@teselagen/ove 0.5.3 → 0.5.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/index.cjs.js +83 -52
- package/index.es.js +83 -52
- package/index.umd.js +83 -52
- package/package.json +3 -3
package/index.cjs.js
CHANGED
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@@ -52982,31 +52982,36 @@ const renderBlueprintRadioGroup = /* @__PURE__ */ __name((_e) => {
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52982
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const optionsToUse = getOptions$1(options);
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52983
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if (options.some((opt) => {
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52984
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if (opt.value === "true") {
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52985
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-
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52985
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return true;
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}
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52987
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-
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52988
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-
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-
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52990
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-
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52991
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selectedValue: input.value,
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52992
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label: void 0,
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52993
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onChange: function(e2) {
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52994
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let val2 = e2.target.value;
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if (val2 === "true") {
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val2 = true;
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}
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52998
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if (val2 === "false") {
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52999
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val2 = false;
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}
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if (val2 === "") {
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val2 = false;
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53003
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}
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53004
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input.onChange(val2);
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onFieldSubmit(val2);
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},
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options: optionsToUse
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53008
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})
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52987
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return false;
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52988
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})) {
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52989
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throw new Error(
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52990
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'RadioGroup values cannot be strings of "true" or "false", they must be actual booleans'
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53009
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);
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52992
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}
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52993
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return /* @__PURE__ */ React$2.createElement(
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52994
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core$5.RadioGroup,
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__spreadProps(__spreadValues(__spreadValues({}, input), removeUnwantedProps(rest)), {
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52996
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selectedValue: input.value,
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label: void 0,
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onChange: function(e2) {
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52999
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let val2 = e2.target.value;
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53000
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if (val2 === "true") {
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53001
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val2 = true;
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53002
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}
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53003
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if (val2 === "false") {
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val2 = false;
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}
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53006
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if (val2 === "") {
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53007
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val2 = false;
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53008
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}
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53009
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input.onChange(val2);
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53010
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onFieldSubmit(val2);
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53011
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},
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options: optionsToUse
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})
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);
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}, "renderBlueprintRadioGroup");
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const _RenderReactColorPicker = class _RenderReactColorPicker extends React$2.Component {
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constructor() {
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@@ -93528,19 +93533,38 @@ function flattenSequenceArray(parsingResultArray, opts2) {
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return parsingResultArray;
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}
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__name(flattenSequenceArray, "flattenSequenceArray");
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+
function wrapOriginSpanningFeatures(locArrayInput, sequenceLength, inclusive1BasedStart, inclusive1BasedEnd) {
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const locArrayOutput = locArrayInput.map((loc) => __spreadValues({}, loc));
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for (let i = 0; i < locArrayOutput.length - 1; i++) {
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const firstFeature = locArrayOutput[i];
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const secondFeature = locArrayOutput[i + 1];
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if (firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) && secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)) {
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locArrayOutput[i] = {
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start: firstFeature.start,
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end: secondFeature.end
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};
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locArrayOutput.splice(i + 1, 1);
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}
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}
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return locArrayOutput;
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}
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__name(wrapOriginSpanningFeatures, "wrapOriginSpanningFeatures");
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function parseFeatureLocation(locStr, isProtein2, inclusive1BasedStart, inclusive1BasedEnd, isCircular, sequenceLength) {
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locStr = locStr.trim();
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-
const
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locStr.
