@teselagen/ove 0.5.13 → 0.5.14

package/index.es.js

@@ -14453,10 +14453,10 @@ var _objectKeysInternal = /* @__PURE__ */ __name(function(object3, names2) {
   return result;
 }, "_objectKeysInternal");
 var _enumBugKeys = "constructor,hasOwnProperty,isPrototypeOf,propertyIsEnumerable,toLocaleString,toString,valueOf".split(",");
-var $keys$3 = _objectKeysInternal;
+var $keys$2 = _objectKeysInternal;
 var enumBugKeys$1 = _enumBugKeys;
 var _objectKeys = Object.keys || /* @__PURE__ */ __name(function keys(O2) {
-  return $keys$3(O2, enumBugKeys$1);
+  return $keys$2(O2, enumBugKeys$1);
 }, "keys");
 var _objectGops = {};
 _objectGops.f = Object.getOwnPropertySymbols;
@@ -14889,11 +14889,11 @@ var ArrayProto = Array.prototype;
 var _isArrayIter = /* @__PURE__ */ __name(function(it) {
   return it !== void 0 && (Iterators.Array === it || ArrayProto[ITERATOR] === it);
 }, "_isArrayIter");
-var $defineProperty$4 = require_objectDp();
+var $defineProperty$3 = require_objectDp();
 var createDesc$2 = _propertyDesc;
 var _createProperty = /* @__PURE__ */ __name(function(object3, index2, value) {
   if (index2 in object3)
-    $defineProperty$4.f(object3, index2, createDesc$2(0, value));
+    $defineProperty$3.f(object3, index2, createDesc$2(0, value));
   else
     object3[index2] = value;
 }, "_createProperty");
@@ -15141,13 +15141,21 @@ var _isArray = Array.isArray || /* @__PURE__ */ __name(function isArray(arg) {
 }, "isArray");
 var _objectGopnExt = {};
 var _objectGopn = {};
-var $keys$2 = _objectKeysInternal;
-var hiddenKeys = _enumBugKeys.concat("length", "prototype");
-_objectGopn.f = Object.getOwnPropertyNames || /* @__PURE__ */ __name(function getOwnPropertyNames(O2) {
-  return $keys$2(O2, hiddenKeys);
-}, "getOwnPropertyNames");
+var hasRequired_objectGopn;
+function require_objectGopn() {
+  if (hasRequired_objectGopn)
+    return _objectGopn;
+  hasRequired_objectGopn = 1;
+  var $keys2 = _objectKeysInternal;
+  var hiddenKeys = _enumBugKeys.concat("length", "prototype");
+  _objectGopn.f = Object.getOwnPropertyNames || /* @__PURE__ */ __name(function getOwnPropertyNames4(O2) {
+    return $keys2(O2, hiddenKeys);
+  }, "getOwnPropertyNames");
+  return _objectGopn;
+}
+__name(require_objectGopn, "require_objectGopn");
 var toIObject$2 = _toIobject;
-var gOPN$1 = _objectGopn.f;
+var gOPN$1 = require_objectGopn().f;
 var toString$4 = {}.toString;
 var windowNames = typeof window == "object" && window && Object.getOwnPropertyNames ? Object.getOwnPropertyNames(window) : [];
 var getWindowNames = /* @__PURE__ */ __name(function(it) {
@@ -15157,7 +15165,7 @@ var getWindowNames = /* @__PURE__ */ __name(function(it) {
     return windowNames.slice();
   }
 }, "getWindowNames");
-_objectGopnExt.f = /* @__PURE__ */ __name(function getOwnPropertyNames2(it) {
+_objectGopnExt.f = /* @__PURE__ */ __name(function getOwnPropertyNames(it) {
   return windowNames && toString$4.call(it) == "[object Window]" ? getWindowNames(it) : gOPN$1(toIObject$2(it));
 }, "getOwnPropertyNames");
 var _objectGopd = {};
@@ -15247,9 +15255,9 @@ var isSymbol$7 = USE_NATIVE && typeof $Symbol.iterator == "symbol" ? function(it
 } : function(it) {
   return it instanceof $Symbol;
 };
-var $defineProperty$3 = /* @__PURE__ */ __name(function defineProperty3(it, key, D2) {
+var $defineProperty$2 = /* @__PURE__ */ __name(function defineProperty3(it, key, D2) {
   if (it === ObjectProto)
-    $defineProperty$3(OPSymbols, key, D2);
+    $defineProperty$2(OPSymbols, key, D2);
   anObject(it);
   key = toPrimitive(key, true);
   anObject(D2);
