@teselagen/ove 0.0.14 → 0.0.15

package/src/Editor/style.css

@@ -0,0 +1,235 @@
+@import url(darkmode.css);
+.veEditor {
+  position: relative;
+  flex-grow: 1;
+}
+
+.taProductViewer {
+  display: flex;
+}
+
+.RowViewSide,
+.CircularViewSide {
+  width: 100%;
+}
+.ve-clickable {
+  cursor: pointer;
+  opacity: 0.7;
+}
+.ve-clickable:hover {
+  opacity: 1;
+}
+.ve-clickable-black {
+  cursor: pointer;
+  color: rgb(78, 78, 78);
+}
+.ve-clickable-black:hover {
+  color: black;
+}
+
+.veRightClickTabMenu {
+  opacity: 0.4;
+}
+.veRightClickTabMenu:hover {
+  opacity: 1;
+}
+
+.reflex-layout > .reflex-element {
+  overflow: hidden !important;
+}
+.reflex-layout.reflex-container {
+  height: inherit !important;
+}
+
+.preview-mode-container {
+  display: flex;
+  align-items: center;
+  flex-direction: column;
+  flex-grow: 1;
+  width: fit-content;
+  height: fit-content;
+
+  /* border: 1px solid black; */
+}
+.preview-mode-container > div {
+  -moz-box-shadow: 0 0 3px #ccc;
+  -webkit-box-shadow: 0 0 3px #ccc;
+  box-shadow: 0 0 3px #ccc;
+  padding: 2px;
+}
+
+.preview-mode-view-fullscreen {
+  top: 1%;
+  left: 1%;
+  /* transform: translateX(-50%) translateY(-50%); */
+  position: absolute;
+  display: flex;
+
+  /* opacity: .9; */
+}
+
+/* .preview-mode-container>div:hover .preview-mode-view-fullscreen {
+ opacity: 1;
+} */
+
+.preview-mode-view-fullscreen:hover {
+  background: #0e5a8a;
+}
+.bp3-tag.tg-smallTag {
+  transform: scale(0.8);
+}
+
+.veSearchLayer {
+  cursor: pointer;
+
+  stroke: gold !important;
+  fill: gold !important;
+  background: gold !important;
+  border-right-color: yellow !important;
+}
+.veSearchLayerActive {
+  stroke: red !important;
+  fill: red !important;
+  background: red !important;
+}
+.notCaret.veSearchLayerBottomStrand:after {
+  content: "";
+  display: block;
+  position: absolute;
+  right: 0px;
+  bottom: -15px;
+  opacity: 1 !important;
+  width: 0;
+  height: 0;
+  border-top: 15px solid transparent;
+  border-bottom: 15px solid transparent;
+  border-right: 15px solid gold;
+}
+.veSearchLayerActive.veSearchLayerBottomStrand:after {
+  border-right-color: red !important;
+}
+.notCaret.veSearchLayerBottomStrand:before {
+  content: "";
+  display: block;
+  position: absolute;
+  left: 1px;
+  bottom: -15px;
+  opacity: 1 !important;
+  width: 0;
+  height: 0;
+  border-top: 15px solid transparent;
+  border-bottom: 15px solid transparent;
+  border-right: 15px solid gold;
+}
+.veSearchLayerActive.veSearchLayerBottomStrand:before {
+  border-right-color: red !important;
+}
+
+.veSearchLayer.veCaret {
+  cursor: pointer;
+}
+
+.veRowView,
+.veCircularView {
+  outline: none;
+}
+
+@keyframes blinker {
+  50% {
+    opacity: 0;
+  }
+}
+
+.veVectorInteractionWrapper .veSelectionLayer:not(.veCaret) {
+  background: gray;
+  fill: gray;
+}
+.veVectorInteractionWrapper:focus .veSelectionLayer:not(.veCaret) {
+  fill: #0099ff;
+  background: #0099ff;
+}
+.tg-simple-dna-view .veSelectionLayer:not(.veCaret) {
+  fill: #0099ff;
+  background: #0099ff;
+}
+
+.veVectorInteractionWrapper:focus .veCaret:not(.selectionLayerCaret) {
+  animation: blinker 1s step-start infinite;
+}
+/* this is the little handles above the selection carets */
+.veEditor :not(.veSearchLayer).selectionLayerCaret::after {
+  content: " ";
+  display: block;
+  width: 0;
+  height: 0;
+  border-left: 5px solid transparent;
+  border-right: 5px solid transparent;
+  border-top: 10px solid black;
+  position: absolute;
+  z-index: 1000;
+  top: -7px;
+  left: -4px;
+}
+.bp3-dark .veEditor :not(.veSearchLayer).selectionLayerCaret::after {
+  border-top: 10px solid white;
+}
+.vePolygonCaretHandle,
+.veEditor .veSearchLayer .vePolygonCaretHandle {
+  display: none;
+}
+.veEditor .vePolygonCaretHandle {
+  display: inherit;
+}
+.bp3-dark .veEditor .vePolygonCaretHandle {
+  fill: white;
+}
+.bp3-dark .veTabActive {
+  color: #48aff0 !important;
+  border-bottom-color: #48aff0 !important;
+}
+
+[cmd="filterPartsByTagCmd"] > .bp3-text-overflow-ellipsis {
+  overflow: visible;
+}
+.vePart {
+  fill-opacity: 0;
+}
+
+.vePart text,
+text.vePart,
+tspan.vePart {
+  fill-opacity: 1;
+}
+.veTopRightContainer {
+  position: absolute;
+  top: 5px;
+  right: 5px;
+  display: flex;
+}
+
+.ve-draggable-tabs {
+  display: flex;
+  align-items: flex-end;
+  flex: 0 0 auto;
+  flex-direction: row;
+  overflow-x: auto;
+  border-bottom: 1px solid #f5f8fa;
+  padding-top: 3px;
+  padding-bottom: 3px;
+}
+
+.ve-draggable-tabs.is-dragging-over {
+  background: #e5f3ff;
+}
+
+.bp3-dark .veEditor .ve-draggable-tabs {
+  color: #f5f8fa !important;
+  border-bottom: 1px solid #4a4b4b;
+}
+
+.bp3-dark .veEditor .ve-draggable-tabs.is-dragging-over {
+  background: #0c5174;
+}
+.ve-draggable-tabs::-webkit-scrollbar {
+  display: none;
+}