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-
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const positionsArray = [];
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const locationParts = locStr.split(",");
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93556
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locationParts.forEach((locPart) => {
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const extractedPositions = locPart.match(/(\d+)/g);
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if (extractedPositions === null) {
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return;
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}
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positionsArray.push(extractedPositions[0]);
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positionsArray.push(extractedPositions[1] || extractedPositions[0]);
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});
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const locArray = [];
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93538
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-
for (let i = 0; i <
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-
const start2 = parseInt(
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-
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if (isNaN(end2)) {
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93542
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end2 = start2;
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-
}
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for (let i = 0; i < positionsArray.length; i += 2) {
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const start2 = parseInt(positionsArray[i], 10) - (inclusive1BasedStart ? 0 : 1);
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const end2 = parseInt(positionsArray[i + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
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const location2 = {
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start: start2,
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end: end2
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@@ -93549,20 +93573,16 @@ function parseFeatureLocation(locStr, isProtein2, inclusive1BasedStart, inclusiv
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isProtein2 ? convertAACaretPositionOrRangeToDna(location2) : location2
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);
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}
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-
if (isCircular) {
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-
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-
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-
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-
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locArray.splice(i + 1, 1);
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}
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}
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if (isCircular && sequenceLength) {
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return wrapOriginSpanningFeatures(
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locArray,
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sequenceLength,
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inclusive1BasedStart,
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inclusive1BasedEnd
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);
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} else {
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return locArray;
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}
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93565
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-
return locArray;
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}
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__name(parseFeatureLocation, "parseFeatureLocation");
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function genbankToJson(string2, options = {}) {
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@@ -93659,7 +93679,7 @@ function genbankToJson(string2, options = {}) {
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parseOrigin(line, key);
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break;
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case genbankAnnotationKey.END_SEQUENCE_TAG:
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-
endSeq();
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endSeq(options);
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break;
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case genbankAnnotationKey.DEFINITION_TAG:
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line = line.replace(/DEFINITION/, "");
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@@ -93764,9 +93784,9 @@ function genbankToJson(string2, options = {}) {
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}
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});
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return results;
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93767
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-
function endSeq() {
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+
function endSeq(options2) {
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hasFoundLocus = false;
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93769
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postProcessCurSeq();
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postProcessCurSeq(options2);
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resultsArray.push(result || { success: false });
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}
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__name(endSeq, "endSeq");
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@@ -93780,11 +93800,13 @@ function genbankToJson(string2, options = {}) {
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}
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}
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__name(addMessage, "addMessage");
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-
function postProcessCurSeq() {
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function postProcessCurSeq(options2) {
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if (result && result.parsedSequence && result.parsedSequence.features) {
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for (let i = 0; i < result.parsedSequence.features.length; i++) {
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result.parsedSequence.features[i] = postProcessGenbankFeature(
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result.parsedSequence.features[i]
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result.parsedSequence.features[i],
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result.parsedSequence,
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options2
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);
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}
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}
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@@ -94030,7 +94052,7 @@ function genbankToJson(string2, options = {}) {
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return runon;
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}
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__name(isKeywordRunon, "isKeywordRunon");
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-
function postProcessGenbankFeature(feat) {
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function postProcessGenbankFeature(feat, parsedSequence, options2) {
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if (feat.notes.label) {
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feat.name = feat.notes.label[0];
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} else if (feat.notes.gene) {
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@@ -94063,6 +94085,15 @@ function genbankToJson(string2, options = {}) {
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feat.arrowheadType = feat.notes.direction[0].toUpperCase() === "BOTH" ? "BOTH" : feat.notes.direction[0].toUpperCase() === "NONE" ? "NONE" : void 0;
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delete feat.notes.direction;
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}
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if (parsedSequence.circular) {
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const { inclusive1BasedStart: inclusive1BasedStart2, inclusive1BasedEnd: inclusive1BasedEnd2 } = options2;
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94090
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feat.locations = wrapOriginSpanningFeatures(
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feat.locations,
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parsedSequence.sequence.length,
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inclusive1BasedStart2,
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94094
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inclusive1BasedEnd2
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);
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94096
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}
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return feat;
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}
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__name(postProcessGenbankFeature, "postProcessGenbankFeature");
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@@ -125363,7 +125394,7 @@ function showFileDialog({ multiple = false, onSelect }) {
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}
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__name(showFileDialog, "showFileDialog");
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const name = "@teselagen/ove";
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-
const version = "0.5.
