@teselagen/ove 0.7.28 → 0.7.30-beta.1

package/getTrackFromEvent.js

@@ -1,25 +0,0 @@
-import { getClientX, getClientY } from "../utils/editorUtils";
-
-export function getTrackFromEvent(event, allTracks) {
-  const trackContainers = document.querySelectorAll(
-    ".alignmentViewTrackContainer"
-  );
-  let track;
-  trackContainers.forEach(t => {
-    const mouseX = getClientX(event) + document.body.scrollLeft;
-    const mouseY = getClientY(event) + document.body.scrollTop;
-    if (
-      mouseX >= t.getBoundingClientRect().left &&
-      mouseX <=
-        t.getBoundingClientRect().left + t.getBoundingClientRect().width &&
-      mouseY >= t.getBoundingClientRect().top &&
-      mouseY <= t.getBoundingClientRect().top + t.getBoundingClientRect().height
-    ) {
-      const index = t.getAttribute("data-alignment-track-index");
-      track = allTracks[index];
-      track.index = index;
-      return true;
-    }
-  });
-  return track;
-}

package/getVisibleStartEnd.js

@@ -1,7 +0,0 @@
-export function getVisibleStartEnd({ scrollData, width }) {
-  const { percentScrolled, viewportWidth } = scrollData;
-
-  const visibleStart = percentScrolled * (width - viewportWidth);
-  const visibleEnd = visibleStart + viewportWidth;
-  return { visibleEnd, visibleStart };
-}

package/getXStartAndWidthFromNonCircularRange.js

@@ -1,12 +0,0 @@
-import { getRangeLength } from "@teselagen/range-utils";
-
-export default function getXStartAndWidthFromNonCircularRange(
-  range,
-  charWidth
-) {
-  const rangeLength = getRangeLength(range);
-  return {
-    width: rangeLength * charWidth,
-    xStart: range.start * charWidth
-  };
-}

package/getXStartAndWidthOfRangeWrtRow.js

@@ -1,27 +0,0 @@
-import { normalizePositionByRangeLength } from "@teselagen/range-utils";
-import { isNumber } from "lodash-es";
-
-export default function getXStartAndWidthOfRangeWrtRow({
-  range,
-  row,
-  charWidth,
-  sequenceLength,
-  gapsBefore = 0,
-  gapsInside = 0
-}) {
-  const xStart =
-    ((!isNumber(gapsBefore) ? 0 : gapsBefore) +
-      normalizePositionByRangeLength(range.start - row.start, sequenceLength)) *
-    charWidth;
-  const obj = {
-    xStart,
-    width:
-      (gapsInside +
-        normalizePositionByRangeLength(
-          range.end + 1 - range.start,
-          sequenceLength + 1
-        )) *
-      charWidth
-  };
-  return obj;
-}

package/getXStartAndWidthOfRowAnnotation.js

@@ -1,19 +0,0 @@
-export default function getXStartAndWidthOfRowAnnotation(
-  range,
-  bpsPerRow,
-  charWidth,
-  gapsBefore = 0,
-  gapsInside = 0
-) {
-  const startOffset = range.start % bpsPerRow;
-  const toReturn = {
-    startOffset,
-    xStart: (startOffset + gapsBefore) * charWidth,
-    width: getWidth(range, charWidth, gapsInside)
-  };
-  return toReturn;
-}
-
-export function getWidth(range, charWidth, gapsInside = 0) {
-  return (range.end + 1 - range.start + gapsInside) * charWidth;
-}

package/getYOffset.js

@@ -1,15 +0,0 @@
-export default function getYOffset(iTree, start, end) {
-  //get all potentially overlapping annotations
-
-  const potentiallyOverlappingAnnotations = iTree.search(start, end);
-  //we don't want to render the new annotation on top of any of these potentially overlapping annotations
-  const potentialPositionsForNewAnnotation =
-    potentiallyOverlappingAnnotations.map(() => true);
-  potentiallyOverlappingAnnotations.forEach(function (otherAnnotation) {
-    potentialPositionsForNewAnnotation[otherAnnotation.yOffset] = false;
-  });
-  //get first occurence of empty yOffset
-  const yOffset = potentialPositionsForNewAnnotation.indexOf(true);
-  //if there are no empty slots, make a new slot
-  return yOffset > -1 ? yOffset : potentialPositionsForNewAnnotation.length;
-}

