@teselagen/ove 0.3.50 → 0.3.51

package/index.umd.js

@@ -45118,7 +45118,15 @@ ${latestSubscriptionCallbackError.current.stack}
   var _objectGops = {};
   _objectGops.f = Object.getOwnPropertySymbols;
   var _objectPie = {};
-  _objectPie.f = {}.propertyIsEnumerable;
+  var hasRequired_objectPie;
+  function require_objectPie() {
+    if (hasRequired_objectPie)
+      return _objectPie;
+    hasRequired_objectPie = 1;
+    _objectPie.f = {}.propertyIsEnumerable;
+    return _objectPie;
+  }
+  __name(require_objectPie, "require_objectPie");
   var defined$1 = _defined;
   var _toObject = /* @__PURE__ */ __name(function(it) {
     return Object(defined$1(it));
@@ -45132,7 +45140,7 @@ ${latestSubscriptionCallbackError.current.stack}
     var DESCRIPTORS2 = _descriptors;
     var getKeys2 = _objectKeys;
     var gOPS2 = _objectGops;
-    var pIE2 = _objectPie;
+    var pIE2 = require_objectPie();
     var toObject2 = _toObject;
     var IObject2 = require_iobject();
     var $assign = Object.assign;
@@ -45769,7 +45777,7 @@ ${latestSubscriptionCallbackError.current.stack}
   }, "_wksDefine");
   var getKeys = _objectKeys;
   var gOPS$1 = _objectGops;
-  var pIE$1 = _objectPie;
+  var pIE$1 = require_objectPie();
   var _enumKeys = /* @__PURE__ */ __name(function(it) {
     var result = getKeys(it);
     var getSymbols2 = gOPS$1.f;
@@ -45810,7 +45818,7 @@ ${latestSubscriptionCallbackError.current.stack}
     return windowNames && toString$3.call(it) == "[object Window]" ? getWindowNames(it) : gOPN$1(toIObject$2(it));
   }, "getOwnPropertyNames");
   var _objectGopd = {};
-  var pIE = _objectPie;
+  var pIE = require_objectPie();
   var createDesc$1 = _propertyDesc;
   var toIObject$1 = _toIobject;
   var toPrimitive$1 = _toPrimitive$1;
@@ -45990,7 +45998,7 @@ ${latestSubscriptionCallbackError.current.stack}
     $GOPD.f = $getOwnPropertyDescriptor;
     $DP.f = $defineProperty;
     _objectGopn.f = gOPNExt.f = $getOwnPropertyNames;
-    _objectPie.f = $propertyIsEnumerable;
+    require_objectPie().f = $propertyIsEnumerable;
     $GOPS.f = $getOwnPropertySymbols;
     if (DESCRIPTORS && !_library) {
       redefine(ObjectProto, "propertyIsEnumerable", $propertyIsEnumerable);
@@ -114744,7 +114752,9 @@ ${latestSubscriptionCallbackError.current.stack}
   }
   __name(arrayRotate, "arrayRotate");
   function rotateSequenceDataToPosition(sequenceData2, caretPosition2, options) {
-    const newSequenceData = tidyUpSequenceData(sequenceData2, options);
+    const newSequenceData = tidyUpSequenceData(sequenceData2, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
     newSequenceData.sequence = rotateBpsToPosition(
       newSequenceData.sequence,
       caretPosition2
@@ -114781,7 +114791,7 @@ ${latestSubscriptionCallbackError.current.stack}
   __name(adjustAnnotationsToInsert, "adjustAnnotationsToInsert");
   function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert, _existingSequenceData, caretPositionOrRange, options = {}) {
     const { maintainOriginSplit } = options;
-    let existingSequenceData = tidyUpSequenceData(_existingSequenceData, options);
+    let existingSequenceData = tidyUpSequenceData(_existingSequenceData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
     const sequenceDataToInsert = tidyUpSequenceData(
       _sequenceDataToInsert,
       options
@@ -114799,6 +114809,7 @@ ${latestSubscriptionCallbackError.current.stack}
           return acc[type] = [];
         }, {})), {
           sequence: "",
+          doNotRemoveInvalidChars: true,
           proteinSequence: "",
           chromatogramData: void 0
         }),
@@ -122829,7 +122840,7 @@ ${latestSubscriptionCallbackError.current.stack}
     if (!range2)
       return seqData;
     const { exclude = {}, excludePartial = {} } = options;
-    const seqDataToUse = tidyUpSequenceData(seqData, options);
+    const seqDataToUse = tidyUpSequenceData(seqData, __spreadValues({ doNotRemoveInvalidChars: true }, options));
     annotationTypes.forEach((type) => {
       delete seqDataToUse[`filtered${lodashExports.startCase(type)}`];
     });
@@ -122880,9 +122891,9 @@ ${latestSubscriptionCallbackError.current.stack}
           }
         });
       });
-      return tidyUpSequenceData(toRet, options);
+      return tidyUpSequenceData(toRet, __spreadValues({ doNotRemoveInvalidChars: true }, options));
     }
-    return tidyUpSequenceData(seqDataToReturn, options);
+    return tidyUpSequenceData(seqDataToReturn, __spreadValues({ doNotRemoveInvalidChars: true }, options));