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125397
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+
const version = "0.5.3";
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const main = "./src/index.js";
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const exports$1 = {
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".": {
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package/index.es.js
CHANGED
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@@ -52964,31 +52964,36 @@ const renderBlueprintRadioGroup = /* @__PURE__ */ __name((_e) => {
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52964
52964
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const optionsToUse = getOptions$1(options);
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52965
52965
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if (options.some((opt) => {
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if (opt.value === "true") {
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52967
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-
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return true;
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}
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52969
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-
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-
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52971
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-
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-
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selectedValue: input.value,
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52974
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label: void 0,
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-
onChange: function(e2) {
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-
let val2 = e2.target.value;
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52977
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-
if (val2 === "true") {
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-
val2 = true;
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52979
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-
}
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52980
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-
if (val2 === "false") {
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-
val2 = false;
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52982
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-
}
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52983
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-
if (val2 === "") {
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52984
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-
val2 = false;
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52985
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-
}
|
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52986
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-
input.onChange(val2);
|
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52987
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-
onFieldSubmit(val2);
|
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52988
|
-
},
|
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52989
|
-
options: optionsToUse
|
|
52990
|
-
})
|
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52969
|
+
return false;
|
|
52970
|
+
})) {
|
|
52971
|
+
throw new Error(
|
|
52972
|
+
'RadioGroup values cannot be strings of "true" or "false", they must be actual booleans'
|
|
52991
52973
|
);
|
|
52974
|
+
}
|
|
52975
|
+
return /* @__PURE__ */ React__default$1.createElement(
|
|
52976
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+
RadioGroup,
|
|
52977
|
+
__spreadProps(__spreadValues(__spreadValues({}, input), removeUnwantedProps(rest)), {
|
|
52978
|
+
selectedValue: input.value,
|
|
52979
|
+
label: void 0,
|
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52980
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+
onChange: function(e2) {
|
|
52981
|
+
let val2 = e2.target.value;
|
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52982
|
+
if (val2 === "true") {
|
|
52983
|
+
val2 = true;
|
|
52984
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+
}
|
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52985
|
+
if (val2 === "false") {
|
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52986
|
+
val2 = false;
|
|
52987
|
+
}
|
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52988
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+
if (val2 === "") {
|
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52989
|
+
val2 = false;
|
|
52990
|
+
}
|
|
52991
|
+
input.onChange(val2);
|
|
52992
|
+
onFieldSubmit(val2);
|
|
52993
|
+
},
|
|
52994
|
+
options: optionsToUse
|
|
52995
|
+
})
|
|
52996
|
+
);
|
|
52992
52997
|
}, "renderBlueprintRadioGroup");
|
|
52993
52998
|
const _RenderReactColorPicker = class _RenderReactColorPicker extends React__default$1.Component {
|
|
52994
52999
|
constructor() {
|
|
@@ -93510,19 +93515,38 @@ function flattenSequenceArray(parsingResultArray, opts2) {
|
|
|
93510
93515
|
return parsingResultArray;
|
|
93511
93516
|
}
|
|
93512
93517
|
__name(flattenSequenceArray, "flattenSequenceArray");
|
|
93518
|
+
function wrapOriginSpanningFeatures(locArrayInput, sequenceLength, inclusive1BasedStart, inclusive1BasedEnd) {
|
|
93519
|
+
const locArrayOutput = locArrayInput.map((loc) => __spreadValues({}, loc));
|
|
93520
|
+
for (let i = 0; i < locArrayOutput.length - 1; i++) {
|
|
93521
|
+
const firstFeature = locArrayOutput[i];
|
|
93522
|
+
const secondFeature = locArrayOutput[i + 1];
|
|
93523
|
+
if (firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) && secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)) {
|
|
93524
|
+
locArrayOutput[i] = {
|
|
93525
|
+
start: firstFeature.start,
|
|
93526
|
+
end: secondFeature.end
|
|
93527
|
+
};
|
|
93528
|
+
locArrayOutput.splice(i + 1, 1);
|
|
93529
|
+
}
|
|
93530
|
+
}
|
|
93531
|
+
return locArrayOutput;
|
|
93532
|
+
}
|
|
93533
|
+
__name(wrapOriginSpanningFeatures, "wrapOriginSpanningFeatures");
|
|
93513
93534
|
function parseFeatureLocation(locStr, isProtein2, inclusive1BasedStart, inclusive1BasedEnd, isCircular, sequenceLength) {
|
|
93514
93535
|
locStr = locStr.trim();
|
|
93515
|
-
const
|
|
93516
|
-
locStr.
