@teselagen/ove 0.7.28 → 0.7.30-beta.1

package/reflex-styles.css

@@ -1,128 +0,0 @@
-.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

@@ -1,9 +0,0 @@
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-    "sources": [
-        "reflex-styles.scss"
-    ],
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-    "file": "reflex-styles.css"
-}

package/relaxLabelAngles.js

@@ -1,157 +0,0 @@
-import { cloneDeep } from "lodash-es";
-
-export default relaxLabelAngles;
-
-function normalizeAngle(angle) {
-  if (angle > Math.PI * 2) {
-    return angle - Math.PI * 2;
-  } else if (angle < 0) {
-    return angle + Math.PI * 2;
-  } else {
-    return angle;
-  }
-}
-
-//this pure function allows the labels to spread out around the circle
-//and groups overlapping labels together if necessary
-function relaxLabelAngles(_labelPoints, spacing, maxradius) {
-  const maxLabelsPerQuadrant = Math.floor(maxradius / spacing) + 4;
-  let labels = cloneDeep(_labelPoints);
-  if (labels.length > maxLabelsPerQuadrant * 4) {
-    //group overlapping labels together
-    labels = combineLabels(labels, maxLabelsPerQuadrant * 4);
-  }
-  // labels = labels.sort(sortLabelsByAngle)
-
-  // Sort labels into four quadrants of the screen.
-  const totalLength = Math.PI * 2;
-
-  let rightTopLabels = [];
-  let rightBottomLabels = [];
-  let leftTopLabels = [];
-  let leftBottomLabels = [];
-
-  let label;
-  for (let i = 0; i < labels.length; i++) {
-    label = labels[i];
-    label.angle = normalizeAngle(label.angle);
-    const labelCenter = label.angle;
-    if (labelCenter <= totalLength / 4) {
-      rightTopLabels.push(label);
-    } else if (
-      labelCenter > totalLength / 4 &&
-      labelCenter <= totalLength / 2
-    ) {
-      rightBottomLabels.push(label);
-    } else if (
-      labelCenter > totalLength / 2 &&
-      labelCenter <= (3 * totalLength) / 4
-    ) {
-      leftBottomLabels.push(label);
-    } else {
-      leftTopLabels.push(label);
-    }
-  }
-
-  function repositionAndGroupLabels(labels /* logtrue */) {
-    const extraSpaces = Math.max(maxLabelsPerQuadrant - labels.length, 0);
-    let lastLabelYPosition = 0 - spacing / 2; // spacing to count label height
-    let lastlabel;
-    return labels
-      .map(function (label, idx) {
-        if (Math.abs(lastLabelYPosition) > maxradius + 80) {
-          lastlabel.labelAndSublabels.push(label);
-          lastlabel.labelIds[label.id] = true;
-          return false;
-        }
-        lastlabel = label;
-        if (label.y < lastLabelYPosition) {
-          const naturalSlot = Math.floor(Math.abs(label.y / spacing));
-          if (naturalSlot > extraSpaces) {
-            if (idx < naturalSlot && extraSpaces > 0) {
-              lastLabelYPosition = label.y;
-            }
-            label.y = lastLabelYPosition;
-          }
-          let x = Math.sqrt(Math.pow(maxradius, 2) - Math.pow(label.y, 2));
-          if (!x) x = 0;
-          label.x = label.x > 0 ? x : -x;
-          lastLabelYPosition = label.y - spacing;
-        } else {
-          label.y = lastLabelYPosition;
-          lastLabelYPosition = label.y - spacing;
-        }
-        return label;
-      })
-      .filter(function (l) {
-        return !!l;
-      });
-  }
-
-  // Scale Right Top Labels
-  let labelsToReturn = [];
-  rightTopLabels = rightTopLabels.sort(sortLabelsByAngleReverse);
-  labelsToReturn = labelsToReturn.concat(
-    repositionAndGroupLabels(rightTopLabels, true)
-  );
-
-  // Scale Right Bottom Labels
-  rightBottomLabels = rightBottomLabels.sort(sortLabelsByAngle);
-  labelsToReturn = labelsToReturn.concat(
-    flipLabelYs(repositionAndGroupLabels(flipLabelYs(rightBottomLabels)))
-  );
-
-  // Scale Left Bottom Labels
-  leftBottomLabels = leftBottomLabels.sort(sortLabelsByAngleReverse);
-  labelsToReturn = labelsToReturn.concat(
-    flipLabelYs(repositionAndGroupLabels(flipLabelYs(leftBottomLabels)))
-  );
-
-  // Scale Left Top Labels
-  leftTopLabels = leftTopLabels.sort(sortLabelsByAngle);
-  labelsToReturn = labelsToReturn.concat(
-    repositionAndGroupLabels(leftTopLabels)
-  );
-
-  return labelsToReturn;
-
-  function flipLabelYs(labels) {
-    return labels.map(function (label) {
-      label.y = -label.y;
-      return label;
-    });
-  }
-}
-
-// function sortLabelsByHeight(a, b) {
-//   return b.innerPoint.y - a.innerPoint.y
-// }
-
-function sortLabelsByAngle(a, b) {
-  return a.angle - b.angle;
-}
-function sortLabelsByAngleReverse(b, a) {
-  return a.angle - b.angle;
-}
-
-//function that groups labels that fall within the same angle together
-function combineLabels(labels, numberOfBuckets) {
-  const buckets = {};
-  Object.keys(labels).forEach(function (key) {
-    const label = labels[key];
-
-    const bucket = Math.floor(
-      (label.annotationCenterAngle / 6.29) * numberOfBuckets
-    );
-    if (!buckets[bucket]) {
-      buckets[bucket] = label;
-    } else {
-      buckets[bucket].labelAndSublabels.push(label);
-      buckets[bucket].labelIds[label.id] = true;
-    }
-  });
-  const combinedLabels = Object.keys(buckets).map(function (key) {
-    return buckets[key];
-  });
-  return combinedLabels;
-}