   }
   __name(getSequenceDataBetweenRange, "getSequenceDataBetweenRange");
   function getAnnotationsBetweenRange(annotationsToBeAdjusted, range2, maxLength, shouldExcludePartial) {
@@ -122929,7 +122940,7 @@ ${latestSubscriptionCallbackError.current.stack}
     const newSeqObj = Object.assign({}, seqObj, {
       sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
     });
-    return tidyUpSequenceData(newSeqObj, options);
+    return tidyUpSequenceData(newSeqObj, __spreadValues({ doNotRemoveInvalidChars: true }, options));
   }
   __name(getComplementSequenceAndAnnotations, "getComplementSequenceAndAnnotations");
   function getCutsiteType(restrictionEnzyme) {
@@ -122977,7 +122988,7 @@ ${latestSubscriptionCallbackError.current.stack}
   function getReverseComplementSequenceAndAnnoations(pSeqObj, options = {}) {
     const seqObj = tidyUpSequenceData(
       getSequenceDataBetweenRange(pSeqObj, options.range),
-      options
+      __spreadValues({ doNotRemoveInvalidChars: true }, options)
     );
     const newSeqObj = Object.assign(
       {},
@@ -122997,7 +123008,9 @@ ${latestSubscriptionCallbackError.current.stack}
         return acc;
       }, {})
     );
-    return tidyUpSequenceData(newSeqObj, options);
+    return tidyUpSequenceData(newSeqObj, __spreadValues({
+      doNotRemoveInvalidChars: true
+    }, options));
   }
   __name(getReverseComplementSequenceAndAnnoations, "getReverseComplementSequenceAndAnnoations");
   function guessIfSequenceIsDnaAndNotProtein(seq, options = {}) {
@@ -123943,6 +123956,30 @@ ${latestSubscriptionCallbackError.current.stack}
     return parsingResultArray;
   }
   __name(flattenSequenceArray, "flattenSequenceArray");
+  function parseFeatureLocation(locStr, isProtein2, inclusive1BasedStart, inclusive1BasedEnd) {
+    locStr = locStr.trim();
+    const locArr = [];
+    locStr.replace(/(\d+)/g, function(string2, match2) {
+      locArr.push(match2);
+    });
+    const locArray = [];
+    for (let i2 = 0; i2 < locArr.length; i2 += 2) {
+      const start2 = parseInt(locArr[i2], 10) - (inclusive1BasedStart ? 0 : 1);
+      let end2 = parseInt(locArr[i2 + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
+      if (isNaN(end2)) {
+        end2 = start2;
+      }
+      const location2 = {
+        start: start2,
+        end: end2
+      };
+      locArray.push(
+        isProtein2 ? convertAACaretPositionOrRangeToDna(location2) : location2
+      );
+    }
+    return locArray;
+  }
+  __name(parseFeatureLocation, "parseFeatureLocation");
   function genbankToJson(string2, options = {}) {
     const {
       inclusive1BasedStart,
@@ -124267,7 +124304,15 @@ ${latestSubscriptionCallbackError.current.stack}
       }
       if (isFeatureLineRunon(line, featureLocationIndentation)) {
         if (lastLineWasLocation) {
-          parseFeatureLocation(line.trim(), options);
+          const feat = getCurrentFeature();
+          feat.locations = feat.locations.concat(
+            parseFeatureLocation(
+              line.trim(),
+              options.isProtein,
+              inclusive1BasedStart,
+              inclusive1BasedEnd
+            )
+          );
           lastLineWasLocation = true;
         } else {
           if (currentFeatureNote) {
@@ -124293,7 +124338,14 @@ ${latestSubscriptionCallbackError.current.stack}
           const feat = getCurrentFeature();
           feat.type = key2;
           feat.strand = strand;
-          parseFeatureLocation(val2, options);
+          feat.locations = feat.locations.concat(
+            parseFeatureLocation(
+              val2,
+              options.isProtein,
+              inclusive1BasedStart,
+              inclusive1BasedEnd
+            )
+          );
           lastLineWasLocation = true;
         }
       }
@@ -124316,29 +124368,6 @@ ${latestSubscriptionCallbackError.current.stack}
       return qual;
     }
     __name(isNote, "isNote");
-    function parseFeatureLocation(locStr, options2) {
-      locStr = locStr.trim();
-      const locArr = [];
-      locStr.replace(/(\d+)/g, function(string22, match2) {
-        locArr.push(match2);
-      });
-      for (let i2 = 0; i2 < locArr.length; i2 += 2) {
-        const start2 = parseInt(locArr[i2], 10) - (inclusive1BasedStart ? 0 : 1);
-        let end2 = parseInt(locArr[i2 + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
-        if (isNaN(end2)) {
-          end2 = start2;
-        }
-        const location2 = {
-          start: start2,
-          end: end2
