Added menu items for exporting both DNA and AA as FASTA TeselaGen#61

ryan-stackwave · Feb 28, 2024 · db5d481 · db5d481
1 parent 31250ca
commit db5d481
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Showing 5 changed files with 25 additions and 12 deletions.
diff --git a/packages/bio-parsers/src/jsonToFasta.js b/packages/bio-parsers/src/jsonToFasta.js
@@ -14,13 +14,13 @@ export default function jsonToFasta(jsonSequence, options) {
     proteinSequence
   } = cleanedData;
 
-  options = options || {};
-  let seqToUse = sequence;
-  let sizeToUse = size;
-  if (isProtein && proteinSequence && !options?.useDNA) {
-    seqToUse = proteinSequence;
-    sizeToUse = proteinSize;
-  }
+  options = {
+    sequence: isProtein && proteinSequence ? proteinSequence : size,
+    size: isProtein && proteinSequence ? proteinSize : sequence,
+    ...options
+  };
+  const seqToUse = options.sequence;
+  const sizeToUse = options.size;
   // options.reformatSeqName = options.reformatSeqName === false ? false : true;
   let fastaString = "";
   fastaString += `>${name || "Untitled Sequence"}|`;

diff --git a/packages/ove/src/MenuBar/defaultConfig.js b/packages/ove/src/MenuBar/defaultConfig.js
@@ -41,8 +41,8 @@ export default [
         showInSearchMenu: true,
         submenu: [
           { cmd: "exportSequenceAsGenbank" },
-          { cmd: "exportSequenceAsFasta" },
           { cmd: "exportDNASequenceAsFasta" },
+          { cmd: "exportProteinSequenceAsFasta" },
           { cmd: "exportSequenceAsTeselagenJson" }
         ]
       },

diff --git a/packages/ove/src/SimpleCircularOrLinearView.js b/packages/ove/src/SimpleCircularOrLinearView.js
@@ -291,8 +291,8 @@ const DownloadBtn = withHandlers({ exportSequenceToFile })(props => {
           showContextMenu(
             [
               "exportSequenceAsGenbank",
-              "exportSequenceAsFasta",
               "exportDNASequenceAsFasta",
+              "exportProteinSequenceAsFasta",
               "exportSequenceAsTeselagenJson"
             ],
             [

diff --git a/packages/ove/src/ToolBar/downloadTool.js b/packages/ove/src/ToolBar/downloadTool.js
@@ -28,8 +28,8 @@ const Dropdown = withEditorProps(props => {
       {createCommandMenu(
         [
           "exportSequenceAsGenbank",
-          "exportSequenceAsFasta",
           "exportDNASequenceAsFasta",
+          "exportProteinSequenceAsFasta",
           "exportSequenceAsTeselagenJson"
         ],
         getCommands({ props })

diff --git a/packages/ove/src/commands/index.js b/packages/ove/src/commands/index.js
@@ -270,8 +270,21 @@ const fileCommandDefs = {
   },
   exportDNASequenceAsFasta: {
     name: "Download DNA FASTA File",
-    isHidden: props => !isProtein(props) || !props.sequenceData.sequence,
-    handler: props => props.exportSequenceToFile("fasta", { useDNA: true })
+    isHidden: props => !props.sequenceData.sequence,
+    handler: props =>
+      props.exportSequenceToFile("fasta", {
+        sequence: props.sequenceData.sequence,
+        size: props.sequenceData.size
+      })
+  },
+  exportProteinSequenceAsFasta: {
+    name: "Download AA FASTA File",
+    isHidden: props => !props.sequenceData.proteinSequence,
+    handler: props =>
+      props.exportSequenceToFile("fasta", {
+        sequence: props.sequenceData.proteinSequence,
+        size: props.sequenceData.proteinSize
+      })
   },
   exportSequenceAsTeselagenJson: {
     name: "Download Teselagen JSON File",