|
|
93517
|
-
|
|
93536
|
+
const positionsArray = [];
|
|
93537
|
+
const locationParts = locStr.split(",");
|
|
93538
|
+
locationParts.forEach((locPart) => {
|
|
93539
|
+
const extractedPositions = locPart.match(/(\d+)/g);
|
|
93540
|
+
if (extractedPositions === null) {
|
|
93541
|
+
return;
|
|
93542
|
+
}
|
|
93543
|
+
positionsArray.push(extractedPositions[0]);
|
|
93544
|
+
positionsArray.push(extractedPositions[1] || extractedPositions[0]);
|
|
93518
93545
|
});
|
|
93519
93546
|
const locArray = [];
|
|
93520
|
-
for (let i = 0; i <
|
|
93521
|
-
const start2 = parseInt(
|
|
93522
|
-
|
|
93523
|
-
if (isNaN(end2)) {
|
|
93524
|
-
end2 = start2;
|
|
93525
|
-
}
|
|
93547
|
+
for (let i = 0; i < positionsArray.length; i += 2) {
|
|
93548
|
+
const start2 = parseInt(positionsArray[i], 10) - (inclusive1BasedStart ? 0 : 1);
|
|
93549
|
+
const end2 = parseInt(positionsArray[i + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
|
|
93526
93550
|
const location2 = {
|
|
93527
93551
|
start: start2,
|
|
93528
93552
|
end: end2
|
|
@@ -93531,20 +93555,16 @@ function parseFeatureLocation(locStr, isProtein2, inclusive1BasedStart, inclusiv
|
|
|
93531
93555
|
isProtein2 ? convertAACaretPositionOrRangeToDna(location2) : location2
|
|
93532
93556
|
);
|
|
93533
93557
|
}
|
|
93534
|
-
if (isCircular) {
|
|
93535
|
-
|
|
93536
|
-
|
|
93537
|
-
|
|
93538
|
-
|
|
93539
|
-
|
|
93540
|
-
|
|
93541
|
-
|
|
93542
|
-
|
|
93543
|
-
locArray.splice(i + 1, 1);
|
|
93544
|
-
}
|
|
93545
|
-
}
|
|
93558
|
+
if (isCircular && sequenceLength) {
|
|
93559
|
+
return wrapOriginSpanningFeatures(
|
|
93560
|
+
locArray,
|
|
93561
|
+
sequenceLength,
|
|
93562
|
+
inclusive1BasedStart,
|
|
93563
|
+
inclusive1BasedEnd
|
|
93564
|
+
);
|
|
93565
|
+
} else {
|
|
93566
|
+
return locArray;
|
|
93546
93567
|
}
|
|
93547
|
-
return locArray;
|
|
93548
93568
|
}
|
|
93549
93569
|
__name(parseFeatureLocation, "parseFeatureLocation");
|
|
93550
93570
|
function genbankToJson(string2, options = {}) {
|
|
@@ -93641,7 +93661,7 @@ function genbankToJson(string2, options = {}) {
|
|
|
93641
93661
|
parseOrigin(line, key);
|
|
93642
93662
|
break;
|
|
93643
93663
|
case genbankAnnotationKey.END_SEQUENCE_TAG:
|
|
93644
|
-
endSeq();
|
|
93664
|
+
endSeq(options);
|
|
93645
93665
|
break;
|
|
93646
93666
|
case genbankAnnotationKey.DEFINITION_TAG:
|
|
93647
93667
|
line = line.replace(/DEFINITION/, "");
|
|
@@ -93746,9 +93766,9 @@ function genbankToJson(string2, options = {}) {
|
|
|
93746
93766
|
}
|
|
93747
93767
|
});
|
|
93748
93768
|
return results;
|
|
93749
|
-
function endSeq() {
|
|
93769
