@teselagen/ove 0.8.37 → 0.8.39

package/index.cjs.js

@@ -95195,7 +95195,44 @@ function getCurrentDateString() {
   return day2 + "-" + month + "-" + year;
 }
 __name(getCurrentDateString, "getCurrentDateString");
+const standardLineLength = 79;
 function featureNoteInDataToGenbankString(name2, value, options) {
+  const valueString = mangleOrStripUrls(value, options);
+  if (valueString.length > standardLineLength - 25 - name2.length) {
+    const lines = [];
+    let currentIndex = 0;
+    while (currentIndex < valueString.length) {
+      if (currentIndex === 0) {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - name2.length - 24
+        );
+        lines.push(
+          StringUtil.lpad("/", " ", 22) + name2 + '="' + chunk + (currentIndex + standardLineLength - 22 - name2.length >= valueString.length ? '"' : "")
+        );
+        currentIndex += standardLineLength - name2.length - 24;
+      } else {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - 21
+        );
+        if (currentIndex + standardLineLength - 21 >= valueString.length) {
+          const lineString = " ".repeat(21) + chunk;
+          if (lineString.length === standardLineLength) {
+            lines.push(lineString);
+            lines.push(" ".repeat(21) + '"');
+          } else {
+            lines.push(lineString + '"');
+          }
+        } else {
+          const lineString = " ".repeat(21) + chunk;
+          lines.push(lineString);
+        }
+        currentIndex += standardLineLength - 21;
+      }
+    }
+    return lines.join("\r\n");
+  }
   return StringUtil.lpad("/", " ", 22) + name2 + '="' + mangleOrStripUrls(value, options) + '"';
 }
 __name(featureNoteInDataToGenbankString, "featureNoteInDataToGenbankString");
@@ -98059,13 +98096,13 @@ function addCustomEnzyme(newEnz) {
   );
 }
 __name(addCustomEnzyme, "addCustomEnzyme");
-function pareDownAnnotations(annotations, max2) {
+function pareDownAnnotations(annotations, max2, sequenceLength) {
   let annotationsToPass = annotations;
   let paredDown = false;
   if (Object.keys(annotations).length > max2) {
     paredDown = true;
     const sortedAnnotations = sortBy$1(annotations, function(annotation) {
-      return -getRangeLength(annotation);
+      return -getRangeLength(annotation, sequenceLength);
     });
     annotationsToPass = sortedAnnotations.slice(0, max2).reduce(function(obj, item) {
       obj[item.id] = item;
@@ -117208,7 +117245,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.37";
+const version = "0.8.39";
 const packageJson = {
   version
 };
@@ -124606,7 +124643,8 @@ const __LinearView = class __LinearView extends React.Component {
         const maxToShow = (maxAnnotationsToDisplay ? maxAnnotationsToDisplay[type2] : limits[type2]) || 50;
         const [annotations, paredDown] = pareDownAnnotations(
           sequenceData2["filtered" + nameUpper] || sequenceData2[type2] || {},
-          maxToShow
+          maxToShow,
+          sequenceData2.sequence ? sequenceData2.sequence.length : sequenceData2.size || 0
         );
         if (paredDown) {
           this.paredDownMessages.push(
@@ -124896,7 +124934,7 @@ const __LinearView = class __LinearView extends React.Component {
             fullSequence: sequenceData2.sequence,
             emptyText: getEmptyText({ sequenceData: sequenceData2, caretPosition: caretPosition2 }),
             tickSpacing: tickSpacingToUse,
-            annotationVisibility: __spreadValues(__spreadValues(__spreadValues({}, rest.annotationVisibility), (!isLinViewZoomed || this.charWidth < 5) && {
+            annotationVisibility: __spreadValues(__spreadValues(__spreadValues({}, rest.annotationVisibility), (!isLinViewZoomed || this.charWidth < 5) && bpsPerRow >= 50 && {
               translations: false,
               primaryProteinSequence: false,
               reverseSequence: false,
@@ -126797,7 +126835,7 @@ function CircularView(props) {
   }
   const innerRadius = radius - 10;
   const initialRadius = radius;
-  const showSeq = isZoomedIn && rangeToShowLength < 140;
+  const showSeq = rangeToShowLength < 140 && (isZoomedIn || sequenceLength < 50);
   const showSeqText = rangeToShowLength < 80;
   const layersToDraw = [
     { zIndex: 10, layerName: "sequenceChars" },
@@ -127050,7 +127088,7 @@ function CircularView(props) {
         }
       );
       const maxToShow = !isZoomedIn && ((maxAnnotationsToDisplay ? maxAnnotationsToDisplay[layerName] : limits[layerName]) || 50);
-      const [trimmedAndParedAnns, paredDown] = maxToShow ? pareDownAnnotations(trimmedAnnotations, maxToShow) : [trimmedAnnotations];
+      const [trimmedAndParedAnns, paredDown] = maxToShow ? pareDownAnnotations(trimmedAnnotations, maxToShow, sequenceLength) : [trimmedAnnotations];
       if (paredDown) {
         paredDownMessages.push(
           getParedDownWarning({

