@nightingale-elements/nightingale-msa - npm Package Compare versions

Comparing version 4.2.2-alpha.0 to 4.3.0-4.4.0-alpha.0.0

dist/index.d.ts

 import NightingaleMSA from "./nightingale-msa";
-export type * from "./types/types";
 export default NightingaleMSA;
 //# sourceMappingURL=index.d.ts.map

dist/nightingale-msa.d.ts

@@ -7,8 +7,8 @@ import "./components/Canvas/SequenceViewer";
 declare class NightingaleMSA extends NightingaleMSA_base {
-    colorScheme?: string;
-    labelWidth?: number;
-    tileHeight?: number;
-    activeLabel?: string;
-    sampleSize?: number;
-    overlayConservtion?: boolean;
+    colorScheme: string;
+    labelWidth: number;
+    tileHeight: number;
+    activeLabel: string;
+    sampleSize: number;
+    overlayConservtion: boolean;
     worker: Worker;
@@ -28,7 +28,2 @@ private sequenceViewer?;
 export default NightingaleMSA;
-declare global {
-    interface HTMLElementTagNameMap {
-        "nightingale-msa": NightingaleMSA;
-    }
-}
 //# sourceMappingURL=nightingale-msa.d.ts.map

package.json

 {
   "name": "@nightingale-elements/nightingale-msa",
-  "version": "4.2.2-alpha.0",
+  "version": "4.3.0-4.4.0-alpha.0.0",
   "files": [
@@ -32,4 +32,4 @@ "dist",
   "dependencies": {
-    "@nightingale-elements/nightingale-new-core": "^4.2.2-alpha.0",
-    "d3": "7.8.3",
+    "@nightingale-elements/nightingale-new-core": "^4.3.0-4.4.0-alpha.0.0",
+    "d3": "7.8.5",
     "shallowequal": "1.1.0"
@@ -40,3 +40,3 @@ },
   },
-  "gitHead": "e4511f5ac19c04d89db334172e541bc69f222501"
+  "gitHead": "cf26b5f2042eedb559f1ea7136e095414c1f4eca"
 }

src/components/Canvas/CanvasCache.ts

@@ -57,3 +57,3 @@ import * as shallowEqual from "shallowequal";
         Object.keys(this.cache),
-        (k) => this.cache[k].insertionTime
+        (k) => this.cache[k].insertionTime,
       );
@@ -60,0 +60,0 @@ if (oldestKey) delete this.cache[oldestKey];

src/components/Canvas/CanvasTilingGrid.ts

@@ -87,3 +87,3 @@ import CanvasCache from "./CanvasCache";
         tileWidth,
-        tileHeight
+        tileHeight,
       );
@@ -149,3 +149,3 @@ }
       this.props.tileHeight / 2 + 1,
-      this.props.tileWidth
+      this.props.tileWidth,
     );
@@ -152,0 +152,0 @@ }

src/components/Canvas/DraggingComponent.ts

@@ -20,3 +20,3 @@ import { html } from "lit";
 abstract class DraggingComponent extends withZoom(
-  withPosition(withDimensions(NightingaleElement))
+  withPosition(withDimensions(NightingaleElement)),
 ) {
@@ -62,3 +62,3 @@ "use-ctrl-to-zoom" = true;
     newPosition?: RawPosition,
-    oldPosition?: RawPosition
+    oldPosition?: RawPosition,
   ): void;
@@ -78,3 +78,3 @@
       (buffer) =>
-        buffer.getContext("2d", { alpha: "false" }) as CanvasRenderingContext2D
+        buffer.getContext("2d", { alpha: "false" }) as CanvasRenderingContext2D,
     );
@@ -81,0 +81,0 @@ // init

src/components/Canvas/FakeScroll.ts

@@ -70,3 +70,3 @@ import { LitElement, html } from "lit";
           },
-        })
+        }),
       );
@@ -77,3 +77,3 @@ };
     overflow: "hidden" | "auto" | "scroll",
-    { withX = false, withY = false }
+    { withX = false, withY = false },
   ) {
@@ -80,0 +80,0 @@ let show = false;