|
+
function endSeq(options2) {
|
|
93750
93770
|
hasFoundLocus = false;
|
|
93751
|
-
postProcessCurSeq();
|
|
93771
|
+
postProcessCurSeq(options2);
|
|
93752
93772
|
resultsArray.push(result || { success: false });
|
|
93753
93773
|
}
|
|
93754
93774
|
__name(endSeq, "endSeq");
|
|
@@ -93762,11 +93782,13 @@ function genbankToJson(string2, options = {}) {
|
|
|
93762
93782
|
}
|
|
93763
93783
|
}
|
|
93764
93784
|
__name(addMessage, "addMessage");
|
|
93765
|
-
function postProcessCurSeq() {
|
|
93785
|
+
function postProcessCurSeq(options2) {
|
|
93766
93786
|
if (result && result.parsedSequence && result.parsedSequence.features) {
|
|
93767
93787
|
for (let i = 0; i < result.parsedSequence.features.length; i++) {
|
|
93768
93788
|
result.parsedSequence.features[i] = postProcessGenbankFeature(
|
|
93769
|
-
result.parsedSequence.features[i]
|
|
93789
|
+
result.parsedSequence.features[i],
|
|
93790
|
+
result.parsedSequence,
|
|
93791
|
+
options2
|
|
93770
93792
|
);
|
|
93771
93793
|
}
|
|
93772
93794
|
}
|
|
@@ -94012,7 +94034,7 @@ function genbankToJson(string2, options = {}) {
|
|
|
94012
94034
|
return runon;
|
|
94013
94035
|
}
|
|
94014
94036
|
__name(isKeywordRunon, "isKeywordRunon");
|
|
94015
|
-
function postProcessGenbankFeature(feat) {
|
|
94037
|
+
function postProcessGenbankFeature(feat, parsedSequence, options2) {
|
|
94016
94038
|
if (feat.notes.label) {
|
|
94017
94039
|
feat.name = feat.notes.label[0];
|
|
94018
94040
|
} else if (feat.notes.gene) {
|
|
@@ -94045,6 +94067,15 @@ function genbankToJson(string2, options = {}) {
|
|
|
94045
94067
|
feat.arrowheadType = feat.notes.direction[0].toUpperCase() === "BOTH" ? "BOTH" : feat.notes.direction[0].toUpperCase() === "NONE" ? "NONE" : void 0;
|
|
94046
94068
|
delete feat.notes.direction;
|
|
94047
94069
|
}
|
|
94070
|
+
if (parsedSequence.circular) {
|
|
94071
|
+
const { inclusive1BasedStart: inclusive1BasedStart2, inclusive1BasedEnd: inclusive1BasedEnd2 } = options2;
|
|
94072
|
+
feat.locations = wrapOriginSpanningFeatures(
|
|
94073
|
+
feat.locations,
|
|
94074
|
+
parsedSequence.sequence.length,
|
|
94075
|
+
inclusive1BasedStart2,
|
|
94076
|
+
inclusive1BasedEnd2
|
|
94077
|
+
);
|
|
94078
|
+
}
|
|
94048
94079
|
return feat;
|
|
94049
94080
|
}
|
|
94050
94081
|
__name(postProcessGenbankFeature, "postProcessGenbankFeature");
|
|
@@ -125345,7 +125376,7 @@ function showFileDialog({ multiple = false, onSelect }) {
|
|
|
125345
125376
|
}
|
|
125346
125377
|
__name(showFileDialog, "showFileDialog");
|
|
125347
125378
|
const name = "@teselagen/ove";
|
|
125348
|
-
const version = "0.5.