package/relaxLabels_DEPRECATED.js

@@ -1,105 +0,0 @@
-/* eslint-disable */
-// import intervalTree2 from "node-interval-tree";
-// var xRanges = new intervalTree2(0)
-// var yRanges = new intervalTree2(0)
-// iTree.search(start, end)
-// featureITree.add(startAngle, expandedEndAngle, undefined, {...annotationCopy})
-
-let alpha = 1.5; //the larger the alpha, the fewer loops through relax necessary, but too large and things are spaced unevenly
-let spacing = 12;
-let relaxCounter = 0;
-export default function relaxLabels(labelPoints) {
-  let mutableLabelPoints = labelPoints.map(function (point) {
-    return {
-      ...point
-    };
-  });
-  function spreadPointsOutOnCircle(labels) {}
-  function relax() {
-    let again = false;
-    relaxCounter++;
-    mutableLabelPoints.forEach(function (point1, index1) {
-      // var xOverlaps = xRanges.search(point1.x, point1.x + point1.width)
-      // var yOverlaps = yRanges.search(point1.y, point1.y + point1.height)
-      // xOverlaps
-      // xRanges.add(point1.x, point1.x + point1.width, undefined, point1)
-      // yRanges.add(point1.y, point1.y + point1.height, undefined, point1)
-
-      mutableLabelPoints.forEach(function (point2, index2) {
-        // a & b are the same element and don't collide.
-        if (index1 === index2) return;
-
-        // a & b are on opposite sides of the chart and
-        // don't collide
-        if (
-          (point1.x > 0 && point2.x <= 0) ||
-          (point1.x < 0 && point2.x >= 0)
-        ) {
-          return;
-        }
-        // Now let's calculate the distance between
-        // these elements.
-        let deltaY = point1.y - point2.y;
-
-        // Our spacing is greater than our specified spacing,
-        // so they don't collide.
-        if (Math.abs(deltaY) > spacing) return;
-
-        // If the labels collide, we'll push each
-        // of the two labels up and down a little bit.
-        let weight1 = point1.y > 0 ? 0.5 : -0.5;
-        let weight2 = point2.y > 0 ? 0.5 : -0.5;
-        again = true;
-        let sign = deltaY > 0 ? 1 : -1;
-        let adjust = sign * alpha;
-        point1.y += adjust + weight1;
-        point2.y -= adjust + weight2;
-
-        // point1.x += -weight1
-        // point2.x -= -weight2
-      });
-    });
-    // Adjust our line leaders here
-    // so that they follow the labels.
-    if (again && relaxCounter < 1) {
-      relax();
-    }
-  }
-  relax();
-
-  //group colliding labels
-  let stableLabels = [];
-  mutableLabelPoints.forEach(function (point1) {
-    let collision = false;
-    stableLabels.some(function (point2) {
-      // a & b are on opposite sides of the chart and
-      // don't collide
-      if ((point1.x > 0 && point2.x <= 0) || (point1.x < 0 && point2.x >= 0)) {
-        return;
-      }
-      // Now let's calculate the distance between
-      // these elements.
-      let deltaY = point1.y - point2.y;
-
-      // Our spacing is greater than our specified spacing,
-      // so they don't collide.
-      if (Math.abs(deltaY) > spacing) return;
-      // If the labels collide, we'll push each
-      collision = true;
-      point2.labels.push(point1);
-      return true; //stop the loop early
-    });
-    if (!collision) {
-      stableLabels.push({
-        ...point1,
-        labels: [point1]
-      });
-    }
-  });
-  stableLabels = stableLabels.sort(sortLabels);
-  return stableLabels;
-}
-
-function sortLabels(a, b) {
-  return b.y - a.y;
-}

