsCount === 0)
-          this._events = /* @__PURE__ */ Object.create(null);
-        else
-          delete events2[type2];
-      }
-      return this;
-    }
-    if (arguments.length === 0) {
-      var keys3 = Object.keys(events2);
-      var key;
-      for (i = 0; i < keys3.length; ++i) {
-        key = keys3[i];
-        if (key === "removeListener") continue;
-        this.removeAllListeners(key);
-      }
-      this.removeAllListeners("removeListener");
-      this._events = /* @__PURE__ */ Object.create(null);
-      this._eventsCount = 0;
-      return this;
-    }
-    listeners = events2[type2];
-    if (typeof listeners === "function") {
-      this.removeListener(type2, listeners);
-    } else if (listeners !== void 0) {
-      for (i = listeners.length - 1; i >= 0; i--) {
-        this.removeListener(type2, listeners[i]);
-      }
-    }
-    return this;
-  }, "removeAllListeners");
-  function _listeners(target, type2, unwrap2) {
-    var events2 = target._events;
-    if (events2 === void 0)
-      return [];
-    var evlistener = events2[type2];
-    if (evlistener === void 0)
-      return [];
-    if (typeof evlistener === "function")
-      return unwrap2 ? [evlistener.listener || evlistener] : [evlistener];
-    return unwrap2 ? unwrapListeners(evlistener) : arrayClone(evlistener, evlistener.length);
-  }
-  __name(_listeners, "_listeners");
-  EventEmitter.prototype.listeners = /* @__PURE__ */ __name(function listeners(type2) {
-    return _listeners(this, type2, true);
-  }, "listeners");
-  EventEmitter.prototype.rawListeners = /* @__PURE__ */ __name(function rawListeners(type2) {
-    return _listeners(this, type2, false);
-  }, "rawListeners");
-  EventEmitter.listenerCount = function(emitter, type2) {
-    if (typeof emitter.listenerCount === "function") {
-      return emitter.listenerCount(type2);
-    } else {
-      return listenerCount.call(emitter, type2);
-    }
-  };
-  EventEmitter.prototype.listenerCount = listenerCount;
-  function listenerCount(type2) {
-    var events2 = this._events;
-    if (events2 !== void 0) {
-      var evlistener = events2[type2];
-      if (typeof evlistener === "function") {
-        return 1;
-      } else if (evlistener !== void 0) {
-        return evlistener.length;
-      }
-    }
-    return 0;
-  }
-  __name(listenerCount, "listenerCount");
-  EventEmitter.prototype.eventNames = /* @__PURE__ */ __name(function eventNames() {
-    return this._eventsCount > 0 ? ReflectOwnKeys(this._events) : [];
-  }, "eventNames");
-  function arrayClone(arr, n2) {
-    var copy = new Array(n2);
-    for (var i = 0; i < n2; ++i)
-      copy[i] = arr[i];
-    return copy;
-  }
-  __name(arrayClone, "arrayClone");
-  function spliceOne2(list2, index2) {
-    for (; index2 + 1 < list2.length; index2++)
-      list2[index2] = list2[index2 + 1];
-    list2.pop();
-  }
-  __name(spliceOne2, "spliceOne");
-  function unwrapListeners(arr) {
-    var ret = new Array(arr.length);
-    for (var i = 0; i < ret.length; ++i) {
-      ret[i] = arr[i].listener || arr[i];
-    }
-    return ret;
-  }
-  __name(unwrapListeners, "unwrapListeners");
-  function once2(emitter, name2) {
-    return new Promise(function(resolve, reject) {
-      function errorListener(err2) {
-        emitter.removeListener(name2, resolver2);
-        reject(err2);
-      }
-      __name(errorListener, "errorListener");
-      function resolver2() {
-        if (typeof emitter.removeListener === "function") {
-          emitter.removeListener("error", errorListener);
-        }
-        resolve([].slice.call(arguments));
