@teselagen/ove 0.7.28 → 0.7.30-beta.1

package/moveCaret.js

@@ -1,58 +0,0 @@
-const handleMoves = {
-  moveCaretLeftOne: function ({ isProtein, selectionLayer, shiftHeld }) {
-    if (selectionLayer.start > -1 && !shiftHeld) {
-      return 0;
-    }
-    return isProtein ? -3 : -1;
-  },
-  moveCaretRightOne: function ({ isProtein, selectionLayer, shiftHeld }) {
-    if (selectionLayer.start > -1 && !shiftHeld) {
-      return 0;
-    }
-    return isProtein ? 3 : 1;
-  },
-  moveCaretUpARow: function ({ bpsPerRow }) {
-    return -bpsPerRow;
-  },
-  moveCaretDownARow: function ({ bpsPerRow }) {
-    return bpsPerRow;
-  },
-  moveCaretToEndOfRow: function ({ bpsPerRow, caretPosition }) {
-    return bpsPerRow - (caretPosition % bpsPerRow);
-  },
-  moveCaretToStartOfRow: function ({ bpsPerRow, caretPosition }) {
-    let moveBy = -caretPosition % bpsPerRow;
-    if (moveBy === 0) {
-      moveBy = -bpsPerRow;
-    }
-    return moveBy;
-  },
-  moveCaretToStartOfSequence: function ({ caretPosition }) {
-    return -caretPosition;
-  },
-  moveCaretToEndOfSequence: function ({ caretPosition, sequenceLength }) {
-    return sequenceLength - caretPosition;
-  }
-};
-
-function moveCaret({
-  sequenceLength,
-  bpsPerRow,
-  caretPosition,
-  selectionLayer,
-  shiftHeld,
-  isProtein,
-  type
-}) {
-  const moveBy = handleMoves[type]({
-    shiftHeld,
-    sequenceLength,
-    isProtein,
-    bpsPerRow,
-    caretPosition,
-    selectionLayer
-  });
-  return moveBy;
-}
-
-export default moveCaret;

package/name.js

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

package/normalizeAngle.js

@@ -1,3 +0,0 @@
-export function normalizeAngle(a) {
-  return (a + Math.PI * 2) % (Math.PI * 2);
-}

package/normalizeAngleRange.js

@@ -1,9 +0,0 @@
-import { normalizeAngle } from "./normalizeAngle";
-
-export function normalizeAngleRange(r) {
-  return {
-    ...r,
-    start: normalizeAngle(r.start),
-    end: normalizeAngle(r.end)
-  };
-}

package/oligoTool.js

@@ -1,30 +0,0 @@
-import { Icon } from "@blueprintjs/core";
-import React from "react";
-import ToolbarItem from "./ToolbarItem";
-import { connectToEditor } from "../withEditorProps";
-
-export default connectToEditor(editorState => {
-  return {
-    isHidden: editorState.sequenceData && editorState.sequenceData.isProtein,
-
-    toggled:
-      editorState.annotationVisibility &&
-      editorState.annotationVisibility.primers
-  };
-})(({ toolbarItemProps, isHidden, toggled, annotationVisibilityToggle }) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon icon="swap-horizontal" />,
-        onIconClick: function () {
-          annotationVisibilityToggle("primers");
-        },
-        isHidden,
-        toggled,
-        tooltip: "Show Primers",
-        tooltipToggled: "Hide Primers",
-        ...toolbarItemProps
-      }}
-    />
-  );
-});

package/onlyUpdateForKeysDeep.js

@@ -1,31 +0,0 @@
-import { pick } from "lodash-es";
-import { shouldUpdate } from "recompose";
-import { isEqualWith, isFunction } from "lodash-es";
-
-// import deepEqual from "deep-equal";
-
-const onlyUpdateForKeys = propKeys => {
-  const hoc = shouldUpdate((props, nextProps) => {
-    const a = !isEq(pick(nextProps, propKeys), pick(props, propKeys));
-    return a;
-  });
-
-  // if (process.env.NODE_ENV !== "production") {
-  //   return BaseComponent =>
-  //     setDisplayName(wrapDisplayName(BaseComponent, "onlyUpdateForKeys"))(
-  //       hoc(BaseComponent)
-  //     );
-  // }
-  return hoc;
-};
-
-export default onlyUpdateForKeys;
-
-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;
-};

package/orfFrameToColorMap.js

@@ -1,10 +0,0 @@
-const orfFrameToColorMap = {
-  0: "#FF4040",
-  1: "#5E8804",
-  2: "#17569B"
-};
-export default orfFrameToColorMap;
-
-export const getOrfColor = orf => {
-  return orfFrameToColorMap[orf.frame];
-};