package/hoveredAnnotation.js

@@ -1,24 +0,0 @@
-//./caretPosition.js
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const hoveredAnnotationUpdate = createAction("HOVEREDANNOTATIONUPDATE");
-export const hoveredAnnotationClear = createAction("HOVEREDANNOTATIONCLEAR");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [hoveredAnnotationUpdate]: (state, payload) => {
-      return payload || null;
-    },
-    [hoveredAnnotationClear]: () => {
-      return "";
-    }
-  },
-  ""
-);

package/importTool.js

@@ -1,27 +0,0 @@
-import React from "react";
-import { Icon } from "@blueprintjs/core";
-import Dropzone from "react-dropzone";
-import ToolbarItem from "./ToolbarItem";
-import { compose, withHandlers } from "recompose";
-import { importSequenceFromFile, connectToEditor } from "../withEditorProps";
-
-export default compose(
-  connectToEditor(),
-  withHandlers({ importSequenceFromFile })
-)(({ toolbarItemProps, importSequenceFromFile }) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon data-test="veImportTool" icon="export" />,
-        IconWrapper: Dropzone,
-        IconWrapperProps: {
-          multiple: false,
-          style: {},
-          onDrop: files => importSequenceFromFile(files[0])
-        },
-        tooltip: "Click or drag to import and view files (.fasta .gb .dna)",
-        ...toolbarItemProps
-      }}
-    />
-  );
-});

package/index.js

@@ -1,71 +0,0 @@
-import { getReverseComplementSequenceAndAnnotations } from "@teselagen/sequence-utils";
-
-export default function addDashesForMatchStartAndEndForTracks(alignmentTracks) {
-  return alignmentTracks.map((track, i) => {
-    // .filter by the user-specified mismatch overrides (initially [])
-    return {
-      ...track,
-      ...addDashesForMatchStartAndEnd(
-        track,
-        alignmentTracks[0], //send in the ref/template seq every time
-        i === 0
-      )
-    };
-  });
-}
-
-function addDashesForMatchStartAndEnd(
-  { alignmentData, sequenceData: _sequenceData },
-  template,
-  isTemplate
-) {
-  let sequenceData = _sequenceData;
-  const {
-    sequenceData: sequenceDataTemplate,
-    alignmentData: alignmentDataTemplate
-  } = template;
-  let { matchStart = 0, matchEnd = 0, strand } = alignmentData;
-  if (strand === -1) {
-    sequenceData = getReverseComplementSequenceAndAnnotations(sequenceData);
-    const oldMatchEnd = matchEnd;
-    const oldMatchStart = matchStart;
-    matchStart = sequenceData.sequence.length - oldMatchStart;
-    matchEnd = sequenceData.sequence.length - oldMatchEnd;
-  }
-  const { matchStart: matchStartTemplate = 0, matchEnd: matchEndTemplate = 0 } =
-    alignmentDataTemplate;
-  let newAlignmentData;
-  if (isTemplate) {
-    newAlignmentData = {
-      ...alignmentData,
-      sequence:
-        sequenceDataTemplate.sequence.slice(0, matchStartTemplate) +
-        alignmentData.sequence +
-        sequenceDataTemplate.sequence.slice(matchEndTemplate + 1)
-    };
-  } else {
-    newAlignmentData = {
-      ...alignmentData,
-      sequence:
-        sequenceData.sequence.slice(0, matchStart) +
-        alignmentData.sequence +
-        sequenceData.sequence.slice(matchEnd + 1)
-    };
-    newAlignmentData = {
-      ...alignmentData,
-      sequence:
-        "-".repeat(Math.max(matchStartTemplate - matchStart, 0)) +
-        newAlignmentData.sequence +
-        "-".repeat(
-          Math.max(
-            sequenceDataTemplate.sequence.slice(matchEndTemplate + 1).length -
-              (sequenceData.sequence.length - matchEnd) +
-              1,
-            0
-          )
-        )
-    };
-  }
-
-  return { alignmentData: newAlignmentData, sequenceData: sequenceData };
-}