-      }
-      __name(resolver2, "resolver");
-      eventTargetAgnosticAddListener(emitter, name2, resolver2, { once: true });
-      if (name2 !== "error") {
-        addErrorHandlerIfEventEmitter(emitter, errorListener, { once: true });
-      }
-    });
-  }
-  __name(once2, "once");
-  function addErrorHandlerIfEventEmitter(emitter, handler, flags) {
-    if (typeof emitter.on === "function") {
-      eventTargetAgnosticAddListener(emitter, "error", handler, flags);
-    }
-  }
-  __name(addErrorHandlerIfEventEmitter, "addErrorHandlerIfEventEmitter");
-  function eventTargetAgnosticAddListener(emitter, name2, listener, flags) {
-    if (typeof emitter.on === "function") {
-      if (flags.once) {
-        emitter.once(name2, listener);
-      } else {
-        emitter.on(name2, listener);
-      }
-    } else if (typeof emitter.addEventListener === "function") {
-      emitter.addEventListener(name2, /* @__PURE__ */ __name(function wrapListener(arg) {
-        if (flags.once) {
-          emitter.removeEventListener(name2, wrapListener);
-        }
-        listener(arg);
-      }, "wrapListener"));
-    } else {
-      throw new TypeError('The "emitter" argument must be of type EventEmitter. Received type ' + typeof emitter);
-    }
-  }
-  __name(eventTargetAgnosticAddListener, "eventTargetAgnosticAddListener");
-  return events.exports;
-}
-__name(requireEvents, "requireEvents");
 var inherits_browser = { exports: {} };
 var hasRequiredInherits_browser;
 function requireInherits_browser() {
@@ -90441,7 +90055,7 @@ var hasRequiredStreamBrowser;
 function requireStreamBrowser() {
   if (hasRequiredStreamBrowser) return streamBrowser;
   hasRequiredStreamBrowser = 1;
-  streamBrowser = requireEvents().EventEmitter;
+  streamBrowser = require$$0.EventEmitter;
   return streamBrowser;
 }
 __name(requireStreamBrowser, "requireStreamBrowser");
@@ -90522,7 +90136,7 @@ function requireBuffer_list() {
   }
   __name(_toPrimitive2, "_toPrimitive");
   var _require = requireBuffer(), Buffer2 = _require.Buffer;
-  var _require2 = require$$3$1, inspect = _require2.inspect;
+  var _require2 = require$$0, inspect = _require2.inspect;
   var custom = inspect && inspect.custom || "inspect";
   function copyBuffer(src2, target, offset4) {
     Buffer2.prototype.copy.call(src2, target, offset4);
@@ -91863,7 +91477,7 @@ function require_stream_readable() {
   _stream_readable = Readable;
   var Duplex;
   Readable.ReadableState = ReadableState;
-  requireEvents().EventEmitter;
+  require$$0.EventEmitter;
   var EElistenerCount = /* @__PURE__ */ __name(function EElistenerCount2(emitter, type2) {
     return emitter.listeners(type2).length;
   }, "EElistenerCount");
@@ -91879,7 +91493,7 @@ function require_stream_readable() {
     return Buffer2.isBuffer(obj) || obj instanceof OurUint8Array;
   }
   __name(_isUint8Array, "_isUint8Array");
-  var debugUtil = require$$3$1;
+  var debugUtil = require$$0;
   var debug;
   if (debugUtil && debugUtil.debuglog) {
     debug = debugUtil.debuglog("stream");
@@ -92836,7 +92450,7 @@ function requireStreamBrowserify() {
   if (hasRequiredStreamBrowserify) return streamBrowserify;
   hasRequiredStreamBrowserify = 1;
   streamBrowserify = Stream;
-  var EE = requireEvents().EventEmitter;
+  var EE = require$$0.EventEmitter;
   var inherits = requireInherits_browser();
   inherits(Stream, EE);
   Stream.Readable = require_stream_readable();
@@ -116609,7 +116223,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.7";
+const version = "0.8.8";
 const packageJson = {
   version
 };