package/replacementLayers.js

@@ -1,36 +0,0 @@
-//./selectionLayer.js
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-import omit from "lodash/omit";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const replacementLayerClear = createAction("replacementLayerClear");
-export const replacementLayerUpdate = createAction("REPLACEMENT_LAYER_UPDATE");
-export const replacementLayerDelete = createAction("REPLACEMENT_LAYER_DELETE");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [replacementLayerClear]: () => {
-      return {};
-    },
-    [replacementLayerUpdate]: (state, payload) => {
-      return {
-        ...state,
-        [payload.id]: {
-          color: "darkolivegreen",
-          id: payload.id,
-          ...payload.range
-        }
-      };
-    },
-    [replacementLayerDelete]: (state, payload) => {
-      return omit(state, payload.id);
-    }
-  },
-  {}
-);

package/restrictionEnzymes.js

@@ -1,52 +0,0 @@
-import { combineReducers } from "redux";
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-import specialCutsiteFilterOptions from "../constants/specialCutsiteFilterOptions";
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const filteredRestrictionEnzymesUpdate = createAction(
-  "FILTERED_RESTRICTION_ENZYMES_UPDATE"
-);
-export const isEnzymeFilterAndUpdate = createAction("IS_ENZYME_FILTER_AND");
-export const filteredRestrictionEnzymesReset = createAction(
-  "FILTERED_RESTRICTION_ENZYMES_RESET"
-);
-export const filteredRestrictionEnzymesAdd = createAction(
-  "FILTERED_RESTRICTION_ENZYMES_ADD"
-);
-// ------------------------------------
-// Reducer
-// ------------------------------------
-const defaultInitialState = [specialCutsiteFilterOptions.single];
-// let initialState = defaultInitialState;
-// const localDefault = window.localStorage.getItem("tgInitialCutsiteFilter");
-
-// if (localDefault) {
-//   try {
-//     initialState = JSON.parse(localDefault);
-//     if (!Array.isArray(initialState)) throw new Error("Must be an array");
-//   } catch (e) {
-//     initialState = defaultInitialState;
-//   }
-// }
-
-export default combineReducers({
-  //filteredRestrictionEnzymes refer to the enzymes actively included in the react-select filter component
-  isEnzymeFilterAnd: createReducer(
-    {
-      [isEnzymeFilterAndUpdate]: (state, payload) => payload
-    },
-    false
-  ),
-  filteredRestrictionEnzymes: createReducer(
-    {
-      [filteredRestrictionEnzymesReset]: () => defaultInitialState,
-      [filteredRestrictionEnzymesUpdate]: (state, payload) => payload,
-      [filteredRestrictionEnzymesAdd]: function (state, payload) {
-        return [...state, payload];
-      }
-    },
-    defaultInitialState
-  )
-});