|
|
125379
|
+
const version = "0.5.3";
|
|
125349
125380
|
const main = "./src/index.js";
|
|
125350
125381
|
const exports$1 = {
|
|
125351
125382
|
".": {
|
package/index.umd.js
CHANGED
|
@@ -82868,31 +82868,36 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
82868
82868
|
const optionsToUse = getOptions$1(options);
|
|
82869
82869
|
if (options.some((opt) => {
|
|
82870
82870
|
if (opt.value === "true") {
|
|
82871
|
-
|
|
82871
|
+
return true;
|
|
82872
82872
|
}
|
|
82873
|
-
|
|
82874
|
-
|
|
82875
|
-
|
|
82876
|
-
|
|
82877
|
-
selectedValue: input.value,
|
|
82878
|
-
label: void 0,
|
|
82879
|
-
onChange: function(e2) {
|
|
82880
|
-
let val2 = e2.target.value;
|
|
82881
|
-
if (val2 === "true") {
|
|
82882
|
-
val2 = true;
|
|
82883
|
-
}
|
|
82884
|
-
if (val2 === "false") {
|
|
82885
|
-
val2 = false;
|
|
82886
|
-
}
|
|
82887
|
-
if (val2 === "") {
|
|
82888
|
-
val2 = false;
|
|
82889
|
-
}
|
|
82890
|
-
input.onChange(val2);
|
|
82891
|
-
onFieldSubmit(val2);
|
|
82892
|
-
},
|
|
82893
|
-
options: optionsToUse
|
|
82894
|
-
})
|
|
82873
|
+
return false;
|
|
82874
|
+
})) {
|
|
82875
|
+
throw new Error(
|
|
82876
|
+
'RadioGroup values cannot be strings of "true" or "false", they must be actual booleans'
|
|
82895
82877
|
);
|
|
82878
|
+
}
|
|
82879
|
+
return /* @__PURE__ */ React$2.createElement(
|
|
82880
|
+
RadioGroup,
|
|
82881
|
+
__spreadProps(__spreadValues(__spreadValues({}, input), removeUnwantedProps(rest)), {
|
|
82882
|
+
selectedValue: input.value,
|
|
82883
|
+
label: void 0,
|
|
82884
|
+
onChange: function(e2) {
|
|
82885
|
+
let val2 = e2.target.value;
|
|
82886
|
+
if (val2 === "true") {
|
|
82887
|
+
val2 = true;
|
|
82888
|
+
}
|
|
82889
|
+
if (val2 === "false") {
|
|
82890
|
+
val2 = false;
|
|
82891
|
+
}
|
|
82892
|
+
if (val2 === "") {
|
|
82893
|
+
val2 = false;
|
|
82894
|
+
}
|
|
82895
|
+
input.onChange(val2);
|
|
82896
|
+
onFieldSubmit(val2);
|
|
82897
|
+
},
|
|
82898
|
+
options: optionsToUse
|
|
82899
|
+
})
|
|
82900
|
+
);
|
|
82896
82901
|
}, "renderBlueprintRadioGroup");
|
|
82897
82902
|
const _RenderReactColorPicker = class _RenderReactColorPicker extends React$2.Component {
|
|
82898
82903
|
constructor() {
|
|
@@ -123400,19 +123405,38 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
123400
123405
|
return parsingResultArray;
|
|
123401
123406
|
}
|
|
123402
123407
|
__name(flattenSequenceArray, "flattenSequenceArray");
|
|
123408
|
+
function wrapOriginSpanningFeatures(locArrayInput, sequenceLength, inclusive1BasedStart, inclusive1BasedEnd) {
|
|
123409
|
+
const locArrayOutput = locArrayInput.map((loc) => __spreadValues({}, loc));
|
|
123410
|
+
for (let i2 = 0; i2 < locArrayOutput.length - 1; i2++) {
|
|
123411
|
+
const firstFeature = locArrayOutput[i2];
|
|
123412
|
+
const secondFeature = locArrayOutput[i2 + 1];
|
|
123413
|
+
if (firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) && secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)) {
|
|
123414
|
+
locArrayOutput[i2] = {
|
|
123415
|
+
start: firstFeature.start,
|
|
123416
|
+
end: secondFeature.end
|
|
123417
|
+
};
|
|
123418
|
+
locArrayOutput.splice(i2 + 1, 1);
|
|
123419
|
+
}
|
|
123420
|
+
}
|
|
123421
|
+
return locArrayOutput;
|
|
123422
|
+
}
|
|
123423
|
+
__name(wrapOriginSpanningFeatures, "wrapOriginSpanningFeatures");
|
|
123403
123424
|
function parseFeatureLocation(locStr, isProtein2, inclusive1BasedStart, inclusive1BasedEnd, isCircular, sequenceLength) {
|
|
123404
123425
|
locStr = locStr.trim();
|
|
123405
|
-
const
|
|
123406
|
-
locStr.