@@ -138089,6 +137703,7 @@ const PropertySidePanel = /* @__PURE__ */ __name(({ properties: properties2, set
     {
       ref: sidebarRef,
       style: __spreadValues({
+        position: "relative",
         width: isOpen ? 350 : 0,
         minWidth: isOpen ? 350 : 0,
         maxWidth: isOpen ? 350 : 0,
@@ -138108,7 +137723,7 @@ const PropertySidePanel = /* @__PURE__ */ __name(({ properties: properties2, set
       {
         style: {
           position: "absolute",
-          top: 5,
+          top: 0,
           right: 10,
           zIndex: 1,
           cursor: "pointer"
@@ -138333,13 +137948,18 @@ function getLabileSites(alignedSequences, threshold = 0.5) {
   };
 }
 __name(getLabileSites, "getLabileSites");
-const getAlignedAminoAcidSequenceProps = /* @__PURE__ */ __name((tracks) => {
+function parseTracks(tracks) {
   let sequences = {};
   tracks.forEach((at) => {
     sequences = __spreadProps(__spreadValues({}, sequences), {
       [at.alignmentData.name]: at.alignmentData.sequence
     });
   });
+  return sequences;
+}
+__name(parseTracks, "parseTracks");
+const getAlignedAminoAcidSequenceProps = /* @__PURE__ */ __name((tracks) => {
+  const sequences = parseTracks(tracks);
   const identity4 = calculateIdentityMatrix(sequences);
   const { overallIdentity, frequencies } = getIdentityAndFrequencies(sequences);
   const labileSites = getLabileSites(sequences, 0.5);
@@ -138591,6 +138211,10 @@ ${seqDataToCopy}\r
       alignmentHolderTop.current.scrollLeft = scrollPercentageToUse * (alignmentHolderTop.current.scrollWidth - alignmentHolderTop.current.clientWidth);
     }
   }, "scrollAlignmentToPercent");
+  const aminoAcidAlignmentProperties = useMemo$1(() => {
+    if (isPairwise || !alignmentTracks[0].sequenceData.isProtein) return;
+    return getAlignedAminoAcidSequenceProps(alignmentTracks);
+  }, [alignmentTracks, isPairwise]);
   useEffect(() => {
     window.scrollAlignmentToPercent = scrollAlignmentToPercent;
     if (window.Cypress)
@@ -138957,10 +138581,6 @@ ${seqDataToCopy}\r
       annotationLabelVisibility: alignmentVisibilityToolOptions.alignmentAnnotationLabelVisibility
     });
   }, "estimateRowHeight");
-  const aminoAcidAlignmentProperties = useMemo$1(() => {
-    if (isPairwise || !alignmentTracks[0].sequenceData.isProtein) return;
-    return getAlignedAminoAcidSequenceProps(alignmentTracks);
-  }, [alignmentTracks, isPairwise]);
   const renderItem = /* @__PURE__ */ __name((_i, _key, isTemplate, cloneProps) => {
     var _a3, _b2, _c, _d, _e;
     const isDragDisabled = !allowTrackRearrange || isPairwise;
@@ -140023,6 +139643,7 @@ const AlignmentView$1 = compose(
   withEditorProps,
   connect(
     (state2, ownProps) => {
+      var _a2, _b2;
       const {
         VectorEditor: {
           __allEditorsOptions: { alignments: alignments2 }
@@ -140087,6 +139708,8 @@ const AlignmentView$1 = compose(
           togglableAlignmentAnnotationSettings[annotation] = alignmentAnnotationVisibility[annotation];
         }
       });
+      const tracks = parseTracks(alignmentTracks);
+      const labileSites = getLabileSites(tracks, 0.5);
       const annotationsWithCounts = [];
       if (alignmentTracks) {
         let totalNumOfFeatures = 0;
@@ -140101,7 +139724,8 @@ const AlignmentView$1 = compose(
         });
         annotationsWithCounts.push({
           features: totalNumOfFeatures,
-          parts: totalNumOfParts
+          parts: totalNumOfParts,
+          labileSites: (_b2 = (_a2 = labileSites.sites) == null ? void 0 : _a2.length) != null ? _b2 : 0
         });
       } else if (pairwiseAlignments) {
         pairwiseAlignments.forEach((pairwise) => {