Merge pull request #33 from theosanderson/sweep/refactor/color-and-co…

…don-mapping

Refactor getColor and codon mapping into separate files

src/components/SingleRow.jsx

@@ -1,160 +1,9 @@
 import ColorHash from "color-hash";
-import { getReverseComplement, filterFeatures } from "../utils";
+import { getReverseComplement, filterFeatures, } from "../utils";
+import getColor from "../utils/getColor";
+import codonToAminoAcid from "../utils/codonMapping";
 var colorHash = new ColorHash({ lightness: [0.75, 0.9, 0.7, 0.8] });
 
-const getColor = (feature, product) => {
-  switch (feature.type) {
-    case "CDS":
-      switch (feature.name) {
-        case "S":
-          return "#ff7373";
-        case "nsp3":
-          return "#d3ffce";
-
-        case "leader":
-          return "#ff7f50";
-
-        case "nsp2":
-          return "#ddffdd";
-
-        case "nsp4":
-          return "#ff7373";
-
-        case "N":
-          return "#7fffd4";
-        case "E":
-          return "#ff7f50";
-        case "M":
-          return "#eeee88";
-        case "nsp12; RdRp":
-          return "#ff7f50";
-        case "nsp6":
-          return "#ee99ee";
-        case "nsp7":
-          return "#99ee99";
-
-        case "nsp8":
-          return "#ff7373";
-        case "nsp10":
-          return "#d3ffce";
-
-        case "nsp14":
-          return "#ff7f50";
-        case "nsp15":
-          return "#ddffdd";
-        case "nsp16":
-          return "#ffeeee";
-        case "nsp13":
-          return "#ff7f50";
-
-        default:
-          return colorHash.hex(feature.name + product + feature.type);
-      }
-    case "gene":
-      return "blue";
-    case "misc_feature":
-      return "green";
-    case "5'UTR":
-      return "orange";
-    case "3'UTR":
-      return "orange";
-    default:
-      return colorHash.hex(feature.name + product + feature.type);
-  }
-};
-
-const codonToAminoAcid = (codon) => {
-  switch (codon) {
-    case "TTT":
-    case "TTC":
-      return "F";
-    case "TTA":
-    case "TTG":
-    case "CTT":
-    case "CTC":
-    case "CTA":
-    case "CTG":
-      return "L";
-    case "ATT":
-    case "ATC":
-    case "ATA":
-      return "I";
-    case "ATG":
-      return "M";
-    case "GTT":
-    case "GTC":
-    case "GTA":
-    case "GTG":
-      return "V";
-    case "TCT":
-    case "TCC":
-    case "TCA":
-    case "TCG":
-    case "AGT":
-    case "AGC":
-      return "S";
-    case "CCT":
-    case "CCC":
-    case "CCA":
-    case "CCG":
-      return "P";
-    case "ACT":
-    case "ACC":
-    case "ACA":
-    case "ACG":
-      return "T";
-    case "GCT":
-    case "GCC":
-    case "GCA":
-    case "GCG":
-      return "A";
-    case "TAT":
-    case "TAC":
-      return "Y";
-    case "TAA":
-    case "TAG":
-    case "TGA":
-      return "*";
-    case "CAT":
-    case "CAC":
-      return "H";
-    case "CAA":
-    case "CAG":
-      return "Q";
-    case "AAT":
-    case "AAC":
-      return "N";
-    case "AAA":
-    case "AAG":
-      return "K";
-    case "GAT":
-    case "GAC":
-      return "D";
-    case "GAA":
-    case "GAG":
-      return "E";
-    case "TGT":
-    case "TGC":
-      return "C";
-    case "TGG":
-      return "W";
-    case "CGT":
-    case "CGC":
-    case "CGA":
-    case "CGG":
-    case "AGA":
-    case "AGG":
-      return "R";
-    case "GGT":
-    case "GGC":
-    case "GGA":
-    case "GGG":
-      return "G";
-    default:
-      return "X";
-  }
-};
-
 const SingleRow = ({
   parsedSequence,
   rowStart,