|
|
123407
|
-
|
|
123426
|
+
const positionsArray = [];
|
|
123427
|
+
const locationParts = locStr.split(",");
|
|
123428
|
+
locationParts.forEach((locPart) => {
|
|
123429
|
+
const extractedPositions = locPart.match(/(\d+)/g);
|
|
123430
|
+
if (extractedPositions === null) {
|
|
123431
|
+
return;
|
|
123432
|
+
}
|
|
123433
|
+
positionsArray.push(extractedPositions[0]);
|
|
123434
|
+
positionsArray.push(extractedPositions[1] || extractedPositions[0]);
|
|
123408
123435
|
});
|
|
123409
123436
|
const locArray = [];
|
|
123410
|
-
for (let i2 = 0; i2 <
|
|
123411
|
-
const start2 = parseInt(
|
|
123412
|
-
|
|
123413
|
-
if (isNaN(end2)) {
|
|
123414
|
-
end2 = start2;
|
|
123415
|
-
}
|
|
123437
|
+
for (let i2 = 0; i2 < positionsArray.length; i2 += 2) {
|
|
123438
|
+
const start2 = parseInt(positionsArray[i2], 10) - (inclusive1BasedStart ? 0 : 1);
|
|
123439
|
+
const end2 = parseInt(positionsArray[i2 + 1], 10) - (inclusive1BasedEnd ? 0 : 1);
|
|
123416
123440
|
const location2 = {
|
|
123417
123441
|
start: start2,
|
|
123418
123442
|
end: end2
|
|
@@ -123421,20 +123445,16 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
123421
123445
|
isProtein2 ? convertAACaretPositionOrRangeToDna(location2) : location2
|
|
123422
123446
|
);
|
|
123423
123447
|
}
|
|
123424
|
-
if (isCircular) {
|
|
123425
|
-
|
|
123426
|
-
|
|
123427
|
-
|
|
123428
|
-
|
|
123429
|
-
|
|
123430
|
-
|
|
123431
|
-
|
|
123432
|
-
|
|
123433
|
-
locArray.splice(i2 + 1, 1);
|
|
123434
|
-
}
|
|
123435
|
-
}
|
|
123448
|
+
if (isCircular && sequenceLength) {
|
|
123449
|
+
return wrapOriginSpanningFeatures(
|
|
123450
|
+
locArray,
|
|
123451
|
+
sequenceLength,
|
|
123452
|
+
inclusive1BasedStart,
|
|
123453
|
+
inclusive1BasedEnd
|
|
123454
|
+
);
|
|
123455
|
+
} else {
|
|
123456
|
+
return locArray;
|
|
123436
123457
|
}
|
|
123437
|
-
return locArray;
|
|
123438
123458
|
}
|
|
123439
123459
|
__name(parseFeatureLocation, "parseFeatureLocation");
|
|
123440
123460
|
function genbankToJson(string2, options = {}) {
|
|
@@ -123531,7 +123551,7 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
123531
123551
|
parseOrigin(line, key2);
|
|
123532
123552
|
break;
|
|
123533
123553
|
case genbankAnnotationKey.END_SEQUENCE_TAG:
|
|
123534
|
-
endSeq();
|
|
123554
|
+
endSeq(options);
|
|
123535
123555
|
break;
|
|
123536
123556
|
case genbankAnnotationKey.DEFINITION_TAG:
|
|
123537
123557
|
line = line.replace(/DEFINITION/, "");
|
|
@@ -123636,9 +123656,9 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
123636
123656
|
}
|
|
123637
123657
|
});
|
|
123638
123658
|
return results;
|
|
123639
|
-
function endSeq() {
|
|
123659
|
+
function endSeq(options2) {
|
|
123640
123660
|
hasFoundLocus = false;
|
|
123641
|
-
postProcessCurSeq();
|
|
123661
|
+
postProcessCurSeq(options2);
|
|
123642
123662
|
resultsArray.push(result || { success: false });
|
|
123643
123663
|
}
|
|
123644
123664
|
__name(endSeq, "endSeq");
|
|
@@ -123652,11 +123672,13 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
123652
123672
|
}
|
|
123653
123673
|
}
|
|
123654
123674
|
__name(addMessage, "addMessage");
|
