adding doNotProvideIdsForAnnotations flag for tidyUpSequencData; addi…

…ng alternate colorByFamily colors to amino acids

src/proteinAlphabet.js

@@ -4,169 +4,194 @@ module.exports = {
     name: "Alanine",
     threeLettersName: "Ala",
     hydrophobicity: 1.8,
+    colorByFamily: "#00FFFF",
     color: "#FF5C5C"
   },
   R: {
     value: "R",
     name: "Arginine",
     threeLettersName: "Arg",
     hydrophobicity: -4.5,
+    colorByFamily: "#FFC0CB",
     color: "#190000"
   },
   N: {
     value: "N",
     name: "Asparagine",
     threeLettersName: "Asn",
     hydrophobicity: -3.5,
+    colorByFamily: "#D3D3D3",
     color: "#4D0000"
   },
   D: {
     value: "D",
     name: "Aspartic acid",
     threeLettersName: "Asp",
     hydrophobicity: -3.5,
+    colorByFamily: "#EE82EE",
     color: "#4D0000"
   },
   C: {
     value: "C",
     name: "Cysteine",
     threeLettersName: "Cys",
     hydrophobicity: 2.5,
+    colorByFamily: "#FFFF00",
     color: "#FF8080"
   },
   E: {
     value: "E",
     name: "Glutamic acid",
     threeLettersName: "Glu",
     hydrophobicity: -3.5,
+    colorByFamily: "#EE82EE",
     color: "#4D0000"
   },
   Q: {
     value: "Q",
     name: "Glutamine",
     threeLettersName: "Gln",
     hydrophobicity: -3.5,
+    colorByFamily: "#D3D3D3",
     color: "#4D0000"
   },
   G: {
     value: "G",
     name: "Glycine",
     threeLettersName: "Gly",
     hydrophobicity: -0.4,
+    colorByFamily: "#00FFFF",
     color: "#EB0000"
   },
   H: {
     value: "H",
     name: "Histidine",
     threeLettersName: "His",
     hydrophobicity: -3.2,
+    colorByFamily: "#FFC0CB",
     color: "#5C0000"
   },
   I: {
     value: "I",
     name: "Isoleucine ",
     threeLettersName: "Ile",
     hydrophobicity: 4.5,
+    colorByFamily: "#00FFFF",
     color: "#FFE6E6"
   },
   L: {
     value: "L",
     name: "Leucine",
     threeLettersName: "Leu",
     hydrophobicity: 3.8,
+    colorByFamily: "#00FFFF",
     color: "#FFC2C2"
   },
   K: {
     value: "K",
     name: "Lysine",
     threeLettersName: "Lys",
     hydrophobicity: -3.9,
+    colorByFamily: "#FFC0CB",
     color: "#380000"
   },
   M: {
     value: "M",
     name: "Methionine",
     threeLettersName: "Met",
     hydrophobicity: 1.9,
+    colorByFamily: "#FFFF00",
     color: "#FF6161"
   },
   F: {
     value: "F",
     name: "Phenylalanine",
     threeLettersName: "Phe",
     hydrophobicity: 2.8,
+    colorByFamily: "#FFA500",
     color: "#FF8F8F"
   },
   P: {
     value: "P",
     name: "Proline",
     threeLettersName: "Pro",
     hydrophobicity: -1.6,
+    colorByFamily: "#00FFFF",
     color: "#AD0000"
   },
   S: {
     value: "S",
     name: "Serine",
     threeLettersName: "Ser",
     hydrophobicity: -0.8,
+    colorByFamily: "#90EE90",
     color: "#D60000"
   },
   T: {
     value: "T",
     name: "Threonine",
     threeLettersName: "Thr",
     hydrophobicity: -0.7,
+    colorByFamily: "#90EE90",
     color: "#DB0000"
   },
   U: {
     value: "U",
     name: "Selenocysteine",
     threeLettersName: "Sec",
+    colorByFamily: "#FF0000",
     color: "#FF0000"
   },
   W: {
     value: "W",
     name: "Tryptophan",
     threeLettersName: "Trp",
     hydrophobicity: -0.9,
+    colorByFamily: "#FFA500",
     color: "#D10000"
   },
   Y: {
     value: "Y",
     name: "Tyrosine",
     threeLettersName: "Tyr",
     hydrophobicity: -1.3,
+    colorByFamily: "#FFA500",
     color: "#BD0000"
   },
   V: {
     value: "V",
     name: "Valine",
     threeLettersName: "Val",
     hydrophobicity: 4.2,
+    colorByFamily: "#00FFFF",
     color: "#FFD6D6"
   },
   "*": {
     value: "*",
     name: "Stop",
     threeLettersName: "Stop",
+    colorByFamily: "#FF0000",
     color: "#FF0000"
   },
   ".": {
     //tnr: this is actually a deletion/gap character (previously we had this as a stop character which is incorrect) https://www.dnabaser.com/articles/IUPAC%20ambiguity%20codes.html
     value: ".",
     name: "Gap",
-    threeLettersName: "Gap",
+    threeLettersName: "Stop",
+    colorByFamily: "#FF0000",
     color: "#FF0000"
   },
   "-": {
     value: "-",
     name: "Gap",
     threeLettersName: "Gap",
+    colorByFamily: "#FF0000",
     color: "#FF0000"
   },
   B: {
     value: "B",
     threeLettersName: "ND",
+    colorByFamily: "lightpurple",
     color: "lightpurple",
     isAmbiguous: true,
     name: "B",
@@ -175,6 +200,7 @@ module.exports = {
   J: {
     value: "J",
     threeLettersName: "IL",
+    colorByFamily: "lightpurple",
     color: "lightpurple",
     isAmbiguous: true,
     name: "J",
@@ -183,6 +209,7 @@ module.exports = {
   X: {
     value: "X",
     threeLettersName: "ACDEFGHIKLMNPQRSTVWY",
+    colorByFamily: "#FFFFFF",
     color: "lightpurple",
     isAmbiguous: true,
     name: "X",
@@ -191,6 +218,7 @@ module.exports = {
   Z: {
     value: "Z",
     threeLettersName: "QE",
+    colorByFamily: "lightpurple",
     color: "lightpurple",
     isAmbiguous: true,
     name: "Z",