@@ -15274,7 +15282,7 @@ var $defineProperties = /* @__PURE__ */ __name(function defineProperties2(it, P2
   var l2 = keys5.length;
   var key;
   while (l2 > i)
-    $defineProperty$3(it, key = keys5[i++], P2[key]);
+    $defineProperty$2(it, key = keys5[i++], P2[key]);
   return it;
 }, "defineProperties");
 var $create = /* @__PURE__ */ __name(function create2(it, P2) {
@@ -15296,7 +15304,7 @@ var $getOwnPropertyDescriptor = /* @__PURE__ */ __name(function getOwnPropertyDe
     D2.enumerable = true;
   return D2;
 }, "getOwnPropertyDescriptor");
-var $getOwnPropertyNames = /* @__PURE__ */ __name(function getOwnPropertyNames3(it) {
+var $getOwnPropertyNames = /* @__PURE__ */ __name(function getOwnPropertyNames2(it) {
   var names2 = gOPN(toIObject(it));
   var result = [];
   var i = 0;
@@ -15339,8 +15347,8 @@ if (!USE_NATIVE) {
     return this._k;
   }, "toString"));
   $GOPD.f = $getOwnPropertyDescriptor;
-  $DP.f = $defineProperty$3;
-  _objectGopn.f = gOPNExt.f = $getOwnPropertyNames;
+  $DP.f = $defineProperty$2;
+  require_objectGopn().f = gOPNExt.f = $getOwnPropertyNames;
   require_objectPie().f = $propertyIsEnumerable;
   $GOPS.f = $getOwnPropertySymbols;
   if (DESCRIPTORS && !_library) {
@@ -15382,7 +15390,7 @@ $export$2($export$2.S + $export$2.F * !USE_NATIVE, "Object", {
   // 19.1.2.2 Object.create(O [, Properties])
   create: $create,
   // 19.1.2.4 Object.defineProperty(O, P, Attributes)
-  defineProperty: $defineProperty$3,
+  defineProperty: $defineProperty$2,
   // 19.1.2.3 Object.defineProperties(O, Properties)
   defineProperties: $defineProperties,
   // 19.1.2.6 Object.getOwnPropertyDescriptor(O, P)
@@ -37267,16 +37275,25 @@ var getIntrinsic = /* @__PURE__ */ __name(function GetIntrinsic(name2, allowMiss
   return value;
 }, "GetIntrinsic");
 var callBind$3 = { exports: {} };
-var GetIntrinsic$4 = getIntrinsic;
-var $defineProperty$2 = GetIntrinsic$4("%Object.defineProperty%", true) || false;
-if ($defineProperty$2) {
-  try {
-    $defineProperty$2({}, "a", { value: 1 });
-  } catch (e2) {
-    $defineProperty$2 = false;
+var esDefineProperty;
+var hasRequiredEsDefineProperty;
+function requireEsDefineProperty() {
+  if (hasRequiredEsDefineProperty)
+    return esDefineProperty;
+  hasRequiredEsDefineProperty = 1;
+  var GetIntrinsic3 = getIntrinsic;
+  var $defineProperty2 = GetIntrinsic3("%Object.defineProperty%", true) || false;
+  if ($defineProperty2) {
+    try {
+      $defineProperty2({}, "a", { value: 1 });
+    } catch (e2) {
+      $defineProperty2 = false;
+    }
   }
+  esDefineProperty = $defineProperty2;
+  return esDefineProperty;
 }
-var esDefineProperty = $defineProperty$2;
+__name(requireEsDefineProperty, "requireEsDefineProperty");
 var GetIntrinsic$3 = getIntrinsic;
 var $gOPD$1 = GetIntrinsic$3("%Object.getOwnPropertyDescriptor%", true);
 if ($gOPD$1) {
@@ -37287,7 +37304,7 @@ if ($gOPD$1) {
   }
 }
 var gopd$1 = $gOPD$1;
-var $defineProperty$1 = esDefineProperty;
+var $defineProperty$1 = requireEsDefineProperty();
 var $SyntaxError = syntax;
 var $TypeError$4 = type$1;
 var gopd = gopd$1;
@@ -37328,7 +37345,7 @@ var defineDataProperty$1 = /* @__PURE__ */ __name(function defineDataProperty(ob
     throw new $SyntaxError("This environment does not support defining a property as non-configurable, non-writable, or non-enumerable.");
   }
 }, "defineDataProperty");
-var $defineProperty = esDefineProperty;
+var $defineProperty = requireEsDefineProperty();
 var hasPropertyDescriptors = /* @__PURE__ */ __name(function hasPropertyDescriptors2() {
   return !!$defineProperty;
 }, "hasPropertyDescriptors");
