@teselagen/ove 0.0.19 → 0.0.21

package/index.umd.js

@@ -160605,7 +160605,17 @@
           data.size = isProtein ? size * 3 : size;
           data.sequence = await read(size, "utf8");
         } else if (ord(next_byte) === 10) {
-          const strand_dict = { 0: ".", 1: "+", 2: "-", 3: "=" };
+          const strand_dict = {
+            // [strand, arrowheadType]
+            0: [1, "NONE"],
+            // non-directional feature (in that case, the attribute is generally absent altogether)
+            1: [1, "TOP"],
+            // forward strand
+            2: [-1, "BOTTOM"],
+            // reverse strand
+            3: [1, "BOTH"]
+            // bi-directional feature
+          };
           const xml = await read(block_size, "utf8");
           const b = new fxp.XMLParser({
             ignoreAttributes: false,
@@ -160636,7 +160646,8 @@
               name,
               type,
               ...locations?.length > 1 && { locations },
-              strand: strand_dict[directionality],
+              strand: directionality ? strand_dict[directionality][0] : 1,
+              arrowheadType: directionality ? strand_dict[directionality][1] : "NONE",
               start: maxStart,
               end: maxEnd
               // color,
@@ -171108,7 +171119,7 @@
     const isAlreadyProteinEditor = currentEditor.sequenceData && currentEditor.sequenceData.isProtein;
     const isAlreadyRnaEditor = currentEditor.sequenceData && currentEditor.sequenceData.isRna;
     const isAlreadyOligoEditor = currentEditor.sequenceData && currentEditor.sequenceData.isOligo;
-    const reverseSequenceShouldBeUpdate = currentEditor.sequenceData?.isSingleStrandedDNA !== sequenceData?.isSingleStrandedDNA;
+    const reverseSequenceShouldBeUpdate = currentEditor.sequenceData?.isSingleStrandedDNA !== sequenceData?.isSingleStrandedDNA || currentEditor.sequenceData?.isDoubleStrandedRNA !== sequenceData?.isDoubleStrandedRNA;
     const isAlreadySpecialEditor = isAlreadyProteinEditor || isAlreadyRnaEditor || isAlreadyOligoEditor || reverseSequenceShouldBeUpdate;
     let toSpread = {};
     let payload;
@@ -171135,14 +171146,14 @@
             },
             annotationVisibility: {
               caret: true,
-              ...annotationVisibility,
-              //we spread this here to allow the user to override this .. if they must!
               sequence: false,
               reverseSequence: false,
               cutsites: false,
               translations: false,
               aminoAcidNumbers: false,
-              primaryProteinSequence: true
+              primaryProteinSequence: true,
+              ...annotationVisibility
+              //we spread this here to allow the user to override this .. if they must!
             },
             annotationsToSupport: {
               features: true,
@@ -171164,14 +171175,14 @@
             },
             annotationVisibility: {
               caret: true,
-              ...annotationVisibility,
-              //we spread this here to allow the user to override this .. if they must!
               sequence: true,
               cutsites: false,
               reverseSequence: false,
               translations: false,
               aminoAcidNumbers: false,
-              primaryProteinSequence: false
+              primaryProteinSequence: false,
+              ...annotationVisibility
+              //we spread this here to allow the user to override this .. if they must!
             },
             annotationsToSupport: {
               features: true,
@@ -171194,14 +171205,14 @@
             },
             annotationVisibility: {
               caret: true,
-              ...annotationVisibility,
-              //we spread this here to allow the user to override this .. if they must!
               sequence: true,
               cutsites: false,
-              reverseSequence: false,
+              reverseSequence: sequenceData?.isDoubleStrandedRNA,
               translations: false,
               aminoAcidNumbers: false,
-              primaryProteinSequence: false
+              primaryProteinSequence: false,
+              ...annotationVisibility
+              //we spread this here to allow the user to override this .. if they must!
             },
             annotationsToSupport: {
               features: true,
@@ -171225,13 +171236,13 @@
             },
             annotationVisibility: {
               caret: true,
-              ...annotationVisibility,
-              //we spread this here to allow the user to override this .. if they must!
               sequence: true,
               reverseSequence: !sequenceData?.isSingleStrandedDNA,
               translations: false,
               aminoAcidNumbers: false,
-              primaryProteinSequence: false
+              primaryProteinSequence: false,
+              ...annotationVisibility
+              //we spread this here to allow the user to override this .. if they must!
             },
             annotationsToSupport: {
               features: true,
@@ -188154,6 +188165,7 @@ double click --> edit`}`;
       rowTopComp,
       rowBottomComp,
       isProtein,
+      isRna,
       tickSpacing,
       truncateLabelsThatDoNotFit = true,
       aminoAcidNumbersHeight = rowHeights.aminoAcidNumbers.height,
@@ -188218,7 +188230,8 @@ double click --> edit`}`;
     } = annotationVisibility;
     const { sequence = "", cutsites = [] } = row;
     const reverseSequence = getComplementSequenceString(
-      alignmentData && alignmentData.sequence || sequence
+      alignmentData && alignmentData.sequence || sequence,
+      isRna
     );
     const getGaps = reactExports.useMemo(() => {
       if (alignmentData) {
@@ -189924,7 +189937,7 @@ double click --> edit`}`;
   }
 
   const name = "@teselagen/ove";
-  const version = "0.0.18";
+  const version = "0.0.20";
   const main = "./src/index.js";
   const packageJson = {
   	name: name,
@@ -200355,6 +200368,7 @@ double click --> edit`}`;
               },
               isRowView: true,
               isProtein: sequenceData.isProtein,
+              isRna: sequenceData.isRna,
               chromatogramData: sequenceData.chromatogramData,
               sequenceLength: sequenceData.sequence.length,
               bpsPerRow,