-        };
-        const feat = getCurrentFeature();
-        feat.locations.push(
-          options2.isProtein ? convertAACaretPositionOrRangeToDna(location2) : location2
-        );
-      }
-    }
-    __name(parseFeatureLocation, "parseFeatureLocation");
     function parseFeatureNote(line) {
       let newLine;
       newLine = line.trimLeft();
@@ -136592,7 +136621,9 @@ ${seq.sequence}
       if (track2.isUnmapped) {
         return track2;
       }
-      const sequenceData2 = tidyUpSequenceData(track2.sequenceData);
+      const sequenceData2 = tidyUpSequenceData(track2.sequenceData, {
+        doNotRemoveInvalidChars: true
+      });
       const matchHighlightRanges = getRangeMatchesBetweenTemplateAndNonTemplate(
         alignmentTracks[0].alignmentData.sequence,
         track2.alignmentData.sequence
@@ -136652,7 +136683,9 @@ ${seq.sequence}
         const templateSeq = payloadToUse.pairwiseAlignments[0][0];
         const pairwiseOverviewAlignmentTracks = [
           __spreadProps(__spreadValues({}, templateSeq), {
-            sequenceData: tidyUpSequenceData(templateSeq.sequenceData),
+            sequenceData: tidyUpSequenceData(templateSeq.sequenceData, {
+              doNotRemoveInvalidChars: true
+            }),
             alignmentData: { sequence: templateSeq.sequenceData.sequence }
             //remove the gaps from the template sequence
           })
@@ -136681,7 +136714,9 @@ ${seq.sequence}
             }));
           }
           const alignedSeqMinusInserts = __spreadProps(__spreadValues({}, alignedSeq), {
-            sequenceData: __spreadProps(__spreadValues({}, tidyUpSequenceData(alignedSeq.sequenceData)), {
+            sequenceData: __spreadProps(__spreadValues({}, tidyUpSequenceData(alignedSeq.sequenceData, {
+              doNotRemoveInvalidChars: true
+            })), {
               sequence: template.sequenceData.sequence
             }),
             additionalSelectionLayers,
@@ -140039,7 +140074,7 @@ ${seq.sequence}
     }
     const promiseOrVal = (!readOnly2 || alwaysAllowSave || opts2.isSaveAs) && saveHandler && saveHandler(
       opts2,
-      tidyUpSequenceData(sequenceData2, { annotationsAsObjects: true }),
+      tidyUpSequenceData(sequenceData2, { doNotRemoveInvalidChars: true, annotationsAsObjects: true }),
       props,
       updateLastSavedIdToCurrent
     );
@@ -140639,7 +140674,7 @@ ${seq.sequence}
     return JSON.stringify(
       lodashExports.omit(
         cleanUpTeselagenJsonForExport(
-          tidyUpSequenceData(incomingJson, { annotationsAsObjects: false })
+          tidyUpSequenceData(incomingJson, { doNotRemoveInvalidChars: true, annotationsAsObjects: false })
         ),
         [
           "sequenceFragments",
@@ -155101,7 +155136,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
   }
   __name(showFileDialog, "showFileDialog");
   const name = "@teselagen/ove";
-  const version = "0.3.49";
+  const version = "0.3.50";
   const main = "./src/index.js";
   const exports$1 = {
     ".": {
@@ -158231,7 +158266,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
                 }
               }
             ),
-            { annotationsAsObjects: true }
+            { doNotRemoveInvalidChars: true, annotationsAsObjects: true }
           );
           if (!(this.sequenceDataToCopy || {}).textToCopy && !seqData.sequence.length)
             return window.toastr.warning(
@@ -158247,7 +158282,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
             this.handleDnaDelete(false);
             onCut(
               e2,
-              tidyUpSequenceData(seqData, { annotationsAsObjects: true }),
+              tidyUpSequenceData(seqData, { doNotRemoveInvalidChars: true, annotationsAsObjects: true }),
               this.props
             );
             document.body.removeEventListener("cut", this.handleCut);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.3.50",
+  "version": "0.3.51",
   "main": "./src/index.js",
   "exports": {
     ".": {
@@ -13,12 +13,12 @@
     "node": "16.20.2"
   },
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.11",
+    "@teselagen/sequence-utils": "0.3.12",
     "@teselagen/range-utils": "0.3.7",
     "@teselagen/ui": "0.3.38",
     "@teselagen/file-utils": "0.3.9",
     "@teselagen/bounce-loader": "0.3.11",
-    "@teselagen/bio-parsers": "0.4.3",
+    "@teselagen/bio-parsers": "0.4.5",
     "@blueprintjs/core": "3.52.0",
     "@blueprintjs/datetime": "3.23.19",
     "@blueprintjs/icons": "3.33.0",