package/index.es.js

@@ -95177,7 +95177,44 @@ function getCurrentDateString() {
   return day2 + "-" + month + "-" + year;
 }
 __name(getCurrentDateString, "getCurrentDateString");
+const standardLineLength = 79;
 function featureNoteInDataToGenbankString(name2, value, options) {
+  const valueString = mangleOrStripUrls(value, options);
+  if (valueString.length > standardLineLength - 25 - name2.length) {
+    const lines = [];
+    let currentIndex = 0;
+    while (currentIndex < valueString.length) {
+      if (currentIndex === 0) {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - name2.length - 24
+        );
+        lines.push(
+          StringUtil.lpad("/", " ", 22) + name2 + '="' + chunk + (currentIndex + standardLineLength - 22 - name2.length >= valueString.length ? '"' : "")
+        );
+        currentIndex += standardLineLength - name2.length - 24;
+      } else {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - 21
+        );
+        if (currentIndex + standardLineLength - 21 >= valueString.length) {
+          const lineString = " ".repeat(21) + chunk;
+          if (lineString.length === standardLineLength) {
+            lines.push(lineString);
+            lines.push(" ".repeat(21) + '"');
+          } else {
+            lines.push(lineString + '"');
+          }
+        } else {
+          const lineString = " ".repeat(21) + chunk;
+          lines.push(lineString);
+        }
+        currentIndex += standardLineLength - 21;
+      }
+    }
+    return lines.join("\r\n");
+  }
   return StringUtil.lpad("/", " ", 22) + name2 + '="' + mangleOrStripUrls(value, options) + '"';
 }
 __name(featureNoteInDataToGenbankString, "featureNoteInDataToGenbankString");
@@ -98041,13 +98078,13 @@ function addCustomEnzyme(newEnz) {
   );
 }
 __name(addCustomEnzyme, "addCustomEnzyme");
-function pareDownAnnotations(annotations, max2) {
+function pareDownAnnotations(annotations, max2, sequenceLength) {
   let annotationsToPass = annotations;
   let paredDown = false;
   if (Object.keys(annotations).length > max2) {
     paredDown = true;
     const sortedAnnotations = sortBy$1(annotations, function(annotation) {
-      return -getRangeLength(annotation);
+      return -getRangeLength(annotation, sequenceLength);
     });
     annotationsToPass = sortedAnnotations.slice(0, max2).reduce(function(obj, item) {
       obj[item.id] = item;
@@ -117190,7 +117227,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.37";
+const version = "0.8.39";
 const packageJson = {
   version
 };
@@ -124588,7 +124625,8 @@ const __LinearView = class __LinearView extends React__default.Component {
         const maxToShow = (maxAnnotationsToDisplay ? maxAnnotationsToDisplay[type2] : limits[type2]) || 50;
         const [annotations, paredDown] = pareDownAnnotations(
           sequenceData2["filtered" + nameUpper] || sequenceData2[type2] || {},
-          maxToShow
+          maxToShow,
+          sequenceData2.sequence ? sequenceData2.sequence.length : sequenceData2.size || 0
         );
         if (paredDown) {
           this.paredDownMessages.push(
@@ -124878,7 +124916,7 @@ const __LinearView = class __LinearView extends React__default.Component {
             fullSequence: sequenceData2.sequence,
             emptyText: getEmptyText({ sequenceData: sequenceData2, caretPosition: caretPosition2 }),
             tickSpacing: tickSpacingToUse,
-            annotationVisibility: __spreadValues(__spreadValues(__spreadValues({}, rest.annotationVisibility), (!isLinViewZoomed || this.charWidth < 5) && {
+            annotationVisibility: __spreadValues(__spreadValues(__spreadValues({}, rest.annotationVisibility), (!isLinViewZoomed || this.charWidth < 5) && bpsPerRow >= 50 && {
               translations: false,
               primaryProteinSequence: false,
               reverseSequence: false,
@@ -126779,7 +126817,7 @@ function CircularView(props) {
   }
   const innerRadius = radius - 10;
   const initialRadius = radius;
-  const showSeq = isZoomedIn && rangeToShowLength < 140;
+  const showSeq = rangeToShowLength < 140 && (isZoomedIn || sequenceLength < 50);
   const showSeqText = rangeToShowLength < 80;
   const layersToDraw = [
     { zIndex: 10, layerName: "sequenceChars" },
@@ -127032,7 +127070,7 @@ function CircularView(props) {
         }
       );
       const maxToShow = !isZoomedIn && ((maxAnnotationsToDisplay ? maxAnnotationsToDisplay[layerName] : limits[layerName]) || 50);
-      const [trimmedAndParedAnns, paredDown] = maxToShow ? pareDownAnnotations(trimmedAnnotations, maxToShow) : [trimmedAnnotations];
+      const [trimmedAndParedAnns, paredDown] = maxToShow ? pareDownAnnotations(trimmedAnnotations, maxToShow, sequenceLength) : [trimmedAnnotations];
       if (paredDown) {
         paredDownMessages.push(
           getParedDownWarning({