src/utils/codonMapping.js

@@ -0,0 +1,93 @@
+const codonToAminoAcid = (codon) => {
+  switch (codon) {
+    case "TTT":
+    case "TTC":
+      return "F";
+    case "TTA":
+    case "TTG":
+    case "CTT":
+    case "CTC":
+    case "CTA":
+    case "CTG":
+      return "L";
+    case "ATT":
+    case "ATC":
+    case "ATA":
+      return "I";
+    case "ATG":
+      return "M";
+    case "GTT":
+    case "GTC":
+    case "GTA":
+    case "GTG":
+      return "V";
+    case "TCT":
+    case "TCC":
+    case "TCA":
+    case "TCG":
+    case "AGT":
+    case "AGC":
+      return "S";
+    case "CCT":
+    case "CCC":
+    case "CCA":
+    case "CCG":
+      return "P";
+    case "ACT":
+    case "ACC":
+    case "ACA":
+    case "ACG":
+      return "T";
+    case "GCT":
+    case "GCC":
+    case "GCA":
+    case "GCG":
+      return "A";
+    case "TAT":
+    case "TAC":
+      return "Y";
+    case "TAA":
+    case "TAG":
+    case "TGA":
+      return "*";
+    case "CAT":
+    case "CAC":
+      return "H";
+    case "CAA":
+    case "CAG":
+      return "Q";
+    case "AAT":
+    case "AAC":
+      return "N";
+    case "AAA":
+    case "AAG":
+      return "K";
+    case "GAT":
+    case "GAC":
+      return "D";
+    case "GAA":
+    case "GAG":
+      return "E";
+    case "TGT":
+    case "TGC":
+      return "C";
+    case "TGG":
+      return "W";
+    case "CGT":
+    case "CGC":
+    case "CGA":
+    case "CGG":
+    case "AGA":
+    case "AGG":
+      return "R";
+    case "GGT":
+    case "GGC":
+    case "GGA":
+    case "GGG":
+      return "G";
+    default:
+      return "X";
+  }
+};
+
+export default codonToAminoAcid;

src/utils/getColor.js

@@ -0,0 +1,65 @@
+import ColorHash from "color-hash";
+var colorHash = new ColorHash({ lightness: [0.75, 0.9, 0.7, 0.8] });
+
+const getColor = (feature, product) => {
+  switch (feature.type) {
+    case "CDS":
+      switch (feature.name) {
+        case "S":
+          return "#ff7373";
+        case "nsp3":
+          return "#d3ffce";
+
+        case "leader":
+          return "#ff7f50";
+
+        case "nsp2":
+          return "#ddffdd";
+
+        case "nsp4":
+          return "#ff7373";
+
+        case "N":
+          return "#7fffd4";
+        case "E":
+          return "#ff7f50";
+        case "M":
+          return "#eeee88";
+        case "nsp12; RdRp":
+          return "#ff7f50";
+        case "nsp6":
+          return "#ee99ee";
+        case "nsp7":
+          return "#99ee99";
+
+        case "nsp8":
+          return "#ff7373";
+        case "nsp10":
+          return "#d3ffce";
+
+        case "nsp14":
+          return "#ff7f50";
+        case "nsp15":
+          return "#ddffdd";
+        case "nsp16":
+          return "#ffeeee";
+        case "nsp13":
+          return "#ff7f50";
+
+        default:
+          return colorHash.hex(feature.name + product + feature.type);
+      }
+    case "gene":
+      return "blue";
+    case "misc_feature":
+      return "green";
+    case "5'UTR":
+      return "orange";
+    case "3'UTR":
+      return "orange";
+    default:
+      return colorHash.hex(feature.name + product + feature.type);
+  }
+};
+
+export default getColor;