@teselagen/ove 0.7.27 → 0.7.28

package/primerBases.js

@@ -0,0 +1,221 @@
+import React from "react";
+import { map } from "lodash-es";
+import { fudge2, realCharWidth } from "../constants";
+import getYOffset from "../../CircularView/getYOffset";
+import { getRangeLength } from "@teselagen/range-utils";
+import { getStructuredBases } from "./getStructuredBases";
+
+export function getBasesToShow({
+  hidePrimerBases,
+  annotation,
+  annotationRange,
+  charWidth,
+  bpsPerRow,
+  fullSequence,
+  iTree,
+  sequenceLength
+}) {
+  if (hidePrimerBases) return {};
+  const basesToShow = {};
+  if (annotation && annotation.bases) {
+    const fudge = charWidth - realCharWidth;
+    const { forward, primerBindsOn } = annotation;
+
+    const { basesNoInsertsWithMetaData, inserts, aRange } = getStructuredBases({
+      ...annotation,
+      fullSequence,
+      annotationRange,
+      sequenceLength
+    });
+
+    const annLen = getRangeLength(annotation, sequenceLength);
+    const aRangeLen = getRangeLength(annotationRange, sequenceLength);
+    const startOffset = annotationRange.start % bpsPerRow;
+    const endOffset = bpsPerRow - (annotationRange.end % bpsPerRow);
+    basesToShow.insertPaths = "";
+    basesToShow.insertTicks = "";
+    basesToShow.flipAnnotation = !forward;
+    basesToShow.extraHeight = 0;
+    const insertText = [];
+    const level1Height = -10;
+    const level2Height = 11;
+    inserts.forEach((i, n) => {
+      //loop thru all inserts
+      const indexToUse = forward ? i.index : annLen - i.index - 1;
+      if (
+        aRange.start - (primerBindsOn === "5prime" ? 1 : 0) <= indexToUse &&
+        aRange.end + (primerBindsOn === "5prime" ? 1 : 0) >= indexToUse
+      ) {
+        //only draw if insert falls within the annotation range
+        let xStart = i.index - aRange.start - Math.ceil(0.5 * i.bases.length); //calculate initial xStart
+        let xEnd = i.index - aRange.start + Math.floor(0.5 * i.bases.length);
+        if (aRange.end + 3 < xEnd) {
+          xStart -= xEnd - aRange.end - 3;
+          xEnd -= xEnd - aRange.end - 3;
+        }
+        if (i.index === 0) {
+          //for the first chunk, try to make it hang off the end if possible
+          xStart -= xEnd - 1;
+          xEnd -= xEnd - 1;
+        }
+        const forwAnd3Prime = forward;
+
+        if (xStart < -(forwAnd3Prime ? startOffset : endOffset)) {
+          //if the xStart is going to fall off the row to the left, correct it by moving the xStart to the right
+          const offsetLeft =
+            -(forwAnd3Prime ? startOffset : endOffset) - xStart;
+          xStart += offsetLeft;
+          xEnd += offsetLeft;
+        } else if (
+          xEnd + (forwAnd3Prime ? startOffset : endOffset) >
+          bpsPerRow
+        ) {
+          //if the xStart is going to fall off the row to the right, correct it by moving the xStart to the left
+          const offsetLeft =
+            bpsPerRow - xEnd - (forwAnd3Prime ? startOffset : endOffset);
+          xStart += offsetLeft;
+          xEnd += offsetLeft;
+        }
+        // use an interval tree to determine the level the primer insert should be on to not overlap with other inserts
+        const yOffset = getYOffset(iTree, xStart, xEnd);
+        iTree.insert(xStart, xEnd, {
+          //tnr: pass an initial level in the case that the underlying primer ranges themselves are overlapping
+          ...annotationRange,
+          yOffset
+        });
+
+        basesToShow.extraHeight = Math.max(
+          basesToShow.extraHeight,
+          15 + yOffset * 20
+        );
+        const insertStart =
+          (indexToUse - (forward ? aRange.start : aRange.end)) *
+          (!forward && primerBindsOn === "5prime" ? -1 : 1);
+        basesToShow.insertPaths += getInsertPath({
+          xStart,
+          xEnd,
+          charWidth,
+          level: yOffset,
+          insertStart
+        });
+
+        if (indexToUse !== aRange.end + 1 && indexToUse !== -1) {
+          basesToShow.insertTicks += getInsertTick({
+            charWidth,
+            height: level2Height,
+            insertStart
+          });
+        }
+        const textLength = Math.max(
+          0,
+          charWidth * i.bases.length - fudge - fudge2
+        );
+        insertText.push(
+          <text
+            style={{ pointerEvents: "none" }}
+            data-insert-bases={i.bases}
+            className="ve-monospace-font tg-primer-bases-insert"
+            textLength={textLength}
+            transform={
+              forward
+                ? ""
+                : `translate(${aRangeLen * charWidth},-5) scale(-1,-1) `
+            }
+            key={n}
+            x={
+              forward
+                ? (xStart - 1) * charWidth + fudge
+                : xStart * charWidth - fudge / 2
+            }
+            y={level1Height - yOffset * 20 - (forward ? 0 : 5)}
+          >
+            {i.bases.split("").map((b, i) => (
+              <tspan
+                key={i}
+                rotate={forward ? 0 : 180}
+                className="tg-no-match-seq"
+                textLength={textLength}
+              >
+                {b}
+              </tspan>
+            ))}
+          </text>
+        );
+      }
+    });
+
+    const textLength =
+      charWidth * basesNoInsertsWithMetaData.length - fudge - fudge2;
+    basesToShow.baseEl = (
+      <React.Fragment>
+        <text
+          {...{
+            textLength,
+            y: forward ? level2Height : -(basesToShow.extraHeight - 5),
+            x: forward ? fudge / 2 : fudge / 2 + 0.2 /* + diffLen * charWidth */
+          }}
+          style={{ pointerEvents: "none" }}
+          className="ve-monospace-font tg-primer-bases"
+        >
+          {map(
+            basesNoInsertsWithMetaData,
+            ({ b, isMatch, isAmbiguousMatch }, i) => {
+              return (
+                <tspan
+                  key={i}
+                  className={
+                    b === "&"
+                      ? "tg-no-show-seq"
+                      : isMatch
+                        ? ""
+                        : isAmbiguousMatch
+                          ? "tg-ambiguous-match-seq"
+                          : "tg-no-match-seq"
+                  }
+                  textLength={textLength}
+                >
+                  {b}
+                </tspan>
+              );
+            }
+          )}
+        </text>
+        {insertText}
+      </React.Fragment>
+    );
+  }
+  return basesToShow;
+}
+
+function getInsertTick({ insertStart, charWidth, height }) {
+  if (insertStart === 0) return "";
+  const insertLocation = insertStart * charWidth;
+
+  const jutUp = `
+  L ${insertLocation - 1},${height + 5}
+  L ${insertLocation - 1},${height - 4}
+  L ${insertLocation - 1},${height + 5}
+   `;
+  return jutUp;
+}
+
+function getInsertPath({ charWidth, xStart, xEnd, insertStart, level = 0 }) {
+  const insertLocation = insertStart * charWidth;
+  const insertHeight = 15;
+  const levelHeight = -5 - level * 20;
+  const leftX = (xStart - 1) * charWidth;
+  const rightX = (xEnd - 1) * charWidth;
+
+  const jutUp = `
+   L ${insertLocation - 6},${0}
+   L ${insertLocation - 6},${levelHeight}
+   L ${leftX},${levelHeight}
+   L ${leftX},${-insertHeight + levelHeight}
+
+   L ${rightX},${-insertHeight + levelHeight}
+   L ${rightX},${levelHeight}
+   L ${insertLocation + 4},${levelHeight}
+   L ${insertLocation + 4},${0}
+   `;
+  return jutUp;
+}