package/index.umd.js

@@ -124096,7 +124096,44 @@ ${seq.sequence}
     return day2 + "-" + month + "-" + year;
   }
   __name(getCurrentDateString, "getCurrentDateString");
+  const standardLineLength = 79;
   function featureNoteInDataToGenbankString(name2, value, options) {
+    const valueString = mangleOrStripUrls(value, options);
+    if (valueString.length > standardLineLength - 25 - name2.length) {
+      const lines = [];
+      let currentIndex = 0;
+      while (currentIndex < valueString.length) {
+        if (currentIndex === 0) {
+          const chunk = valueString.substring(
+            currentIndex,
+            currentIndex + standardLineLength - name2.length - 24
+          );
+          lines.push(
+            StringUtil.lpad("/", " ", 22) + name2 + '="' + chunk + (currentIndex + standardLineLength - 22 - name2.length >= valueString.length ? '"' : "")
+          );
+          currentIndex += standardLineLength - name2.length - 24;
+        } else {
+          const chunk = valueString.substring(
+            currentIndex,
+            currentIndex + standardLineLength - 21
+          );
+          if (currentIndex + standardLineLength - 21 >= valueString.length) {
+            const lineString = " ".repeat(21) + chunk;
+            if (lineString.length === standardLineLength) {
+              lines.push(lineString);
+              lines.push(" ".repeat(21) + '"');
+            } else {
+              lines.push(lineString + '"');
+            }
+          } else {
+            const lineString = " ".repeat(21) + chunk;
+            lines.push(lineString);
+          }
+          currentIndex += standardLineLength - 21;
+        }
+      }
+      return lines.join("\r\n");
+    }
     return StringUtil.lpad("/", " ", 22) + name2 + '="' + mangleOrStripUrls(value, options) + '"';
   }
   __name(featureNoteInDataToGenbankString, "featureNoteInDataToGenbankString");
@@ -126207,13 +126244,13 @@ ${seq.sequence}
     );
   }
   __name(addCustomEnzyme, "addCustomEnzyme");
-  function pareDownAnnotations(annotations, max2) {
+  function pareDownAnnotations(annotations, max2, sequenceLength) {
     let annotationsToPass = annotations;
     let paredDown = false;
     if (Object.keys(annotations).length > max2) {
       paredDown = true;
       const sortedAnnotations = sortBy$1(annotations, function(annotation) {
-        return -getRangeLength(annotation);
+        return -getRangeLength(annotation, sequenceLength);
       });
       annotationsToPass = sortedAnnotations.slice(0, max2).reduce(function(obj, item) {
         obj[item.id] = item;