src/components/Canvas/SequenceViewer.ts

@@ -100,3 +100,3 @@ import { property, state, customElement } from "lit/decorators.js";
         0,
-        (this.sequences?.length || 1) - 1
+        (this.sequences?.length || 1) - 1,
       ),
@@ -106,3 +106,3 @@ currentViewSequencePosition: clamp(
         0,
-        this.sequences?.maxLength || 0
+        this.sequences?.maxLength || 0,
       ),
@@ -220,3 +220,3 @@ ...position,
         console.error(
-          "Failed to draw scene because couldn't get the tile positions"
+          "Failed to draw scene because couldn't get the tile positions",
         );
@@ -237,3 +237,3 @@ return;
           bubbles: true,
-        })
+        }),
       );
@@ -245,3 +245,3 @@ }
         console.log(
-          `Took ${elapsed} msecs to redraw for ${positions.startXTile} ${positions.startYTile} (redrawnTiles: ${this.redrawnTiles})`
+          `Took ${elapsed} msecs to redraw for ${positions.startXTile} ${positions.startYTile} (redrawnTiles: ${this.redrawnTiles})`,
         );
@@ -257,15 +257,15 @@ }
       0,
-      this.position.currentViewSequencePosition - this.props.cacheElements
+      this.position.currentViewSequencePosition - this.props.cacheElements,
     );
     const startYTile = Math.max(
       0,
-      this.position.currentViewSequence - this.props.cacheElements
+      this.position.currentViewSequence - this.props.cacheElements,
     );
     const endYTile = Math.min(
       this.sequences.length,
-      startYTile + this.stats.nrYTiles + 2 * this.props.cacheElements
+      startYTile + this.stats.nrYTiles + 2 * this.props.cacheElements,
     );
     const endXTile = Math.min(
       this.sequences.maxLength,
-      startXTile + this.stats.nrXTiles + 2 * this.props.cacheElements
+      startXTile + this.stats.nrXTiles + 2 * this.props.cacheElements,
     );
@@ -337,3 +337,3 @@ return { startXTile, startYTile, endXTile, endYTile };
           width,
-          height
+          height,
         );
@@ -405,3 +405,3 @@ }
       regionWidth,
-      regionHeight
+      regionHeight,
     );
@@ -433,3 +433,3 @@ }
       0,
-      sequences.length - 1
+      sequences.length - 1,
     );
@@ -441,3 +441,3 @@ const sequence = sequences[seqNr];
       0,
-      sequence.sequence.length - 1
+      sequence.sequence.length - 1,
     );
@@ -463,3 +463,3 @@ return {
           sequencePosition.i >= feature.sequences.from &&
-          sequencePosition.i <= feature.sequences.to
+          sequencePosition.i <= feature.sequences.to,
       )
@@ -489,3 +489,3 @@ .map((feature) => feature.id || "");
           detail: data,
-        })
+        }),
       );
@@ -579,3 +579,3 @@ }
     this.residueTileCache.updateTileSpecs(
-      residueTileSpecs as ResidueTileOptions
+      residueTileSpecs as ResidueTileOptions,
     );
@@ -582,0 +582,0 @@ }

src/components/Labels.ts

@@ -7,7 +7,7 @@ import { LitElement, html, PropertyValues } from "lit";
 class Labels extends LitElement {
-  @property()
+  @property({ type: Number })
   width = 0;
-  @property()
+  @property({ type: Number })
   height = 0;
-  @property()
+  @property({ type: Number })
   y = 0;
@@ -61,3 +61,3 @@ @state()
                   detail: { label },
-                })
+                }),
               );
@@ -67,3 +67,3 @@ }}
             ${label}
-          </li>`
+          </li>`,
       )}
@@ -70,0 +70,0 @@ </ul>`;

src/index.ts

 import NightingaleMSA from "./nightingale-msa";
-export type * from "./types/types";
 export default NightingaleMSA;

src/nightingale-msa.ts

@@ -17,10 +17,9 @@ import { customElement, property } from "lit/decorators.js";
 import { Region, SequencesMSA } from "./types/types";
+// import ConservationWorker from "web-worker:./workers/conservation.worker";
 