package/orfTool.js

@@ -1,136 +0,0 @@
-import { Icon } from "@blueprintjs/core";
-import React from "react";
-import { orfIcon, CmdCheckbox, CmdDiv, InfoHelper } from "@teselagen/ui";
-import ToolbarItem from "./ToolbarItem";
-import { connectToEditor } from "../withEditorProps";
-import withEditorProps from "../withEditorProps";
-import getCommands from "../commands";
-
-export default connectToEditor(
-  ({ annotationVisibility = {}, toolBar = {} }) => {
-    return {
-      toggled: annotationVisibility.orfs,
-      isOpen: toolBar.openItem === "orfTool"
-    };
-  }
-)(({ toolbarItemProps, toggled, annotationVisibilityToggle, isOpen }) => {
-  return (
-    <ToolbarItem
-      {...{
-        Icon: <Icon data-test="orfTool" icon={orfIcon} />,
-        onIconClick: function () {
-          annotationVisibilityToggle("orfs");
-        },
-        toggled,
-        tooltip: "Show Open Reading Frames",
-        tooltipToggled: "Hide Open Reading Frames",
-        Dropdown: OrfToolDropdown,
-        dropdowntooltip:
-          (!isOpen ? "Show" : "Hide") + " Open Reading Frame Options",
-        ...toolbarItemProps
-      }}
-    />
-  );
-});
-
-const OrfToolDropdown = withEditorProps(
-  class OrfDropdown extends React.Component {
-    constructor(props) {
-      super(props);
-      this.commands = getCommands(this);
-    }
-    render() {
-      return (
-        <div className="veToolbarOrfOptionsHolder">
-          <CmdCheckbox
-            prefix="Show "
-            cmd={this.commands.toggleOrfTranslations}
-          />
-          <CmdCheckbox
-            prefix="Show "
-            cmd={this.commands.useGtgAndCtgAsStartCodons}
-          />
-          <CmdDiv cmd={this.commands.minOrfSizeCmd} />
-          <div className="vespacer" />
-
-          <InfoHelper
-            displayToSide
-            content="To translate an arbitrary area, right click a selection."
-          />
-        </div>
-      );
-    }
-  }
-);
-// const OrfToolDropdown = withEditorProps(function({
-//   useAdditionalOrfStartCodons,
-//   useAdditionalOrfStartCodonsToggle,
-//   annotationVisibility,
-//   annotationVisibilityToggle,
-//   editorName
-// }) {
-//   return (
-//     <div className="veToolbarOrfOptionsHolder">
-//       {/* <div className="vespacer" />
-//       <MinOrfSize editorName={editorName} />
-//       <Checkbox
-//         onChange={function() {
-//           annotationVisibilityToggle("orfTranslations");
-//         }}
-//         disabled={!annotationVisibility.orfs}
-//         checked={annotationVisibility.orfTranslations}
-//         label="Show translations for ORFs"
-//       />
-//       <Checkbox
-//         onChange={function() {
-//           annotationVisibilityToggle("cdsFeatureTranslations");
-//         }}
-//         checked={annotationVisibility.cdsFeatureTranslations}
-//         label="Show translations for CDS features"
-//       />
-//       <Checkbox
-//         onChange={useAdditionalOrfStartCodonsToggle}
-//         checked={useAdditionalOrfStartCodons}
-//         label="Use GTG and CTG as start codons"
-//       /> */}
-//       <div className="vespacer" />
-
-//       <InfoHelper
-//         displayToSide
-//         content="To translate an arbitrary area, right click a selection."
-//       />
-//     </div>
-//   );
-// });
-
-// export const MinOrfSize = connectToEditor(editorState => {
-//   return {
-//     sequenceLength: selectors.sequenceLengthSelector(editorState),
-//     minimumOrfSize: editorState.minimumOrfSize
-//   };
-// })(
-//   ({
-//     minimumOrfSizeUpdate,
-//     sequenceLength,
-//     annotationVisibilityShow,
-//     minimumOrfSize
-//   }) => {
-//     return (
-//       <div data-test="min-orf-size" style={{ display: "flex" }}>
-//         Minimum ORF Size:
-//         <input
-//           type="number"
-//           className={classNames(Classes.INPUT, "minOrfSizeInput")}
-//           onChange={function(event) {
-//             let minimumOrfSize = parseInt(event.target.value, 10);
-//             if (!(minimumOrfSize > -1)) return;
-//             if (minimumOrfSize > sequenceLength) return;
-//             annotationVisibilityShow("orfs");
-//             minimumOrfSizeUpdate(minimumOrfSize);
-//           }}
-//           value={minimumOrfSize}
-//         />
-//       </div>
-//     );
-//   }
-// );