package/inlineFindTool.js

@@ -1,38 +0,0 @@
-import React from "react";
-import { Icon } from "@blueprintjs/core";
-import FindBar from "../FindBar";
-import ToolbarItem from "./ToolbarItem";
-import { connectToEditor } from "../withEditorProps";
-
-export default connectToEditor(({ findTool = {} }) => {
-  return {
-    isOpen: findTool.isOpen
-  };
-})(({ toolbarItemProps, editorName, toggleFindTool, isOpen }) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: !isOpen ? (
-          <div>
-            <Icon data-test="ve-find-tool-toggle" icon="search" />
-            <Icon icon="caret-right" />
-          </div>
-        ) : (
-          <FindBar editorName={editorName} />
-        ),
-        renderIconAbove: isOpen,
-        onIconClick: toggleFindTool,
-        tooltip: isOpen ? (
-          <span>
-            Hide Find Tool <span style={{ fontSize: 10 }}>(Cmd/Ctrl+F)</span>
-          </span>
-        ) : (
-          <span>
-            Show Find Tool <span style={{ fontSize: 10 }}>(Cmd/Ctrl+F)</span>
-          </span>
-        ),
-        ...toolbarItemProps
-      }}
-    />
-  );
-});

package/isElementInViewport.js

@@ -1,29 +0,0 @@
-export function isElWithinAnotherEl(el, container) {
-  if (el.left > container.right) return false;
-  if (el.right < container.left) return false;
-  return true;
-}
-const buffer = 13;
-export function isElWithinAnotherElWithDiff(el, container) {
-  const elWidth = el.right - el.left;
-  const containerWidth = container.right - container.left;
-  const space = containerWidth - elWidth;
-  if (el.right > container.right) {
-    let diff = container.right - el.right - space / 2;
-    if (el.left + diff < container.left + buffer) {
-      //too far to the left -- aka diff too negative
-      diff += container.left + buffer - el.left - diff;
-    }
-    return [false, diff];
-  }
-
-  if (el.left < container.left) {
-    let diff = container.left - el.left + space / 2;
-    if (el.right + diff + buffer > container.right) {
-      //too far to the right -- aka diff too big
-      diff -= el.right + diff + buffer - container.right;
-    }
-    return [false, diff];
-  }
-  return [true];
-}

package/isEnzymeFilterAndSelector.js

@@ -1 +0,0 @@
-export default state => state.restrictionEnzymes.isEnzymeFilterAnd;

package/isTargetWithinEl.js

@@ -1,6 +0,0 @@
-// function Ident({ children }) {
-//   return children;
-// }
-export function isTargetWithinEl(event, selector) {
-  return event.target.closest(selector);
-}

package/labelLineIntensity.js

@@ -1,25 +0,0 @@
-import { createReducer } from "redux-act";
-
-import createAction from "./utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const changeLabelLineIntensity = createAction(
-  "changeLabelLineIntensity"
-);
-
-const newVal = window.localStorage.getItem("labelLineIntensity");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [changeLabelLineIntensity]: (state, payload) => {
-      localStorage.setItem("labelLineIntensity", payload);
-      return payload;
-    }
-  },
-  newVal ? parseFloat(newVal) : 0.1 //  0.1 (low) || 0.4 (med) || 0.7 (high) || 1.0 (full)
-);

package/labelSize.js

@@ -1,23 +0,0 @@
-import { createReducer } from "redux-act";
-
-import createAction from "./utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const changeLabelSize = createAction("changeLabelSize");
-
-const newVal = window.localStorage.getItem("labelSize");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [changeLabelSize]: (state, payload) => {
-      localStorage.setItem("labelSize", payload);
-      return payload;
-    }
-  },
-  newVal ? parseInt(newVal) : 8 //  8 is 100% label size
-);