@@ -37397,7 +37414,7 @@ var setFunctionLength = /* @__PURE__ */ __name(function setFunctionLength2(fn4,
   var $apply = GetIntrinsic3("%Function.prototype.apply%");
   var $call = GetIntrinsic3("%Function.prototype.call%");
   var $reflectApply = GetIntrinsic3("%Reflect.apply%", true) || bind3.call($call, $apply);
-  var $defineProperty2 = esDefineProperty;
+  var $defineProperty2 = requireEsDefineProperty();
   var $max = GetIntrinsic3("%Math.max%");
   module2.exports = /* @__PURE__ */ __name(function callBind2(originalFunction) {
     if (typeof originalFunction !== "function") {
@@ -49864,7 +49881,7 @@ var KNOWN_STATICS = {
   arity: true
 };
 var defineProperty$3 = Object.defineProperty;
-var getOwnPropertyNames4 = Object.getOwnPropertyNames;
+var getOwnPropertyNames3 = Object.getOwnPropertyNames;
 var getOwnPropertySymbols3 = Object.getOwnPropertySymbols;
 var getOwnPropertyDescriptor3 = Object.getOwnPropertyDescriptor;
 var getPrototypeOf = Object.getPrototypeOf;
@@ -49877,7 +49894,7 @@ function hoistNonReactStatics(targetComponent, sourceComponent, blacklist) {
         hoistNonReactStatics(targetComponent, inheritedComponent, blacklist);
       }
     }
-    var keys5 = getOwnPropertyNames4(sourceComponent);
+    var keys5 = getOwnPropertyNames3(sourceComponent);
     if (getOwnPropertySymbols3) {
       keys5 = keys5.concat(getOwnPropertySymbols3(sourceComponent));
     }
@@ -78874,123 +78891,167 @@ function getAminoAcidFromSequenceTriplet(sequenceString) {
   return proteinAlphabet[letter.toUpperCase()];
 }
 __name(getAminoAcidFromSequenceTriplet, "getAminoAcidFromSequenceTriplet");
-function getAminoAcidDataForEachBaseOfDna(originalSequenceString, forward, optionalSubrangeRange, isProteinSequence) {
+function getNextTriplet(index2, sequenceString, exonRange) {
+  let triplet = "";
+  let internalIndex;
+  const codonPositions = [];
+  const isBaseInExon = /* @__PURE__ */ __name((baseIndex) => exonRange.some(
+    (r2) => isPositionWithinRange(baseIndex, r2, sequenceString.length, true, false)
+  ), "isBaseInExon");
+  for (internalIndex = index2; internalIndex < sequenceString.length; internalIndex++) {
+    if (triplet.length === 3) {
+      break;
+    }
+    if (isBaseInExon(internalIndex)) {
+      triplet += sequenceString[internalIndex];
+      codonPositions.push(internalIndex);
+    }
+  }
+  return { triplet, basesRead: internalIndex - index2, codonPositions };
+}
+__name(getNextTriplet, "getNextTriplet");
+function getTranslatedSequenceProperties(originalSequenceString, forward, optionalSubrangeRange, isProteinSequence) {
   const originalSequenceStringLength = isProteinSequence ? originalSequenceString.length * 3 : originalSequenceString.length;
   let sequenceString = originalSequenceString;
-  let startOffset = 0;
+  const translationRange = { start: 0, end: originalSequenceStringLength - 1 };
   if (optionalSubrangeRange) {
     sequenceString = getSequenceWithinRange(
       optionalSubrangeRange,
       originalSequenceString
     );
-    startOffset = optionalSubrangeRange.start;
+    translationRange.start = optionalSubrangeRange.start;
+    translationRange.end = optionalSubrangeRange.end;
   }
   const sequenceStringLength = isProteinSequence ? sequenceString.length * 3 : sequenceString.length;
-  const aminoAcidDataForEachBaseOfDNA = [];
-  let codonRange;
-  let revCompGapLength = 0;
-  let aminoAcidIndex = 0;
-  if (!forward) {
-    aminoAcidIndex = Math.floor((sequenceStringLength - 1) / 3);
-    revCompGapLength = sequenceStringLength % 3;
-    codonRange = translateRange(
-      {
-        start: 0,