package/primerLengthsToHide.js

@@ -0,0 +1,27 @@
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const updatePrimerLengthsToHide = createAction(
+  "updatePrimerLengthsToHide"
+);
+export const togglePrimerLengthsToHide = createAction(
+  "togglePrimerLengthsToHide"
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createMergedDefaultStateReducer(
+  {
+    [updatePrimerLengthsToHide]: (state, payload) => {
+      return { ...state, ...payload };
+    },
+    [togglePrimerLengthsToHide]: state => {
+      return { ...state, enabled: !state["enabled"] };
+    }
+  },
+  { enabled: false, min: 0, max: 40 }
+);

package/primers.js

@@ -0,0 +1,19 @@
+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+import upsertDeleteActionGenerator from "./upsertDeleteActionGenerator";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const upsertPrimer = createAction("UPSERT_PRIMER");
+export const deletePrimer = createAction("DELETE_PRIMER");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    ...upsertDeleteActionGenerator(upsertPrimer, deletePrimer)
+  },
+  {}
+);

package/primersSelector.js

@@ -0,0 +1,8 @@
+import { createSelector } from "reselect";
+import sequenceDataSelector from "./sequenceDataSelector";
+
+function primersRawSelector(sequenceData) {
+  return sequenceData.primers;
+}
+
+export default createSelector(sequenceDataSelector, primersRawSelector);