package/restrictionEnzymesSelector.js

@@ -1,34 +0,0 @@
-import { forEach } from "lodash-es";
-import { createSelector } from "reselect";
-import {
-  defaultEnzymesByName,
-  aliasedEnzymesByName
-} from "@teselagen/sequence-utils";
-
-export default createSelector(
-  () => defaultEnzymesByName,
-  (state, additionalEnzymes) => {
-    return additionalEnzymes;
-  },
-  () => localStorage.getItem("enzymeGroups"), //it should recompute if the enzyme groups change in localstorage
-  (defaultEnzymesByName, additionalEnzymes) => {
-    const enzymesFromGroups = {};
-    forEach(window.getExistingEnzymeGroups(), group => {
-      forEach(group, enzymeName => {
-        const enzyme = { ...aliasedEnzymesByName, ...additionalEnzymes }[
-          enzymeName.toLowerCase()
-        ];
-        if (!enzyme) {
-          console.warn("ruh roh, no enzyme found for: ", enzymeName);
-        } else {
-          enzymesFromGroups[enzymeName.toLowerCase()] = enzyme;
-        }
-      });
-    });
-    return {
-      ...defaultEnzymesByName,
-      ...additionalEnzymes,
-      ...enzymesFromGroups
-    };
-  }
-);

package/rowviewContants.js

@@ -1,3 +0,0 @@
-export const defaultCharWidth = 9;
-export const defaultContainerWidth = 400;
-export const defaultMarginWidth = 50;

package/ruler.css

@@ -1,89 +0,0 @@
-/* .managerListLadder {
-  height: 265px;
-  overflow: visible;
-  border: 1px solid #E0E0E0;
-  padding: 0 !important;
-  position: fixed;
-  width: 225px;
-}
-
-.left {
-  border-color: black;
-  position: absolute;
-  height: 5px;
-  width: 80%;
-}
-
-.right {
-  border-color: black;
-  position: absolute;
-  height: 5px;
-  width: 80%;
-}
-
-.tooltip {
-  position: absolute;
-  height: 0;
-}
-
-.tooltip .tooltiptext {
-  visibility: hidden;
-  position: absolute;
-  width: auto;
-  background-color: black;
-  color: white;
-  text-align: left;
-  padding: 5px;
-  font-size: 7pt;
-  bottom: 5px;
-  white-space: nowrap;
-  border-radius: 6px;
-}
-
-.tooltip .tooltiptext::after {
-  content: " ";
-  /* i don't know what this content attribute does, but it works... */
-/* position: absolute;
-  top: 100%;
-  left: 50%;
-  margin-left: -5px;
-  border-width: 5px;
-  border-style: solid;
-  border-color: black transparent transparent transparent;
-}
-
-.tooltip:hover .tooltiptext {
-  visibility: visible;
-}
-
-.rightLabel {
-  margin-right: 2%;
-  margin-left: 60%;
-  position: relative;
-}
-
-.leftLabel {
-  margin-left: 2%;
-  margin-right: 60%;
-  position: relative;
-}
-
-.block {
-  height: 265px;
-  max-height: none;
-  padding-bottom: 40px;
-  padding-top: 10px;
-  overflow: scroll;
-}
-
-.fragmentsNumLabel {
-  text-align: left;
-  padding: 0 5px;
-  color: #333333;
-  height: 30px;
-  width: 100%;
-}
- 
-
-
-*/

package/saveTool.js

@@ -1,44 +0,0 @@
-import React from "react";
-import { Icon } from "@blueprintjs/core";
-import ToolbarItem from "./ToolbarItem";
-import { connectToEditor, handleSave } from "../withEditorProps";
-import { withHandlers } from "recompose";
-import { compose } from "redux";
-
-export default compose(
-  connectToEditor(
-    ({ readOnly, sequenceData = {}, lastSavedId = "134%!@#%!@#%!@%" }) => {
-      return {
-        readOnly: readOnly,
-        sequenceData: sequenceData,
-        hasBeenSaved:
-          sequenceData.stateTrackingId === "initialLoadId" ||
-          sequenceData.stateTrackingId === lastSavedId
-      };
-    }
-  ),
-  withHandlers({ handleSave })
-)(({
-  toolbarItemProps,
-  alwaysAllowSave,
-  handleSave,
-  readOnly,
-  hasBeenSaved,
-  onSave
-}) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon data-test="saveTool" icon="floppy-disk" />,
-        onIconClick: handleSave,
-        disabled: alwaysAllowSave ? false : !onSave || hasBeenSaved || readOnly,
-        tooltip: (
-          <span>
-            Save <span style={{ fontSize: 10 }}>(Cmd/Ctrl+S)</span>
-          </span>
-        ),
-        ...toolbarItemProps
-      }}
-    />
-  );
-});