-        end: revCompGapLength - 1
-      },
-      startOffset,
+  if (!isProteinSequence && !forward) {
+    sequenceString = getReverseComplementSequenceString(sequenceString);
+  }
+  const absoluteExonRange = !isProteinSequence && optionalSubrangeRange && optionalSubrangeRange.locations ? optionalSubrangeRange.locations : [translationRange];
+  const exonRange = absoluteExonRange.map((range2) => {
+    let outputRange = translateRange(
+      range2,
+      -translationRange.start,
       originalSequenceStringLength
     );
-    if (revCompGapLength > 0) {
-      for (let i = 0; i < revCompGapLength; i++) {
-        aminoAcidDataForEachBaseOfDNA.push({
-          aminoAcid: getAminoAcidFromSequenceTriplet("xxx"),
-          //fake xxx triplet returns the ambiguous X amino acid
-          positionInCodon: revCompGapLength - i - 1,
-          aminoAcidIndex,
-          sequenceIndex: codonRange.start + i,
-          codonRange,
-          fullCodon: false
-        });
-      }
-      aminoAcidIndex--;
+    if (!forward) {
+      outputRange = flipRelativeRange(
+        outputRange,
+        { start: 0, end: sequenceStringLength - 1 },
+        sequenceStringLength
+      );
     }
+    return outputRange;
+  });
+  return {
+    sequenceString,
+    translationRange,
+    sequenceStringLength,
+    originalSequenceStringLength,
+    exonRange
+  };
+}
+__name(getTranslatedSequenceProperties, "getTranslatedSequenceProperties");
+function positionInCdsToPositionInMainSequence(index2, forward, translationRange, mainSequenceLength) {
+  let outputRange = translateRange(
+    { start: index2, end: index2 },
+    translationRange.start,
+    mainSequenceLength
+  );
+  if (!forward) {
+    outputRange = flipRelativeRange(
+      outputRange,
+      translationRange,
+      mainSequenceLength
+    );
   }
-  for (let index2 = 2 + revCompGapLength; index2 < sequenceStringLength; index2 += 3) {
+  return outputRange.start;
+}
+__name(positionInCdsToPositionInMainSequence, "positionInCdsToPositionInMainSequence");
+function getAminoAcidDataForEachBaseOfDna(originalSequenceString, forward, optionalSubrangeRange, isProteinSequence) {
+  const {
+    sequenceString,
+    translationRange,
+    sequenceStringLength,
+    originalSequenceStringLength,
+    exonRange
+  } = getTranslatedSequenceProperties(
+    originalSequenceString,
+    forward,
+    optionalSubrangeRange,
+    isProteinSequence
+  );
+  const aminoAcidDataForEachBaseOfDNA = [];
+  for (let index2 = 0; index2 < sequenceStringLength; index2 += 3) {
     let aminoAcid;
+    const aminoAcidIndex = index2 / 3;
+    let codonPositionsInCDS;
+    let basesRead;
     if (isProteinSequence) {
-      aminoAcid = proteinAlphabet[sequenceString[(index2 - 2) / 3].toUpperCase()];
+      codonPositionsInCDS = [0, 1, 2].map((i) => index2 + i);
+      basesRead = 3;
+      aminoAcid = proteinAlphabet[sequenceString[index2 / 3].toUpperCase()];
     } else {
-      let triplet = sequenceString.slice(index2 - 2, index2 + 1);
-      if (!forward) {
-        triplet = getReverseComplementSequenceString(triplet);
-      }
-      aminoAcid = getAminoAcidFromSequenceTriplet(triplet);
-    }
-    codonRange = translateRange(
-      {
-        start: index2 - 2,
-        end: index2
-      },
-      startOffset,
-      originalSequenceStringLength
+      const {
+        triplet,
+        basesRead: _basesRead,
+        codonPositions
+      } = getNextTriplet(index2, sequenceString, exonRange);
+      basesRead = _basesRead;
+      codonPositionsInCDS = codonPositions;