package/src/Editor/userDefinedHandlersAndOpts.js

@@ -0,0 +1,56 @@
+export const userDefinedHandlersAndOpts = [
+  "defaultLinkedOligoMessage",
+  "allowMultipleFeatureDirections",
+  "getAdditionalEditAnnotationComps",
+  "getAdditionalCreateOpts",
+  "getLinkedOligoLink",
+  "additionalTopRightToolbarButtons",
+  "getCustomAutoAnnotateList",
+  "allowPartsToOverlapSelf",
+  "allowPrimerBasesToBeEdited",
+  "truncateLabelsThatDoNotFit",
+  "smartCircViewLabelRender",
+  "onConfigureFeatureTypesClick",
+  "allPartTags",
+  "editTagsLink",
+  "readOnly",
+  "shouldAutosave",
+  "hideSingleImport",
+  "beforeAnnotationCreate",
+  "disableSetReadOnly",
+  "showReadOnly",
+  "showCircularity",
+  "onHiddenEnzymeAdd",
+  "showMoleculeType",
+  "showAvailability",
+  "showCicularViewInternalLabels",
+  "showGCContentByDefault",
+  "GCDecimalDigits",
+  "onlyShowLabelsThatDoNotFit",
+  "fullscreenMode",
+  "maxAnnotationsToDisplay",
+  "onNew",
+  "onImport",
+  "onSave",
+  "onSaveAs",
+  "alwaysAllowSave",
+  "generatePng",
+  "onRename",
+  "getVersionList",
+  "getSequenceAtVersion",
+  "onDuplicate",
+  "onSelectionOrCaretChanged",
+  "beforeSequenceInsertOrDelete",
+  "enzymeManageOverride",
+  "enzymeGroupsOverride",
+  "additionalEnzymes",
+  "onDelete",
+  "onCopy",
+  "autoAnnotateFeatures",
+  "autoAnnotateParts",
+  "autoAnnotatePrimers",
+  "onCreateNewFromSubsequence",
+  "onPreviewModeFullscreenClose",
+  "onPaste",
+  "menuFilter"
+];

package/src/EnzymeViewer/index.js

@@ -0,0 +1,81 @@
+import { Icon } from "@blueprintjs/core";
+import React from "react";
+import copyToClipboard from "copy-to-clipboard";
+
+import RowItem from "../RowItem";
+import "./style.css";
+import classNames from "classnames";
+import { noop } from "lodash";
+
+export default ({
+  extraClasses = "",
+  sequence = "nnnnn",
+  paddingEnd = "-------",
+  paddingStart = "-------",
+  reverseSnipPosition,
+  forwardSnipPosition,
+  charWidth = 13,
+  noCopy
+}) => {
+  const seqPlusPadding = paddingStart + sequence + paddingEnd;
+
+  return (
+    <div
+      style={{ cursor: noCopy ? "" : "pointer", position: "relative" }}
+      onClick={
+        noCopy
+          ? noop
+          : () => {
+              copyToClipboard(sequence);
+              window.toastr.success("Recognition Site Copied");
+            }
+      }
+      className={classNames("enzyme-rowitem", extraClasses, { noCopy })}
+    >
+      <Icon
+        className="tg-icon-duplicate-inner"
+        style={{ display: "none", position: "absolute", top: 3, left: 3 }}
+        icon="duplicate"
+      ></Icon>
+      <RowItem
+        {...{
+          charWidth,
+          tickSpacing: 1,
+          annotationVisibility: {
+            cutsites: true,
+            cutsiteLabels: false,
+            axis: false,
+            reverseSequence: true,
+            sequence: true
+          },
+          annotationLabelVisibility: {
+            cutsites: false
+          },
+          sequenceLength: seqPlusPadding.length,
+          bpsPerRow: seqPlusPadding.length,
+          row: {
+            sequence: seqPlusPadding,
+            start: 0,
+            end: seqPlusPadding.length - 1,
+            cutsites: {
+              fake1: {
+                annotation: {
+                  recognitionSiteRange: {
+                    start: paddingStart.length,
+                    end: paddingStart.length + sequence.length - 1
+                  },
+                  topSnipBeforeBottom:
+                    forwardSnipPosition < reverseSnipPosition,
+                  bottomSnipPosition: paddingStart.length + reverseSnipPosition,
+                  topSnipPosition: paddingStart.length + forwardSnipPosition,
+                  id: "fake1",
+                  restrictionEnzyme: {}
+                }
+              }
+            }
+          }
+        }}
+      />
+    </div>
+  );
+};

package/src/EnzymeViewer/style.css

@@ -0,0 +1,6 @@
+.enzyme-rowitem {
+  z-index: 1;
+}
+.enzyme-rowitem:not(.noCopy):hover .tg-icon-duplicate-inner {
+  display: block !important;
+}