motif search fixes (#177)

Author: mlacadie

src/components/motifsearch/motifsearchresultset.tsx

@@ -154,7 +154,7 @@ export const MotifSearchResultSet: React.FC<{
           <MotifResult
             key={i}
             alignment={alignment}
-            query={rpwm}
+            query={pwm}
           />
         ),
         info: (

src/components/motifsearch/motifutil.ts

@@ -43,20 +43,23 @@ const PCMAP: { [letter: string]: number[] } = {
 };
 
 export const regexToPWM = (regex: any) => {
+  //brackets being seen as 5%B and 5%D, have to decode first
+  const decodedpwm = decodeURIComponent(regex);
   const pwm = [];
-  const lregex = regex.toLowerCase();
+  const lregex = decodedpwm.toLowerCase();
   let inBracket = false,
     cbracket = [0.0, 0.0, 0.0, 0.0],
     ccount = 0.0;
   for (let i = 0; i < lregex.length; ++i) {
+    console.log(cbracket)
     if (inBracket) {
       if (lregex[i] === "]") {
         inBracket = false;
         for (let j = 0; j < cbracket.length; ++j) cbracket[j] /= ccount;
         pwm.push(cbracket);
         cbracket = [0.0, 0.0, 0.0, 0.0];
         ccount = 0.0;
-      } else if (ACMAP[lregex[i]] && cbracket[ACMAP[lregex[i]]] === 0.0) {
+      } else if ((ACMAP[lregex[i]] || lregex[i] === "a") && cbracket[ACMAP[lregex[i]]] === 0.0) {
         ccount += 1.0;
         cbracket[ACMAP[lregex[i]]] = 1.0;
       }

src/components/motifsearchbar.tsx

@@ -28,7 +28,16 @@ const MotifSearchbar: React.FC<MotifSearchBarProps> = ({dark}) => {
     const regex = /^[acgtwsmkrybdhvn\[\]]*$/i; // Match allowed letters and brackets
     const bracketBalanced = (input.match(/\[/g)?.length || 0) === (input.match(/\]/g)?.length || 0);
 
-    if (regex.test(input) && bracketBalanced) {
+    // Find all content inside brackets
+    const bracketMatches = input.match(/\[([^\[\]]+)\]/g);
+
+    const onlyACGTInside = bracketMatches
+    ? bracketMatches.every(group =>
+        /^[acgt]+$/i.test(group.slice(1, -1))
+      )
+    : true;
+
+    if (regex.test(input) && bracketBalanced && onlyACGTInside) {
       setValidSearch(true);
     } else {
       setValidSearch(false);