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.0.19",
+  "version": "0.0.21",
   "main": "./src/index.js",
   "dependencies": {
-    "@teselagen/sequence-utils": "0.1.20",
-    "@teselagen/range-utils": "0.1.19",
-    "@teselagen/ui": "0.0.24",
-    "@teselagen/file-utils": "0.2.26",
-    "@teselagen/bounce-loader": "0.0.13",
-    "@teselagen/bio-parsers": "0.1.25",
+    "@teselagen/sequence-utils": "0.1.23",
+    "@teselagen/range-utils": "0.1.22",
+    "@teselagen/ui": "0.0.27",
+    "@teselagen/file-utils": "0.2.29",
+    "@teselagen/bounce-loader": "0.0.16",
+    "@teselagen/bio-parsers": "0.1.28",
     "@blueprintjs/core": "3.52.0",
     "@blueprintjs/datetime": "3.23.19",
     "@blueprintjs/icons": "3.33.0",

package/src/RowItem/index.js

@@ -74,6 +74,7 @@ export default function RowItem(props) {
     rowTopComp,
     rowBottomComp,
     isProtein,
+    isRna,
     tickSpacing,
     truncateLabelsThatDoNotFit = true,
     aminoAcidNumbersHeight = rowHeights.aminoAcidNumbers.height,
@@ -141,7 +142,8 @@ export default function RowItem(props) {
   const { sequence = "", cutsites = [] } = row;
 
   const reverseSequence = getComplementSequenceString(
-    (alignmentData && alignmentData.sequence) || sequence
+    (alignmentData && alignmentData.sequence) || sequence,
+    isRna
   );
   const getGaps = useMemo(() => {
     if (alignmentData) {

package/src/RowView/index.js

@@ -367,6 +367,7 @@ class _RowView extends React.Component {
               },
               isRowView: true,
               isProtein: sequenceData.isProtein,
+              isRna: sequenceData.isRna,
               chromatogramData: sequenceData.chromatogramData,
               sequenceLength: sequenceData.sequence.length,
               bpsPerRow,

package/src/updateEditor.js

@@ -25,7 +25,9 @@ export default function updateEditor(
     currentEditor.sequenceData && currentEditor.sequenceData.isOligo;
   const reverseSequenceShouldBeUpdate =
     currentEditor.sequenceData?.isSingleStrandedDNA !==
-    sequenceData?.isSingleStrandedDNA;
+      sequenceData?.isSingleStrandedDNA ||
+    currentEditor.sequenceData?.isDoubleStrandedRNA !==
+      sequenceData?.isDoubleStrandedRNA;
 
   const isAlreadySpecialEditor =
     isAlreadyProteinEditor ||
@@ -60,13 +62,13 @@ export default function updateEditor(
 
           annotationVisibility: {
             caret: true,
-            ...annotationVisibility, //we spread this here to allow the user to override this .. if they must!
             sequence: false,
             reverseSequence: false,
             cutsites: false,
             translations: false,
             aminoAcidNumbers: false,
-            primaryProteinSequence: true
+            primaryProteinSequence: true,
+            ...annotationVisibility //we spread this here to allow the user to override this .. if they must!
           },
           annotationsToSupport: {
             features: true,
@@ -87,13 +89,13 @@ export default function updateEditor(
           },
           annotationVisibility: {
             caret: true,
-            ...annotationVisibility, //we spread this here to allow the user to override this .. if they must!
             sequence: true,
             cutsites: false,
             reverseSequence: false,
             translations: false,
             aminoAcidNumbers: false,
-            primaryProteinSequence: false
+            primaryProteinSequence: false,
+            ...annotationVisibility //we spread this here to allow the user to override this .. if they must!
           },
           annotationsToSupport: {
             features: true,
@@ -114,13 +116,13 @@ export default function updateEditor(
           },
           annotationVisibility: {
             caret: true,
-            ...annotationVisibility, //we spread this here to allow the user to override this .. if they must!
             sequence: true,
             cutsites: false,
-            reverseSequence: false,
+            reverseSequence: sequenceData?.isDoubleStrandedRNA,
             translations: false,
             aminoAcidNumbers: false,
-            primaryProteinSequence: false
+            primaryProteinSequence: false,
+            ...annotationVisibility //we spread this here to allow the user to override this .. if they must!
           },
           annotationsToSupport: {
             features: true,
@@ -143,12 +145,12 @@ export default function updateEditor(
           },
           annotationVisibility: {
             caret: true,
-            ...annotationVisibility, //we spread this here to allow the user to override this .. if they must!
             sequence: true,
             reverseSequence: !sequenceData?.isSingleStrandedDNA,
             translations: false,
             aminoAcidNumbers: false,
-            primaryProteinSequence: false
+            primaryProteinSequence: false,
+            ...annotationVisibility //we spread this here to allow the user to override this .. if they must!
           },
           annotationsToSupport: {
             features: true,