package/ladderDefaults.js

@@ -1,25 +0,0 @@
-export const ladderDefaults = [
-  {
-    value: "geneRuler1KB",
-    label: "GeneRuler 1kb + DNA 75-20,000 bp",
-    markings: [
-      20000, 10000, 7000, 5000, 4000, 3000, 2000, 1500, 1000, 700, 500, 400,
-      300, 200, 75
-    ]
-  },
-  {
-    value: "geneRuler100BP",
-    label: "GeneRuler 100bp + DNA 100-3000 bp",
-    markings: [
-      3000, 2000, 1500, 1200, 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100
-    ]
-  },
-  {
-    value: "invitrogen1KbPlus",
-    label: "Invitrogen 1kb + DNA 100-15,000 bp",
-    markings: [
-      15000, 10000, 8000, 7000, 6000, 5000, 4000, 3000, 2000, 1500, 1000, 850,
-      650, 500, 400, 300, 200, 100
-    ]
-  }
-];

package/lastSavedId.js

@@ -1,20 +0,0 @@
-//./caretPosition.js
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const lastSavedIdUpdate = createAction("lastSavedIdUpdate"); //NOTE!!:: second argument sanitizes actions so no payload is passed
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [lastSavedIdUpdate]: (state, payload) => {
-      return payload;
-    }
-  },
-  null
-);

package/lineageLines.js

@@ -1,11 +0,0 @@
-import { createReducer } from "redux-act";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-// export const caretPositionClear = createAction('caretPositionClear')
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer({}, []);

package/makeStore.js

@@ -1,34 +0,0 @@
-//optionally connect to the redux store
-import { createStore, combineReducers, applyMiddleware, compose } from "redux";
-import VectorEditor, { vectorEditorMiddleware } from "../redux";
-import thunk from "redux-thunk";
-import { reducer as form } from "redux-form";
-
-const makeStore = () => {
-  const composeEnhancer =
-    (window.__REDUX_DEVTOOLS_EXTENSION_COMPOSE__ &&
-      window.__REDUX_DEVTOOLS_EXTENSION_COMPOSE__({
-        name: "createVectorEditor",
-        latency: 1000,
-        // serialize: {
-        //   replacer: (key, value) => {
-        //   }
-        // },
-        actionsDenylist: ["HOVEREDANNOTATIONUPDATE", "HOVEREDANNOTATIONCLEAR"]
-      })) ||
-    compose;
-
-  const store = createStore(
-    combineReducers({
-      form,
-      VectorEditor: VectorEditor()
-    }),
-    undefined,
-    composeEnhancer(
-      applyMiddleware(thunk, vectorEditorMiddleware) //your store should be redux-thunk connected for the VectorEditor component to work
-    )
-  );
-  return store;
-};
-
-export default makeStore;

package/massageTickSpacing.js

@@ -1,19 +0,0 @@
-import { some } from "lodash-es";
-
-export function massageTickSpacing(spacing) {
-  let toRet = spacing;
-  if (spacing < 15) {
-    return 10;
-  }
-  some(
-    [20, 50, 100, 500, 1000, 2000, 5000, 10000, 50000, 100000, 1000000],
-    val => {
-      if (spacing < val) {
-        toRet = val;
-        return true;
-      }
-    }
-  );
-
-  return toRet;
-}

package/materiallyAvailable.js

@@ -1,19 +0,0 @@
-import { createReducer } from "redux-act";
-import createAction from "../utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const updateAvailability = createAction("updateAvailability");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [updateAvailability]: (state, payload) => {
-      return payload;
-    }
-  },
-  true
-);