@@ -145306,7 +145343,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     input.click();
   }
   __name(showFileDialog, "showFileDialog");
-  const version = "0.8.37";
+  const version = "0.8.39";
   const packageJson = {
     version
   };
@@ -151102,7 +151139,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           const maxToShow = (maxAnnotationsToDisplay ? maxAnnotationsToDisplay[type2] : limits[type2]) || 50;
           const [annotations, paredDown] = pareDownAnnotations(
             sequenceData2["filtered" + nameUpper] || sequenceData2[type2] || {},
-            maxToShow
+            maxToShow,
+            sequenceData2.sequence ? sequenceData2.sequence.length : sequenceData2.size || 0
           );
           if (paredDown) {
             this.paredDownMessages.push(
@@ -151392,7 +151430,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
               fullSequence: sequenceData2.sequence,
               emptyText: getEmptyText({ sequenceData: sequenceData2, caretPosition: caretPosition2 }),
               tickSpacing: tickSpacingToUse,
-              annotationVisibility: __spreadValues(__spreadValues(__spreadValues({}, rest.annotationVisibility), (!isLinViewZoomed || this.charWidth < 5) && {
+              annotationVisibility: __spreadValues(__spreadValues(__spreadValues({}, rest.annotationVisibility), (!isLinViewZoomed || this.charWidth < 5) && bpsPerRow >= 50 && {
                 translations: false,
                 primaryProteinSequence: false,
                 reverseSequence: false,
@@ -153293,7 +153331,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     }
     const innerRadius = radius - 10;
     const initialRadius = radius;
-    const showSeq = isZoomedIn && rangeToShowLength < 140;
+    const showSeq = rangeToShowLength < 140 && (isZoomedIn || sequenceLength < 50);
     const showSeqText = rangeToShowLength < 80;
     const layersToDraw = [
       { zIndex: 10, layerName: "sequenceChars" },
@@ -153546,7 +153584,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           }
         );
         const maxToShow = !isZoomedIn && ((maxAnnotationsToDisplay ? maxAnnotationsToDisplay[layerName] : limits[layerName]) || 50);
-        const [trimmedAndParedAnns, paredDown] = maxToShow ? pareDownAnnotations(trimmedAnnotations, maxToShow) : [trimmedAnnotations];
+        const [trimmedAndParedAnns, paredDown] = maxToShow ? pareDownAnnotations(trimmedAnnotations, maxToShow, sequenceLength) : [trimmedAnnotations];
         if (paredDown) {
           paredDownMessages.push(
             getParedDownWarning({

