@teselagen/ove 0.0.14 → 0.0.16

package/src/redux/annotationVisibility.js

@@ -0,0 +1,196 @@
+import { omit } from "lodash";
+
+//./caretPosition.js
+
+import createAction from "./utils/createMetaAction";
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+
+export const visibilityDefaultValues = {
+  featureTypesToHide: {},
+  featureIndividualToHide: {},
+  partIndividualToHide: {},
+  primerIndividualToHide: {},
+  features: true,
+  warnings: true,
+  assemblyPieces: true,
+  chromatogram: true,
+  lineageAnnotations: true,
+  translations: true,
+  parts: true,
+  orfs: false,
+  orfTranslations: false,
+  cdsFeatureTranslations: true,
+  axis: true,
+  cutsites: true,
+  // cutsites: true,
+  cutsitesInSequence: true,
+  primers: true,
+  dnaColors: false,
+  sequence: true,
+  reverseSequence: true,
+  fivePrimeThreePrimeHints: true,
+  axisNumbers: true
+};
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const annotationVisibilityToggle = createAction(
+  "annotationVisibilityToggle"
+);
+//eg: annotationVisibilityToggle('features')
+export const annotationVisibilityHide = createAction(
+  "annotationVisibilityHide"
+);
+export const annotationVisibilityShow = createAction(
+  "annotationVisibilityShow"
+);
+export const hideFeatureTypes = createAction("hideFeatureTypes");
+export const showFeatureTypes = createAction("showFeatureTypes");
+export const resetFeatureTypesToHide = createAction("resetFeatureTypesToHide");
+export const hideFeatureIndividual = createAction("hideFeatureIndividual");
+export const showFeatureIndividual = createAction("showFeatureIndividual");
+export const resetFeatureIndividualToHide = createAction(
+  "resetFeatureIndividualToHide"
+);
+export const hidePrimerIndividual = createAction("hidePrimerIndividual");
+export const showPrimerIndividual = createAction("showPrimerIndividual");
+export const resetPrimerIndividualToHide = createAction(
+  "resetPrimerIndividualToHide"
+);
+export const hidePartIndividual = createAction("hidePartIndividual");
+export const showPartIndividual = createAction("showPartIndividual");
+export const resetPartIndividualToHide = createAction(
+  "resetPartIndividualToHide"
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+const annotationVisibility = createMergedDefaultStateReducer(
+  {
+    [resetPartIndividualToHide]: (state) => {
+      return {
+        ...state,
+        partIndividualToHide: {}
+      };
+    },
+    [showPartIndividual]: (state, payload) => {
+      return {
+        ...state,
+        parts: true,
+        partIndividualToHide: omit(state.partIndividualToHide, payload)
+      };
+    },
+    [hidePartIndividual]: (state, payload) => {
+      return {
+        ...state,
+        partIndividualToHide: {
+          ...state.partIndividualToHide,
+          ...payload.reduce((acc, key) => {
+            acc[key] = true;
+            return acc;
+          }, {})
+        }
+      };
+    },
+    [resetFeatureIndividualToHide]: (state) => {
+      return {
+        ...state,
+        featureIndividualToHide: {}
+      };
+    },
+    [showFeatureIndividual]: (state, payload) => {
+      return {
+        ...state,
+        features: true,
+        featureIndividualToHide: omit(state.featureIndividualToHide, payload)
+      };
+    },
+    [hideFeatureIndividual]: (state, payload) => {
+      return {
+        ...state,
+        featureIndividualToHide: {
+          ...state.featureIndividualToHide,
+          ...payload.reduce((acc, key) => {
+            acc[key] = true;
+            return acc;
+          }, {})
+        }
+      };
+    },
+    [resetPrimerIndividualToHide]: (state) => {
+      return {
+        ...state,
+        primerIndividualToHide: {}
+      };
+    },
+    [showPrimerIndividual]: (state, payload) => {
+      return {
+        ...state,
+        primers: true,
+        primerIndividualToHide: omit(state.primerIndividualToHide, payload)
+      };
+    },
+    [hidePrimerIndividual]: (state, payload) => {
+      return {
+        ...state,
+        primerIndividualToHide: {
+          ...state.primerIndividualToHide,
+          ...payload.reduce((acc, key) => {
+            acc[key] = true;
+            return acc;
+          }, {})
+        }
+      };
+    },
+    [resetFeatureTypesToHide]: (state) => {
+      return {
+        ...state,
+        featureTypesToHide: {}
+      };
+    },
+    [showFeatureTypes]: (state, payload) => {
+      return {
+        ...state,
+        featureTypesToHide: omit(state.featureTypesToHide, payload)
+      };
+    },
+    [hideFeatureTypes]: (state, payload) => {
+      return {
+        ...state,
+        featureTypesToHide: {
+          ...state.featureTypesToHide,
+          ...payload.reduce((acc, key) => {
+            acc[key] = true;
+            return acc;
+          }, {})
+        }
+      };
+    },
+    [annotationVisibilityToggle]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: !state[payload],
+        ...(payload === "orfs" && state.orfs === state.orfTranslations
+          ? { orfTranslations: !state.orfTranslations }
+          : null)
+      };
+    },
+    [annotationVisibilityHide]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: false
+      };
+    },
+    [annotationVisibilityShow]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: true
+      };
+    }
+  },
+  visibilityDefaultValues
+);
+
+export default annotationVisibility;