package/printTool.js

@@ -0,0 +1,31 @@
+//TNRTODO this needs to be fixed and implemented
+import React from "react";
+import print from "./veToolbarIcons/print.png";
+
+export default () => {
+  return {
+    Icon: <img src={print} alt="Print Vector" />,
+    onIconClick: function () {
+      // var myPrintContent = document.getElementById('printdiv');
+      // var myPrintWindow = window.open(windowUrl, windowName, 'left=300,top=100,width=400,height=400');
+      // myPrintWindow.document.write(myPrintContent.innerHTML);
+      // myPrintWindow.document.getElementById('hidden_div').style.display='block'
+      // myPrintWindow.document.close();
+      // myPrintWindow.focus();
+      // myPrintWindow.print();
+      // myPrintWindow.close();
+      // return false;
+      // print();
+      // var content = document.getElementById("divcontents");
+      // document.appendChild(con)
+      // var pri = document.getElementById("ifmcontentstoprint").contentWindow;
+      // pri.document.open();
+      // pri.document.write(content.innerHTML);
+      // pri.document.close();
+      // pri.focus();
+      // pri.print();
+      // downloadSequenceData(sequenceData || )
+    },
+    tooltip: "Print Vector"
+  };
+};

package/propertiesTool.js

@@ -0,0 +1,40 @@
+import createAction from "./utils/createMetaAction";
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+// export const propertiesViewToggle = createAction(
+//   "TOGGLE_PROPERTIES_VIEW",
+//   () => {}
+// ); //NOTE!!:: second argument sanitizes actions so no payload is passed
+// export const propertiesViewOpen = createAction(
+//   "Open_PROPERTIES_VIEW",
+//   () => {}
+// ); //NOTE!!:: second argument sanitizes actions so no payload is passed
+export const propertiesViewTabUpdate = createAction("propertiesViewTabUpdate"); //NOTE!!:: second argument sanitizes actions so no payload is passed
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createMergedDefaultStateReducer(
+  {
+    [propertiesViewTabUpdate]: (
+      state,
+      tabId,
+      selectedAnnotationOrAnnotationId
+    ) => {
+      return {
+        ...state,
+        selectedAnnotationId: selectedAnnotationOrAnnotationId
+          ? selectedAnnotationOrAnnotationId.id ||
+            selectedAnnotationOrAnnotationId
+          : undefined,
+        tabId
+      };
+    }
+  },
+  {
+    tabId: "general"
+  }
+);

package/proteinUtils.js

@@ -0,0 +1,3 @@
+export function divideBy3(num, shouldDivideBy3) {
+  return shouldDivideBy3 ? Math.floor(num / 3) : num;
+}

package/pureNoFunc.js

@@ -0,0 +1,18 @@
+import { shouldUpdate } from "recompose";
+import { isEqualWith, isFunction } from "lodash-es";
+
+const isEq = (o1, o2) => {
+  const isEq = isEqualWith(o1, o2, function (val1, val2) {
+    if (isFunction(val1) && isFunction(val2)) {
+      return val1 === val2 || val1.toString() === val2.toString();
+    }
+  });
+  return isEq;
+};
+
+const pure = BaseComponent => {
+  const hoc = shouldUpdate((props, nextProps) => !isEq(props, nextProps));
+  return hoc(BaseComponent);
+};
+
+export default pure;

package/readOnly.js

@@ -0,0 +1,25 @@
+//./caretPosition.js
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+import { noop } from "lodash-es";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const toggleReadOnlyMode = createAction("TOGGLE_READ_ONLY_MODE", noop); //NOTE!!:: second argument sanitizes actions so no payload is passed
+export const updateReadOnlyMode = createAction("UPDATE_READ_ONLY_MODE");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [updateReadOnlyMode]: (state, payload) => {
+      return payload;
+    },
+    [toggleReadOnlyMode]: state => {
+      return !state;
+    }
+  },
+  true
+);

package/redoTool.js

@@ -0,0 +1,30 @@
+import React from "react";
+import { Icon } from "@blueprintjs/core";
+import ToolbarItem from "./ToolbarItem";
+import { connectToEditor } from "../withEditorProps";
+
+export default connectToEditor(editorState => {
+  return {
+    disabled: !(
+      editorState.sequenceDataHistory &&
+      editorState.sequenceDataHistory.future &&
+      editorState.sequenceDataHistory.future.length
+    )
+  };
+})(({ toolbarItemProps, redo, disabled }) => {
+  return (
+    <ToolbarItem
+      {...{
+        Icon: <Icon data-test="veRedoTool" icon="redo" />,
+        disabled,
+        onIconClick: redo,
+        tooltip: (
+          <span>
+            Redo <span style={{ fontSize: 10 }}>(Cmd/Ctrl+Shift+Z)</span>
+          </span>
+        ),
+        ...toolbarItemProps
+      }}
+    />
+  );
+});