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.8.37",
+  "version": "0.8.39",
   "main": "./src/index.js",
   "type": "module",
   "repository": "https://github.com/TeselaGen/tg-oss",
@@ -15,7 +15,7 @@
     "@blueprintjs/core": "3.54.0",
     "@hello-pangea/dnd": "16.2.0",
     "@risingstack/react-easy-state": "^6.3.0",
-    "@teselagen/bio-parsers": "0.4.35",
+    "@teselagen/bio-parsers": "0.4.36",
     "@teselagen/file-utils": "0.3.23",
     "@teselagen/range-utils": "0.3.20",
     "@teselagen/react-list": "0.8.18",

package/src/CircularView/index.js

@@ -241,7 +241,8 @@ export function CircularView(props) {
   }
   const innerRadius = radius - 10;
   const initialRadius = radius;
-  const showSeq = isZoomedIn && rangeToShowLength < 140;
+  const showSeq =
+    rangeToShowLength < 140 && (isZoomedIn || sequenceLength < 50);
   const showSeqText = rangeToShowLength < 80;
 
   //RENDERING CONCEPTS:
@@ -521,7 +522,7 @@ export function CircularView(props) {
             : limits[layerName]) ||
             50);
         const [trimmedAndParedAnns, paredDown] = maxToShow
-          ? pareDownAnnotations(trimmedAnnotations, maxToShow)
+          ? pareDownAnnotations(trimmedAnnotations, maxToShow, sequenceLength)
           : [trimmedAnnotations];
 
         if (paredDown) {

package/src/LinearView/index.js

@@ -118,7 +118,10 @@ class _LinearView extends React.Component {
           : limits[type]) || 50;
       const [annotations, paredDown] = pareDownAnnotations(
         sequenceData["filtered" + nameUpper] || sequenceData[type] || {},
-        maxToShow
+        maxToShow,
+        sequenceData.sequence
+          ? sequenceData.sequence.length
+          : sequenceData.size || 0
       );
 
       if (paredDown) {
@@ -363,13 +366,14 @@ class _LinearView extends React.Component {
                 tickSpacing: tickSpacingToUse,
                 annotationVisibility: {
                   ...rest.annotationVisibility,
-                  ...((!isLinViewZoomed || this.charWidth < 5) && {
-                    translations: false,
-                    primaryProteinSequence: false,
-                    reverseSequence: false,
-                    sequence: false,
-                    cutsitesInSequence: false
-                  }),
+                  ...((!isLinViewZoomed || this.charWidth < 5) &&
+                    bpsPerRow >= 50 && {
+                      translations: false,
+                      primaryProteinSequence: false,
+                      reverseSequence: false,
+                      sequence: false,
+                      cutsitesInSequence: false
+                    }),
                   ...annotationVisibilityOverrides
                 },
                 ...RowItemProps

package/src/utils/editorUtils.js

@@ -111,13 +111,13 @@ export function addCustomEnzyme(newEnz) {
   );
 }
 
-export function pareDownAnnotations(annotations, max) {
+export function pareDownAnnotations(annotations, max, sequenceLength) {
   let annotationsToPass = annotations;
   let paredDown = false;
   if (Object.keys(annotations).length > max) {
     paredDown = true;
     const sortedAnnotations = sortBy(annotations, function (annotation) {
-      return -getRangeLength(annotation);
+      return -getRangeLength(annotation, sequenceLength);
     });
     annotationsToPass = sortedAnnotations.slice(0, max).reduce(function (
       obj,

package/utils/editorUtils.d.ts

@@ -21,7 +21,7 @@ export function getEmptyText({ sequenceData, caretPosition }: {
 export function tryToRefocusEditor(): void;
 export function getCustomEnzymes(): any;
 export function addCustomEnzyme(newEnz: any): void;
-export function pareDownAnnotations(annotations: any, max: any): any[];
+export function pareDownAnnotations(annotations: any, max: any, sequenceLength: any): any[];
 export function getParedDownWarning({ nameUpper, maxToShow, isAdjustable }: {
     nameUpper: any;
     maxToShow: any;