package/src/redux/annotationsToSupport.js

@@ -0,0 +1,104 @@
+import createAction from "./utils/createMetaAction";
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+
+//this determines whether or not to
+const initialSupportedTypes = {
+  parts: true,
+  features: true,
+  translations: true,
+  primers: true,
+  cutsites: true,
+  orfs: true,
+  warnings: true,
+  assemblyPieces: true,
+  lineageAnnotations: true
+};
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const annotationSupportToggle = createAction("annotationSupportToggle");
+//eg: annotationSupportToggle('features')
+export const annotationSupportOn = createAction("annotationSupportOn");
+export const annotationSupportOff = createAction("annotationSupportOff");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createMergedDefaultStateReducer(
+  {
+    [annotationSupportToggle]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: !state[payload]
+      };
+    },
+    [annotationSupportOn]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: false
+      };
+    },
+    [annotationSupportOff]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: true
+      };
+    }
+  },
+  initialSupportedTypes
+);
+
+// import createAction from "./utils/createMetaAction";
+// import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+
+// //this determines whether or not to
+// const initialSupportedTypes = {
+//   parts: true,
+//   features: true,
+//   translations: true,
+//   primers: true,
+//   cutsites: true,
+//   orfs: true,
+//   warnings: true,
+//   assemblyPieces: true,
+//   lineageAnnotations: true
+// };
+
+// // ------------------------------------
+// // Actions
+// // ------------------------------------
+// export const annotationSupportToggle = createAction(
+//   "ANNOTATION_SUPPORT_TOGGLE"
+// );
+
+// export const annotationSupportOn = createAction("ANNOTATION_SUPPORT_ON");
+// export const annotationSupportOff = createAction("ANNOTATION_SUPPORT_OFF");
+
+// export default function (state = initialSupportedTypes, action) {
+//   switch (action.type) {
+//     case "ANNOTATION_SUPPORT_TOGGLE":
+//       return {
+//         ...state,
+//         [action.payload]: !state[action.payload]
+//       };
+//     case "ANNOTATION_SUPPORT_ON":
+//       return {
+//         ...state,
+//         [action.payload]: true
+//       };
+//     case "ANNOTATION_SUPPORT_OFF":
+//       return {
+//         ...state,
+//         [action.payload]: false
+//       };
+//     default:
+//       if (action.mergeStateDeep) {
+//         return {
+//           ...initialSupportedTypes,
+//           ...state
+//         };
+//       }
+//       return state;
+//   }
+// }

package/src/redux/caretPosition.js

@@ -0,0 +1,27 @@
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const caretPositionClear = createAction("CARET_POSITION_CLEAR");
+export const caretPositionUpdate = createAction("CARET_POSITION_UPDATE");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    SELECTION_LAYER_UPDATE: () => {
+      //clear the caret if the selection layer is updated!
+      return -1;
+    },
+    [caretPositionClear]: () => {
+      return -1;
+    },
+    [caretPositionUpdate]: (unused, payload) => {
+      return typeof payload === "string" ? parseInt(payload, 10) : payload;
+    }
+  },
+  -1
+);