+      aminoAcid = triplet.length === 3 ? getAminoAcidFromSequenceTriplet(triplet) : getAminoAcidFromSequenceTriplet("xxx");
+    }
+    const absoluteCodonPositions = codonPositionsInCDS.map(
+      (i) => positionInCdsToPositionInMainSequence(
+        i,
+        forward,
+        translationRange,
+        originalSequenceStringLength
+      )
     );
-    aminoAcidDataForEachBaseOfDNA.push({
-      aminoAcid,
-      //gap amino acid
-      positionInCodon: forward ? 0 : 2,
-      aminoAcidIndex,
-      sequenceIndex: codonRange.start,
-      codonRange,
-      fullCodon: true
-    });
-    aminoAcidDataForEachBaseOfDNA.push({
-      aminoAcid,
-      //gap amino acid
-      positionInCodon: 1,
-      aminoAcidIndex,
-      sequenceIndex: codonRange.start + 1,
-      codonRange,
-      fullCodon: true
-    });
-    aminoAcidDataForEachBaseOfDNA.push({
-      aminoAcid,
-      //gap amino acid
-      positionInCodon: forward ? 2 : 0,
-      aminoAcidIndex,
-      sequenceIndex: codonRange.start + 2,
-      codonRange,
-      fullCodon: true
-    });
-    if (forward) {
-      aminoAcidIndex++;
-    } else {
-      aminoAcidIndex--;
+    const codonRange = forward ? {
+      start: absoluteCodonPositions[0],
+      end: absoluteCodonPositions[codonPositionsInCDS.length - 1]
+    } : {
+      start: absoluteCodonPositions[codonPositionsInCDS.length - 1],
+      end: absoluteCodonPositions[0]
+    };
+    let positionInCodon = 0;
+    for (let i = 0; i < basesRead; i++) {
+      const posInCds = i + index2;
+      if (codonPositionsInCDS.includes(posInCds)) {
+        aminoAcidDataForEachBaseOfDNA.push({
+          aminoAcid,
+          positionInCodon,
+          aminoAcidIndex,
+          sequenceIndex: absoluteCodonPositions[i],
+          codonRange,
+          fullCodon: codonPositionsInCDS.length === 3
+        });
+        positionInCodon++;
+      } else {
+        aminoAcidDataForEachBaseOfDNA.push({
+          aminoAcid: null,
+          positionInCodon: null,
+          aminoAcidIndex: null,
+          sequenceIndex: positionInCdsToPositionInMainSequence(
+            posInCds,
+            forward,
+            translationRange,
+            originalSequenceStringLength
+          ),
+          codonRange: null,
+          fullCodon: null
+        });
+      }
     }
-  }
-  const lengthOfEndBpsNotCoveredByAminoAcids = sequenceStringLength - aminoAcidDataForEachBaseOfDNA.length;
-  codonRange = translateRange(
-    {
-      start: sequenceStringLength - lengthOfEndBpsNotCoveredByAminoAcids,
-      end: sequenceStringLength - 1
-    },
-    startOffset,
-    originalSequenceStringLength
-  );
-  for (let j = 0; j < lengthOfEndBpsNotCoveredByAminoAcids; j++) {
-    aminoAcidDataForEachBaseOfDNA.push({
-      aminoAcid: getAminoAcidFromSequenceTriplet("xxx"),
-      //fake xxx triplet returns the gap amino acid
-      positionInCodon: j,
-      aminoAcidIndex,
-      sequenceIndex: codonRange.start + j,
-      fullCodon: false,
-      codonRange
-    });
+    index2 += basesRead - codonPositionsInCDS.length;
   }
   if (sequenceStringLength !== aminoAcidDataForEachBaseOfDNA.length) {
     throw new Error("something went wrong!");
   }
+  if (!forward) {
+    aminoAcidDataForEachBaseOfDNA.reverse();
+  }
   return aminoAcidDataForEachBaseOfDNA;
 }
 __name(getAminoAcidDataForEachBaseOfDna, "getAminoAcidDataForEachBaseOfDna");
@@ -118604,7 +118665,7 @@ function AASliver(props) {
         fill: color2 || "gray"
       }
     )),
-    !isFiller && /* @__PURE__ */ React__default$1.createElement(
+    (!isFiller || isTruncatedEnd && isTruncatedStart) && /* @__PURE__ */ React__default$1.createElement(