package/middleware.js

@@ -1,112 +0,0 @@
-//vectorEditorMiddleware
-//used to add undo/redo abilities to OVE
-
-// To Batch actions together use this api:
-// deleteFeature([id1, id2], {
-//   batchUndoStart: true
-// });
-// upsertFeature(
-// {
-//   ...feat1,
-//   id: uuid(),
-//   start: start - 1,
-//   end: end - 1,
-//   name
-// },
-// {
-//   batchUndoEnd: true
-// }
-// );
-
-export default store => next => action => {
-  if (action.meta && action.meta.disregardUndo) {
-    return next(action);
-  }
-  const disregardUndo = true;
-  if (action.type === "VE_UNDO" || action.type === "VE_REDO") {
-    const { VectorEditor } = store.getState();
-    const editorName = action.meta.editorName;
-    const editorState = VectorEditor[editorName];
-    const stack =
-      editorState.sequenceDataHistory[
-        action.type === "VE_UNDO" ? "past" : "future"
-      ] || [];
-    const stateToUse = stack[stack.length - 1];
-    store.dispatch({
-      type: action.type === "VE_UNDO" ? "VE_UNDO_META" : "VE_REDO_META",
-      payload: {
-        sequenceData: editorState.sequenceData,
-        selectionLayer: editorState.selectionLayer,
-        caretPosition: editorState.caretPosition
-      },
-      meta: { editorName, disregardUndo }
-    });
-    store.dispatch({
-      type: "SEQUENCE_DATA_UPDATE",
-      payload: stateToUse.sequenceData,
-      meta: { editorName, disregardUndo }
-    });
-    if (stateToUse.caretPosition > -1) {
-      store.dispatch({
-        type: "CARET_POSITION_UPDATE",
-        payload: stateToUse.caretPosition,
-        meta: { editorName, disregardUndo }
-      });
-    } else {
-      store.dispatch({
-        type: "SELECTION_LAYER_UPDATE",
-        payload: { ...stateToUse.selectionLayer, forceUpdate: Math.random() },
-        meta: { editorName, disregardUndo }
-      });
-    }
-    store.dispatch({
-      type: "VE_SEQUENCE_CHANGED", //used for external autosave functionality
-      payload: {
-        sequenceData: stateToUse.sequenceData,
-        editorName
-      },
-      meta: { editorName, disregardUndo: true }
-    });
-    return next(action);
-  } else {
-    //pass batchUndoStart, batchUndoMiddle and batchUndoEnd to group actions together
-    const { batchUndoEnd, batchUndoStart, batchUndoMiddle } = action.meta || {};
-    //get editor state(s)
-    const OldVectorEditor = store.getState().VectorEditor;
-    const result = next(action);
-    const NewVectorEditor = store.getState().VectorEditor;
-    Object.keys(NewVectorEditor).forEach(editorName => {
-      const newEditorState = NewVectorEditor[editorName];
-      const oldEditorState = OldVectorEditor[editorName];
-      if (
-        oldEditorState &&
-        oldEditorState.sequenceData &&
-        oldEditorState.sequenceData !== newEditorState.sequenceData
-      ) {
-        const { sequenceData, selectionLayer, caretPosition } = oldEditorState;
-        !batchUndoEnd &&
-          !batchUndoMiddle &&
-          store.dispatch({
-            type: "ADD_TO_UNDO_STACK",
-            payload: {
-              selectionLayer,
-              sequenceData,
-              caretPosition
-            },
-            meta: { editorName, disregardUndo }
-          });
-        !batchUndoStart &&
-          !batchUndoMiddle &&
-          store.dispatch({
-            type: "VE_SEQUENCE_CHANGED", //used for external autosave functionality
-            payload: {
-              sequenceData: newEditorState.sequenceData,
-              editorName
-            },
-            meta: { editorName, disregardUndo: true }
-          });
-      }
-    });
-    return result;
-  }
-};

package/minimumOrfSize.js

@@ -1,24 +0,0 @@
-//./caretPosition.js
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const minimumOrfSizeUpdate = createAction("minimumOrfSizeUpdate");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createReducer(
-  {
-    [minimumOrfSizeUpdate]: (state, payload) => {
-      return payload;
-    }
-  },
-  300
-);
-
-export function getMinimumOrfSize(state) {
-  return state;
-}

package/minimumOrfSizeSelector.js

@@ -1,2 +0,0 @@
-const minimumOrfSizeSelector = state => state.minimumOrfSize;
-export default minimumOrfSizeSelector;

package/modalActions.js

@@ -1,3 +0,0 @@
-// ------------------------------------
-// Actions
-// ------------------------------------