package/orfsSelector.js

@@ -1,15 +0,0 @@
-import circularSelector from "./circularSelector";
-import sequenceSelector from "./sequenceSelector";
-import minimumOrfSizeSelector from "./minimumOrfSizeSelector";
-import { findOrfsInPlasmid } from "@teselagen/sequence-utils";
-import { createSelector } from "reselect";
-
-export default createSelector(
-  sequenceSelector,
-  circularSelector,
-  minimumOrfSizeSelector,
-  state => state.useAdditionalOrfStartCodons,
-  findOrfsInPlasmid
-);
-
-//tiny

package/panelsShown.js

@@ -1,294 +0,0 @@
-import { map, flatMap } from "lodash-es";
-import { createReducer } from "redux-act";
-import createAction from "./utils/createMetaAction";
-import { removeItem } from "../utils/arrayUtils";
-import immer from "immer";
-
-//manages which tab panels are shown in the editor
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const panelsShownUpdate = createAction("PANELS_SHOWN_UPDATE");
-export const addPanelIfItDoesntAlreadyExist = createAction(
-  "addPanelIfItDoesntAlreadyExist"
-);
-export const togglePanelFullScreen = createAction("togglePanelFullScreen");
-export const collapsePanel = createAction("collapsePanel");
-export const closePanel = createAction("closePanel");
-export const _collapseSplitScreen = createAction("_collapseSplitScreen");
-export const setPanelAsActive = createAction("setPanelAsActive");
-export const flipActiveTabFromLinearOrCircularIfNecessary = createAction(
-  "flipActiveTabFromLinearOrCircularIfNecessary"
-);
-export const expandTabToSplitScreen = createAction("expandTabToSplitScreen");
-export const propertiesViewOpen = (unused, meta) => {
-  return setPanelAsActive("properties", meta);
-};
-export const createNewDigest = (unused, meta) => {
-  return dispatch => {
-    dispatch(
-      addPanelIfItDoesntAlreadyExist(
-        {
-          id: "digestTool",
-          name: "New Digest",
-          active: true,
-          canClose: true
-        },
-        meta
-      )
-    );
-    dispatch(setPanelAsActive("digestTool", meta));
-  };
-};
-export const createNewPCR = (unused, meta) => {
-  return dispatch => {
-    dispatch(
-      addPanelIfItDoesntAlreadyExist(
-        {
-          id: "pcrTool",
-          name: "New PCR",
-          active: true,
-          canClose: true
-        },
-        meta
-      )
-    );
-    dispatch(setPanelAsActive("pcrTool", meta));
-  };
-};
-
-export const createNewAlignment = (payload, meta) => {
-  return dispatch => {
-    dispatch(
-      addPanelIfItDoesntAlreadyExist(
-        {
-          type: "alignment",
-          name: "New Alignment",
-          active: true,
-          canClose: true,
-          ...payload
-        },
-        meta
-      )
-    );
-    dispatch(setPanelAsActive(payload.id, meta));
-  };
-};
-
-export const createNewMismatchesList = (payload, meta) => {
-  return dispatch => {
-    dispatch(
-      addPanelIfItDoesntAlreadyExist(
-        {
-          type: "mismatches",
-          name: "Mismatches",
-          active: true,
-          canClose: true,
-          ...payload
-        },
-        meta
-      )
-    );
-    dispatch(setPanelAsActive(payload.id, meta));
-  };
-};
-
-export const collapseSplitScreen = (activePanelId, meta) => {
-  return dispatch => {
-    dispatch(_collapseSplitScreen(activePanelId, meta));
-    activePanelId && dispatch(setPanelAsActive(activePanelId, meta));
-  };
-};
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-const reducer = createReducer(
-  {
-    [addPanelIfItDoesntAlreadyExist]: (state, panelToAdd) => {
-      if (
-        !state.some(panelGroup => {
-          return panelGroup.some(({ id }) => {
-            return id === panelToAdd.id;
-          });
-        })
-      ) {
-        return state.map((panelGroup, index) => {
-          if (index === 0) return [panelToAdd, ...panelGroup];
-          return panelGroup;
-        });
-      }
-      return state;
-    },
-    [panelsShownUpdate]: (state, payload) => {
-      return payload.filter(group => group.length); //filter out any empty groups
-    },
-    [flipActiveTabFromLinearOrCircularIfNecessary]: (state, setCircActive) => {
-      const newState = immer(state, s => {
-        s.forEach(g => {
-          flipActiveForGroup(g, setCircActive);
-        });
-      });
-
-      return newState;
-    },
-    [closePanel]: (state, idToClose) => {
-      const newState = state.map(group => {
-        let indexToClose;
-        group.forEach(({ id }, i) => {
-          if (id === idToClose) indexToClose = i;
-        });
-        if (indexToClose > -1) {
-          const newPanels = removeItem(group, indexToClose);
-          let mostRecentIndex = 0;
-          newPanels.forEach(p => {
-            if (
-              (p.lastActive || 0) > (newPanels[mostRecentIndex].lastActive || 0)