package/src/redux/charWidth.js

@@ -0,0 +1,22 @@
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const updateSequenceSpacing = createAction("updateSequenceSpacing");
+
+const newVal = window.localStorage.getItem("charWidth");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [updateSequenceSpacing]: (state, payload) => {
+      localStorage.setItem("charWidth", payload);
+      return payload;
+    }
+  },
+  newVal || 9
+);

package/src/redux/copyOptions.js

@@ -0,0 +1,34 @@
+//./caretPosition.js
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const toggleCopyOption = createAction("TOGGLE_COPY_OPTION"); //NOTE!!:: second argument sanitizes actions so no payload is passed
+
+export const defaultCopyOptions = {
+  features: true,
+  partialFeatures: false,
+  parts: true,
+  partialParts: false
+};
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [toggleCopyOption]: (state, type) => {
+      return {
+        ...state,
+        ...(type === "partialFeatures" && !state[type] && { features: true }),
+        ...(type === "partialParts" && !state[type] && { parts: true }),
+        ...(type === "features" && { partialFeatures: !state[type] }),
+        ...(type === "parts" && { partialParts: !state[type] }),
+        [type]: !state[type]
+      };
+    }
+  },
+  defaultCopyOptions
+);

package/src/redux/createYourOwnEnzyme.js

@@ -0,0 +1,39 @@
+//./selectionLayer.js
+import { createReducer, createAction } from "redux-act";
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const createYourOwnEnzymeUpdate = createAction(
+  "CREATE_YOUR_OWN_ENZYME_UPDATE"
+);
+export const createYourOwnEnzymeReset = createAction(
+  "CREATE_YOUR_OWN_ENZYME_RESET"
+);
+export const createYourOwnEnzymeClose = createAction(
+  "CREATE_YOUR_OWN_ENZYME_CLOSE"
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+const initialValues = {
+  name: "Example Enzyme",
+  sequence: "ggatcc",
+  chop_top_index: 1,
+  chop_bottom_index: 5,
+  isOpen: false
+};
+export default createReducer(
+  {
+    [createYourOwnEnzymeClose]: () => {
+      return { ...initialValues, isOpen: false };
+    },
+    [createYourOwnEnzymeReset]: (state, payload = {}) => {
+      return { ...initialValues, ...payload };
+    },
+    [createYourOwnEnzymeUpdate]: (state, payload) => {
+      return payload;
+    }
+  },
+  initialValues
+);

package/src/redux/deletionLayers.js

@@ -0,0 +1,36 @@
+//./deletionLayers.js
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+import omit from "lodash/omit";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const deletionLayerClear = createAction("deletionLayerClear");
+export const deletionLayerUpdate = createAction("DELETION_LAYER_UPDATE");
+export const deletionLayerDelete = createAction("DELETION_LAYER_DELETE");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [deletionLayerClear]: () => {
+      return {};
+    },
+    [deletionLayerUpdate]: (state, payload) => {
+      return {
+        ...state,
+        [payload.id]: {
+          color: "firebrick",
+          id: payload.id,
+          ...payload.range
+        }
+      };
+    },
+    [deletionLayerDelete]: (state, payload) => {
+      return omit(state, payload.id);
+    }
+  },
+  {}
+);

package/src/redux/digestTool.js

@@ -0,0 +1,34 @@
+import createAction from "./utils/createMetaAction";
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const updateSelectedFragment = createAction("updateSelectedFragment");
+export const updateComputePartialDigest = createAction(
+  "updateComputePartialDigest"
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createMergedDefaultStateReducer(
+  {
+    [updateSelectedFragment]: (state, payload) => {
+      return {
+        ...state,
+        selectedFragment: payload
+      };
+    },
+    [updateComputePartialDigest]: (state, payload) => {
+      return {
+        ...state,
+        computePartialDigest: payload
+      };
+    }
+  },
+  {
+    selectedFragment: undefined,
+    computePartialDigest: false
+  }
+);