package/src/redux/alignments.js

@@ -79,7 +79,9 @@ function addHighlightedDifferences(alignmentTracks) {
     if (track.isUnmapped) {
       return track;
     }
-    const sequenceData = tidyUpSequenceData(track.sequenceData);
+    const sequenceData = tidyUpSequenceData(track.sequenceData, {
+      doNotRemoveInvalidChars: true
+    });
     const matchHighlightRanges = getRangeMatchesBetweenTemplateAndNonTemplate(
       alignmentTracks[0].alignmentData.sequence,
       track.alignmentData.sequence
@@ -179,7 +181,9 @@ export default (state = {}, { payload = {}, type }) => {
         {
           //add the template seq as the first track in the Pairwise Alignment Overview
           ...templateSeq,
-          sequenceData: tidyUpSequenceData(templateSeq.sequenceData),
+          sequenceData: tidyUpSequenceData(templateSeq.sequenceData, {
+            doNotRemoveInvalidChars: true
+          }),
           alignmentData: { sequence: templateSeq.sequenceData.sequence } //remove the gaps from the template sequence
         }
       ]; // start with just the template seq in there!
@@ -213,7 +217,9 @@ export default (state = {}, { payload = {}, type }) => {
         const alignedSeqMinusInserts = {
           ...alignedSeq,
           sequenceData: {
-            ...tidyUpSequenceData(alignedSeq.sequenceData),
+            ...tidyUpSequenceData(alignedSeq.sequenceData, {
+              doNotRemoveInvalidChars: true
+            }),
             sequence: template.sequenceData.sequence
           },
           additionalSelectionLayers,

package/src/withEditorInteractions/index.js

@@ -283,7 +283,7 @@ function VectorInteractionHOC(Component /* options */) {
               }
             }
           ),
-        { annotationsAsObjects: true }
+        { doNotRemoveInvalidChars: true, annotationsAsObjects: true }
       );
 
       if (
@@ -314,7 +314,7 @@ function VectorInteractionHOC(Component /* options */) {
         this.handleDnaDelete(false);
         onCut(
           e,
-          tidyUpSequenceData(seqData, { annotationsAsObjects: true }),
+          tidyUpSequenceData(seqData, { doNotRemoveInvalidChars: true,annotationsAsObjects: true }),
           this.props
         );
         document.body.removeEventListener("cut", this.handleCut);

package/src/withEditorProps/index.js

@@ -160,7 +160,7 @@ export const handleSave =
       saveHandler &&
       saveHandler(
         opts,
-        tidyUpSequenceData(sequenceData, { annotationsAsObjects: true }),
+        tidyUpSequenceData(sequenceData, { doNotRemoveInvalidChars: true,annotationsAsObjects: true }),
         props,
         updateLastSavedIdToCurrent
       );
@@ -869,7 +869,7 @@ function jsonToJson(incomingJson) {
   return JSON.stringify(
     omit(
       cleanUpTeselagenJsonForExport(
-        tidyUpSequenceData(incomingJson, { annotationsAsObjects: false })
+        tidyUpSequenceData(incomingJson, { doNotRemoveInvalidChars: true,annotationsAsObjects: false })
       ),
       [
         "sequenceFragments",