package/reflex-styles.css

@@ -0,0 +1,128 @@
+.reflex-layout.reflex-container {
+  justify-content: flex-start;
+  /* align items in Main Axis */
+  align-items: stretch;
+  /* align items in Cross Axis */
+  align-content: stretch;
+  display: -webkit-box;
+  /* OLD - iOS 6-, Safari 3.1-6 */
+  display: -moz-box;
+  /* OLD - Firefox 19- (buggy but mostly works) */
+  display: -ms-flexbox;
+  /* TWEENER - IE 10 */
+  display: -webkit-flex;
+  /* NEW - Chrome */
+  display: flex;
+  position: relative;
+  height: 100%;
+  width: 100%;
+}
+
+.reflex-layout.reflex-container.horizontal {
+  flex-direction: column;
+}
+
+.reflex-layout.reflex-container.vertical {
+  flex-direction: row;
+}
+
+.reflex-layout > .reflex-element {
+  position: relative;
+  overflow: auto;
+  height: 100%;
+  width: 100%;
+}
+
+.reflex-layout > .reflex-splitter {
+  background-color: #f1f1f1;
+  z-index: 100;
+}
+
+.reflex-layout > .reflex-splitter.active,
+.reflex-layout > .reflex-splitter:hover {
+  background-color: #cccccc;
+  transition: all 1s ease;
+}
+
+.reflex-layout.horizontal > .reflex-splitter {
+  border-bottom: 1px solid #f1f1f1;
+  border-top: 1px solid #f1f1f1;
+  cursor: row-resize;
+  width: 100%;
+  height: 2px;
+}
+
+.reflex-layout.horizontal > .reflex-splitter:hover,
+.reflex-layout.horizontal > .reflex-splitter.active {
+  border-bottom: 1px solid #cccccc;
+  border-top: 1px solid #cccccc;
+}
+
+.reflex-layout.vertical > .reflex-splitter {
+  border-right: 1px solid #f1f1f1;
+  border-left: 1px solid #f1f1f1;
+  cursor: col-resize;
+  height: 95%;
+  width: 2px;
+  margin-top: 33px;
+}
+.bp3-dark .reflex-layout.vertical > .reflex-splitter {
+  border-right: 1px solid #4a4b4b;
+  border-left: 1px solid #4a4b4b;
+}
+
+.reflex-layout.vertical > .reflex-splitter:hover,
+.reflex-layout.vertical > .reflex-splitter.active {
+  border-right: 1px solid #cccccc;
+  border-left: 1px solid #cccccc;
+}
+
+.reflex-layout > .reflex-splitter.reflex-thin {
+  -moz-box-sizing: border-box;
+  -webkit-box-sizing: border-box;
+  box-sizing: border-box;
+  background: #000;
+  -moz-background-clip: padding;
+  -webkit-background-clip: padding;
+  background-clip: padding-box;
+  opacity: 0.2;
+  z-index: 100;
+}
+
+.reflex-layout
+  > .reflex-splitter.reflex-thin.active
+  .reflex-layout
+  > .reflex-splitter.reflex-thin:hover {
+  transition: all 1.5s ease;
+  opacity: 0.5;
+}
+
+.reflex-layout.horizontal > .reflex-splitter.reflex-thin {
+  border-bottom: 8px solid rgba(255, 255, 255, 0);
+  border-top: 8px solid rgba(255, 255, 255, 0);
+  height: 17px !important;
+  cursor: row-resize;
+  margin: -8px 0;
+  width: 100%;
+}
+
+.reflex-layout.horizontal > .reflex-splitter.reflex-thin.active,
+.reflex-layout.horizontal > .reflex-splitter.reflex-thin:hover {
+  border-bottom: 8px solid #e4e4e4;
+  border-top: 8px solid #e4e4e4;
+}
+
+.reflex-layout.vertical > .reflex-splitter.reflex-thin {
+  border-right: 8px solid rgba(255, 255, 255, 0);
+  border-left: 8px solid rgba(255, 255, 255, 0);
+  width: 17px !important;
+  cursor: col-resize;
+  margin: 0 -8px;
+  height: 100%;
+}
+
+.reflex-layout.vertical > .reflex-splitter.reflex-thin.active,
+.reflex-layout.vertical > .reflex-splitter.reflex-thin:hover {
+  border-right: 8px solid #e4e4e4;
+  border-left: 8px solid #e4e4e4;
+}

package/reflex-styles.css.map

@@ -0,0 +1,9 @@
+{
+    "version": 3,
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+}