package/src/redux/featureLengthsToHide.js

@@ -0,0 +1,27 @@
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const updateFeatureLengthsToHide = createAction(
+  "updateFeatureLengthsToHide"
+);
+export const toggleFeatureLengthsToHide = createAction(
+  "toggleFeatureLengthsToHide"
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createMergedDefaultStateReducer(
+  {
+    [updateFeatureLengthsToHide]: (state, payload) => {
+      return { ...state, ...payload };
+    },
+    [toggleFeatureLengthsToHide]: (state) => {
+      return { ...state, enabled: !state["enabled"] };
+    }
+  },
+  { enabled: false, min: 0, max: 800 }
+);

package/src/redux/findTool.js

@@ -0,0 +1,79 @@
+import createAction from "./utils/createMetaAction";
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+import { noop } from "lodash";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const toggleFindTool = createAction("TOGGLE_FIND_TOOL", noop); //NOTE!!:: second argument sanitizes actions so no payload is passed!
+export const toggleHighlightAll = createAction("toggleHighlightAll", noop); //NOTE!!:: second argument sanitizes actions so no payload is passed!
+export const toggleIsInline = createAction("toggleIsInline", noop); //NOTE!!:: second argument sanitizes actions so no payload is passed!
+export const updateSearchText = createAction("updateSearchText");
+export const updateAmbiguousOrLiteral = createAction(
+  "updateAmbiguousOrLiteral"
+);
+export const updateDnaOrAA = createAction("updateDnaOrAA");
+export const updateMatchNumber = createAction("updateMatchNumber");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createMergedDefaultStateReducer(
+  {
+    [toggleFindTool]: state => {
+      return {
+        ...state,
+        isOpen: !state.isOpen
+      };
+    },
+    [toggleHighlightAll]: state => {
+      return {
+        ...state,
+        highlightAll: !state.highlightAll
+      };
+    },
+    [toggleIsInline]: state => {
+      localStorage.setItem("veFindBarIsExpanded", state.isInline);
+      return {
+        ...state,
+        isInline: !state.isInline
+      };
+    },
+    [updateAmbiguousOrLiteral]: (state, payload) => {
+      return {
+        ...state,
+        matchNumber: 0,
+        ambiguousOrLiteral: payload
+      };
+    },
+    [updateDnaOrAA]: (state, payload) => {
+      return {
+        ...state,
+        matchNumber: 0,
+        dnaOrAA: payload
+      };
+    },
+    [updateSearchText]: (state, payload) => {
+      return {
+        ...state,
+        matchNumber: 0,
+        searchText: payload
+      };
+    },
+    [updateMatchNumber]: (state, payload) => {
+      return {
+        ...state,
+        matchNumber: payload
+      };
+    }
+  },
+  {
+    isOpen: false,
+    isInline: !localStorage.getItem("veFindBarIsExpanded"),
+    searchText: "",
+    dnaOrAA: "DNA",
+    ambiguousOrLiteral: "LITERAL",
+    highlightAll: false,
+    matchNumber: 0
+  }
+);

package/src/redux/frameTranslations.js

@@ -0,0 +1,52 @@
+//./caretPosition.js
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const frameTranslationToggle = createAction("FRAME_TRANSLATION_TOGGLE");
+export const frameTranslationToggleOn = createAction(
+  "FRAME_TRANSLATION_TOGGLE_ON"
+);
+export const frameTranslationToggleOff = createAction(
+  "FRAME_TRANSLATION_TOGGLE_OFF"
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [frameTranslationToggle]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: !state[payload]
+      };
+    },
+    [frameTranslationToggleOn]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: true
+      };
+    },
+    [frameTranslationToggleOff]: (state, payload) => {
+      return {
+        ...state,
+        [payload]: false
+      };
+    }
+  },
+  {
+    "1": false,
+    "2": false,
+    "3": false,
+    "-1": false,
+    "-2": false,
+    "-3": false
+  }
+);
+
+export function getMinimumOrfSize(state) {
+  return state;
+}

package/src/redux/hoveredAnnotation.js

@@ -0,0 +1,24 @@
+//./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 "";
+    }
+  },
+  ""
+);