       "text",
       {
         fontSize: 25,
@@ -118681,18 +118742,39 @@ const _Translation = class _Translation extends React__default$1.Component {
       subrangeStartRelativeToAnnotationStart,
       aminoAcids
     );
+    let prevAaSliver;
+    let nextAaSliver = aminoAcidsForSubrange[1];
+    const lastIndex = aminoAcidsForSubrange.length - 1;
     const translationSVG = aminoAcidsForSubrange.map(
       function(aminoAcidSliver, index2) {
-        const isEndFiller = index2 === 0 && aminoAcidSliver.positionInCodon === (annotation.forward ? 2 : 0);
-        let isTruncatedEnd = index2 === 0 && aminoAcidSliver.positionInCodon === 1;
-        let isTruncatedStart = index2 === aminoAcidsForSubrange.length - 1 && aminoAcidSliver.positionInCodon === 1;
+        if (aminoAcidSliver.positionInCodon === null) {
+          prevAaSliver = aminoAcidSliver;
+          nextAaSliver = aminoAcidsForSubrange[index2 + 2];
+          return /* @__PURE__ */ React__default$1.createElement(
+            "rect",
+            {
+              x: index2 * charWidth2,
+              y: height2 / 2 - height2 / 16,
+              width: charWidth2,
+              height: height2 / 8,
+              fill: "grey",
+              stroke: "black",
+              strokeWidth: 1
+            }
+          );
+        }
+        const isEndFiller = (index2 === 0 || (prevAaSliver == null ? void 0 : prevAaSliver.positionInCodon) === null) && aminoAcidSliver.positionInCodon === (annotation.forward ? 2 : 0);
+        const isStartFiller = (index2 === lastIndex || (nextAaSliver == null ? void 0 : nextAaSliver.positionInCodon) === null) && aminoAcidSliver.positionInCodon === (annotation.forward ? 0 : 2);
+        let isTruncatedEnd = (index2 === 0 || (prevAaSliver == null ? void 0 : prevAaSliver.positionInCodon) === null) && aminoAcidSliver.positionInCodon === 1;
+        let isTruncatedStart = (index2 === lastIndex || (nextAaSliver == null ? void 0 : nextAaSliver.positionInCodon) === null) && aminoAcidSliver.positionInCodon === 1;
         if (!annotation.forward) {
           const holder = isTruncatedEnd;
           isTruncatedEnd = isTruncatedStart;
           isTruncatedStart = holder;
         }
-        const isStartFiller = index2 === aminoAcidsForSubrange.length - 1 && aminoAcidSliver.positionInCodon === (annotation.forward ? 0 : 2);
         if (aminoAcidSliver.positionInCodon !== 1 && !isStartFiller && !isEndFiller) {
+          prevAaSliver = aminoAcidSliver;
+          nextAaSliver = aminoAcidsForSubrange[index2 + 2];
           return null;
         }
         const { gapsInside, gapsBefore } = getGaps2(aminoAcidSliver.codonRange);
@@ -118709,10 +118791,12 @@ const _Translation = class _Translation extends React__default$1.Component {
         } else {
           color2 = aminoAcid.color;
         }
+        prevAaSliver = aminoAcidSliver;
+        nextAaSliver = aminoAcidsForSubrange[index2 + 2];
         return /* @__PURE__ */ React__default$1.createElement(
           AASliver$1,
           {
-            isFiller: isEndFiller || isStartFiller,
+            isFiller: isEndFiller || isStartFiller || isTruncatedEnd && isTruncatedStart,
             isTruncatedEnd,
             isTruncatedStart,
             onClick: function(event) {
@@ -120945,7 +121029,7 @@ function showFileDialog({ multiple = false, onSelect }) {
 }
 __name(showFileDialog, "showFileDialog");
 const name = "@teselagen/ove";
-const version = "0.5.12";
+const version = "0.5.13";
 const main = "./src/index.js";
 const type = "module";
 const exports$1 = {