-            ) {
-              mostRecentIndex = newPanels.indexOf(p);
-            }
-          });
-
-          return newPanels.map((tab, i) => {
-            if (i === mostRecentIndex) return { ...tab, active: true };
-            else {
-              return tab;
-            }
-          });
-        }
-        return group;
-      });
-      return newState.filter(group => group.length); //filter out any empty groups
-    },
-    [_collapseSplitScreen]: state => {
-      return [flatMap(state)];
-    },
-    [expandTabToSplitScreen]: (state, activePanelId) => {
-      let panelToMove;
-      return [
-        state[0]
-          .filter(panel => {
-            if (panel.id === activePanelId) {
-              panelToMove = panel;
-              return false;
-            }
-            return true;
-          })
-          .map((panel, i) => {
-            return i === 0 ? { ...panel, active: true } : panel;
-          }),
-        [{ ...panelToMove, active: true }]
-      ];
-    },
-    [setPanelAsActive]: (state, panelId) => {
-      return map(state, panelGroup => {
-        const isPanelInGroup = panelGroup.some(({ id }) => {
-          return panelId === id;
-        });
-        return panelGroup.map(panel => {
-          return {
-            ...panel,
-            active:
-              panelId === panel.id
-                ? true
-                : isPanelInGroup
-                  ? false
-                  : panel.active
-          };
-        });
-      });
-    },
-    [togglePanelFullScreen]: (state, panelId) => {
-      return map(state, panelGroup => {
-        const isPanelInGroup = panelGroup.some(({ id }) => {
-          return panelId === id;
-        });
-        return panelGroup.map(panel => {
-          return {
-            ...panel,
-            active:
-              panelId === panel.id
-                ? true
-                : isPanelInGroup
-                  ? false
-                  : panel.active,
-            fullScreen:
-              panelId === panel.id
-                ? !panel.fullScreen
-                : isPanelInGroup
-                  ? false
-                  : panel.fullScreen
-          };
-        });
-      });
-    },
-    [collapsePanel]: (state, panelToCloseId) => {
-      return [
-        flatMap(state, panelGroup => {
-          return panelGroup;
-        }).map(panel => {
-          if (panel.id === panelToCloseId) {
-            return {
-              ...panel,
-              active: false
-            };
-          }
-          return panel;
-        })
-      ];
-    }
-  },
-  [
-    [
-      {
-        id: "circular",
-        name: "Circular Map",
-        active: true
-        //   canClose: true
-      },
-      {
-        id: "rail",
-        name: "Linear Map",
-        active: false
-      }
-    ],
-    [
-      {
-        id: "sequence",
-        name: "Sequence Map",
-        active: true
-      },
-      {
-        id: "properties",
-        name: "Properties",
-        active: false
-      }
-    ]
-  ]
-);
-
-export default (state, action) => {
-  const nextState = reducer(state, action);
-  nextState.forEach(pg => {
-    pg.forEach(p => {
-      if (p.active) {
-        p.lastActive = Date.now();
-      }
-    });
-  });
-  return nextState;
-};
-function flipActiveForGroup(group, setCircActive) {
-  const activeTab = group.find(({ active }) => active);
-  if (activeTab?.id === (setCircActive ? "rail" : "circular")) {
-    //we're on the wrong tab type so check if the other tab is in
-    const newTabToActivate = group.find(
-      ({ id }) => id === (setCircActive ? "circular" : "rail")
-    );
-    if (newTabToActivate) {
-      newTabToActivate.active = true;
-      activeTab.active = false;
-    }
-  }
-}

package/partLengthsToHide.js

@@ -1,23 +0,0 @@
-import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
-import createAction from "./utils/createMetaAction";
-
-// ------------------------------------
-// Actions
-// ------------------------------------
-export const updatePartLengthsToHide = createAction("updatePartLengthsToHide");
-export const togglePartLengthsToHide = createAction("togglePartLengthsToHide");
-
-// ------------------------------------
-// Reducer
-// ------------------------------------
-export default createMergedDefaultStateReducer(
-  {
-    [updatePartLengthsToHide]: (state, payload) => {
-      return { ...state, ...payload };
-    },
-    [togglePartLengthsToHide]: state => {
-      return { ...state, enabled: !state["enabled"] };
-    }
-  },
-  { enabled: false, min: 0, max: 800 }
-);

package/partOverhangs.js

@@ -1,6 +0,0 @@
-export const partOverhangs = [
-  "fivePrimeOverhang",
-  "fivePrimeUnderhang",
-  "threePrimeOverhang",
-  "threePrimeUnderhang"
-];