|
123655
|
-
function postProcessCurSeq() {
|
|
123675
|
+
function postProcessCurSeq(options2) {
|
|
123656
123676
|
if (result && result.parsedSequence && result.parsedSequence.features) {
|
|
123657
123677
|
for (let i2 = 0; i2 < result.parsedSequence.features.length; i2++) {
|
|
123658
123678
|
result.parsedSequence.features[i2] = postProcessGenbankFeature(
|
|
123659
|
-
result.parsedSequence.features[i2]
|
|
123679
|
+
result.parsedSequence.features[i2],
|
|
123680
|
+
result.parsedSequence,
|
|
123681
|
+
options2
|
|
123660
123682
|
);
|
|
123661
123683
|
}
|
|
123662
123684
|
}
|
|
@@ -123902,7 +123924,7 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
123902
123924
|
return runon;
|
|
123903
123925
|
}
|
|
123904
123926
|
__name(isKeywordRunon, "isKeywordRunon");
|
|
123905
|
-
function postProcessGenbankFeature(feat) {
|
|
123927
|
+
function postProcessGenbankFeature(feat, parsedSequence, options2) {
|
|
123906
123928
|
if (feat.notes.label) {
|
|
123907
123929
|
feat.name = feat.notes.label[0];
|
|
123908
123930
|
} else if (feat.notes.gene) {
|
|
@@ -123935,6 +123957,15 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
123935
123957
|
feat.arrowheadType = feat.notes.direction[0].toUpperCase() === "BOTH" ? "BOTH" : feat.notes.direction[0].toUpperCase() === "NONE" ? "NONE" : void 0;
|
|
123936
123958
|
delete feat.notes.direction;
|
|
123937
123959
|
}
|
|
123960
|
+
if (parsedSequence.circular) {
|
|
123961
|
+
const { inclusive1BasedStart: inclusive1BasedStart2, inclusive1BasedEnd: inclusive1BasedEnd2 } = options2;
|
|
123962
|
+
feat.locations = wrapOriginSpanningFeatures(
|
|
123963
|
+
feat.locations,
|
|
123964
|
+
parsedSequence.sequence.length,
|
|
123965
|
+
inclusive1BasedStart2,
|
|
123966
|
+
inclusive1BasedEnd2
|
|
123967
|
+
);
|
|
123968
|
+
}
|
|
123938
123969
|
return feat;
|
|
123939
123970
|
}
|
|
123940
123971
|
__name(postProcessGenbankFeature, "postProcessGenbankFeature");
|
|
@@ -154625,7 +154656,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
|
|
|
154625
154656
|
}
|
|
154626
154657
|
__name(showFileDialog, "showFileDialog");
|
|
154627
154658
|
const name = "@teselagen/ove";
|
|
154628
|
-
const version = "0.5.
|
|
154659
|
+
const version = "0.5.3";
|
|
154629
154660
|
const main = "./src/index.js";
|
|
154630
154661
|
const exports$1 = {
|
|
154631
154662
|
".": {
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@teselagen/ove",
|
|
3
|
-
"version": "0.5.
|
|
3
|
+
"version": "0.5.4",
|
|
4
4
|
"main": "./src/index.js",
|
|
5
5
|
"exports": {
|
|
6
6
|
".": {
|
|
@@ -12,10 +12,10 @@
|
|
|
12
12
|
"dependencies": {
|
|
13
13
|
"@teselagen/sequence-utils": "0.3.24",
|
|
14
14
|
"@teselagen/range-utils": "0.3.7",
|
|
15
|
-
"@teselagen/ui": "0.4.
|
|
15
|
+
"@teselagen/ui": "0.4.4",
|
|
16
16
|
"@teselagen/file-utils": "0.3.16",
|
|
17
17
|
"@teselagen/bounce-loader": "0.3.11",
|
|
18
|
-
"@teselagen/bio-parsers": "0.4.
|
|
18
|
+
"@teselagen/bio-parsers": "0.4.16",
|
|
19
19
|
"@blueprintjs/core": "3.52.0",
|
|
20
20
|
"@blueprintjs/datetime": "3.23.19",
|
|
21
21
|
"@blueprintjs/icons": "3.33.0",
|