src/tidyUpAnnotation.js

@@ -10,6 +10,7 @@ module.exports = function tidyUpAnnotation(
     convertAnnotationsFromAAIndices,
     annotationType,
     provideNewIdsForAnnotations,
+    doNotProvideIdsForAnnotations,
     messages = [],
     mutative
   }
@@ -34,7 +35,7 @@ module.exports = function tidyUpAnnotation(
   if (provideNewIdsForAnnotations) {
     annotation.id = bsonObjectid().str;
   }
-  if (!annotation.id && annotation.id !== 0) {
+  if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
     annotation.id = bsonObjectid().str;
     messages.push(
       "Unable to detect valid ID for annotation, setting ID to " + annotation.id

src/tidyUpSequenceData.js

@@ -16,6 +16,7 @@ module.exports = function tidyUpSequenceData(pSeqData, options = {}) {
     additionalValidChars,
     noTranslationData,
     charOverrides,
+    doNotProvideIdsForAnnotations,
     proteinFilterOptions,
     convertAnnotationsFromAAIndices
   } = options;
@@ -143,7 +144,9 @@ module.exports = function tidyUpSequenceData(pSeqData, options = {}) {
           itemId = item.id;
         } else {
           itemId = bsonObjectid().str;
-          item.id = itemId; //assign the newly created id to the item d
+          if (!doNotProvideIdsForAnnotations) {
+            item.id = itemId; //assign the newly created id to the item
+          }
         }
         acc[itemId] = item;
         return acc;

src/tidyUpSequenceData.test.js

@@ -1,3 +1,5 @@
+const assert = require("assert");
+
 const tidyUpSequenceData = require("./tidyUpSequenceData");
 const chai = require("chai");
 const chaiSubset = require("chai-subset");
@@ -78,7 +80,8 @@ describe("tidyUpSequenceData", function() {
           aminoAcid: {
             value: ".",
             name: "Gap",
-            threeLettersName: "Gap",
+            threeLettersName: "Stop",
+            colorByFamily: "#FF0000",
             color: "#FF0000"
           },
           positionInCodon: 0,
@@ -94,7 +97,8 @@ describe("tidyUpSequenceData", function() {
           aminoAcid: {
             value: ".",
             name: "Gap",
-            threeLettersName: "Gap",
+            threeLettersName: "Stop",
+            colorByFamily: "#FF0000",
             color: "#FF0000"
           },
           positionInCodon: 1,
@@ -110,7 +114,8 @@ describe("tidyUpSequenceData", function() {
           aminoAcid: {
             value: ".",
             name: "Gap",
-            threeLettersName: "Gap",
+            threeLettersName: "Stop",
+            colorByFamily: "#FF0000",
             color: "#FF0000"
           },
           positionInCodon: 2,
@@ -250,6 +255,16 @@ describe("tidyUpSequenceData", function() {
     );
     res.features[0].id.should.not.equal(123);
   });
+  it("should not add ids even if the ids are missing if doNotProvideIdsForAnnotations=true", function() {
+    const res = tidyUpSequenceData(
+      {
+        features: [{ start: 4, end: 5 }, {}]
+      },
+      { doNotProvideIdsForAnnotations: true }
+    );
+
+    assert.strictEqual(res.features[0].id, undefined);
+  });
   it("should add the annotationTypePlural field", function() {
     const res = tidyUpSequenceData(
       {