speeding up tidyUpAnnotation by passing featureTypes from tidyUpSeque…

…nceData
TeselaGen · Mar 14, 2023 · 6e0ea2d · 6e0ea2d
1 parent 834e309
commit 6e0ea2d
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/src/tidyUpAnnotation.js b/src/tidyUpAnnotation.js
@@ -15,7 +15,8 @@ module.exports = function tidyUpAnnotation(
     doNotProvideIdsForAnnotations,
     messages = [],
     mutative,
-    allowNonStandardGenbankTypes
+    allowNonStandardGenbankTypes,
+    featureTypes
   }
 ) {
   const { size, circular, isProtein } = sequenceData;
@@ -86,7 +87,7 @@ module.exports = function tidyUpAnnotation(
   if (
     !annotation.type ||
     typeof annotation.type !== "string" ||
-    !some(getFeatureTypes(), function(featureType) {
+    !some(featureTypes || getFeatureTypes(), function(featureType) {
       if (featureType.toLowerCase() === annotation.type.toLowerCase()) {
         annotation.type = featureType; //this makes sure the annotation.type is being set to the exact value of the accepted featureType
         return true;

diff --git a/src/tidyUpSequenceData.js b/src/tidyUpSequenceData.js
@@ -7,6 +7,7 @@ const filterSequenceString = require("./filterSequenceString");
 const tidyUpAnnotation = require("./tidyUpAnnotation");
 const filterAminoAcidSequenceString = require("./filterAminoAcidSequenceString");
 const getDegenerateDnaStringFromAaString = require("./getDegenerateDnaStringFromAAString");
+const { getFeatureTypes } = require("./featureTypesAndColors");
 
 module.exports = function tidyUpSequenceData(pSeqData, options = {}) {
   const {
@@ -100,6 +101,7 @@ module.exports = function tidyUpSequenceData(pSeqData, options = {}) {
   } else {
     seqData.circular = true;
   }
+  const featureTypes = getFeatureTypes();
 
   annotationTypes.forEach(function(annotationType) {
     if (!Array.isArray(seqData[annotationType])) {
@@ -116,6 +118,7 @@ module.exports = function tidyUpSequenceData(pSeqData, options = {}) {
     seqData[annotationType] = seqData[annotationType].filter(annotation => {
       return tidyUpAnnotation(annotation, {
         ...options,
+        featureTypes,
         sequenceData: seqData,
         convertAnnotationsFromAAIndices,
         mutative: true,