-const DEAFULT_TILE_HEIGHT = 20;
-const DEAFULT_COLOR_SCHEME = "clustal2";
 @customElement("nightingale-msa")
 class NightingaleMSA extends withManager(
   withResizable(
-    withHighlight(withMargin(withDimensions(withPosition(NightingaleElement))))
-  )
+    withHighlight(withMargin(withDimensions(withPosition(NightingaleElement)))),
+  ),
 ) {
@@ -30,3 +29,3 @@ @property({
   })
-  colorScheme?: string = DEAFULT_COLOR_SCHEME;
+  colorScheme = "clustal2";
   @property({
@@ -36,3 +35,3 @@ type: Number,
   })
-  labelWidth?: number = 0;
+  labelWidth = 0;
   @property({
@@ -42,3 +41,3 @@ type: Number,
   })
-  tileHeight?: number = DEAFULT_TILE_HEIGHT;
+  tileHeight = 20;
   @property({
@@ -48,3 +47,3 @@ attribute: "active-label",
   })
-  activeLabel?: string = "";
+  activeLabel = "";
   @property({
@@ -54,3 +53,3 @@ type: Number,
   })
-  sampleSize?: number = 20;
+  sampleSize = 20;
   @property({
@@ -60,7 +59,7 @@ type: Boolean,
   })
-  overlayConservtion?: boolean = false;
+  overlayConservtion = false;
 
   worker = new Worker(
-    new URL("./workers/conservation.worker.ts", import.meta.url)
-  );
+    new URL("./workers/conservation.worker.ts", import.meta.url),
+  ); //new ConservationWorker();
 
@@ -77,3 +76,3 @@ private sequenceViewer?: SequenceViewerComponent | null;
           detail: e.data,
-        })
+        }),
       );
@@ -131,4 +130,2 @@ if (e.data.progress === 1) {
     };
-    const labelWidth = this.labelWidth || 0;
-    const tileHeight = this.tileHeight || DEAFULT_TILE_HEIGHT;
     return html`
@@ -139,8 +136,8 @@ ${this["margin-top"] > 0
       <div style=${object2style(containerStyle)}>
-        ${labelWidth > 0
+        ${this.labelWidth > 0
           ? html`<msa-labels
-              width=${labelWidth}
+              width=${this.labelWidth}
               height=${this.height}
-              tile-height=${tileHeight}
-              active-label=${this.activeLabel || ""}
+              tile-height=${this.tileHeight}
+              active-label=${this.activeLabel}
             ></msa-labels>`
@@ -152,5 +149,5 @@ : ""}
           height=${this.height}
-          width=${this.getWidthWithMargins() - labelWidth}
-          color-scheme=${this.colorScheme || DEAFULT_COLOR_SCHEME}
-          tile-height=${tileHeight}
+          width=${this.getWidthWithMargins() - this.labelWidth}
+          color-scheme=${this.colorScheme}
+          tile-height=${this.tileHeight}
           display-start=${this["display-start"] || 0}
@@ -183,3 +180,3 @@ display-end=${this["display-end"] || 0}
           borderColor: this["highlight-color"],
-        } as Region)
+        }) as Region,
     );
@@ -209,7 +206,1 @@ }
 export default NightingaleMSA;
-
-declare global {
-  interface HTMLElementTagNameMap {
-    "nightingale-msa": NightingaleMSA;
-  }
-}

src/utils/ColorScheme.ts

@@ -27,3 +27,3 @@ import schemes from "../colorschemes";
         position,
-        this.conservation
+        this.conservation,
       );
@@ -30,0 +30,0 @@ }

src/utils/mouse.ts

@@ -5,3 +5,3 @@ import { RawPosition } from "../types/types";
   static relative = function (
-    event: MouseEvent | TouchEvent | Touch
+    event: MouseEvent | TouchEvent | Touch,
   ): RawPosition {
@@ -32,3 +32,3 @@ if ((event as TouchEvent).changedTouches !== undefined)
   static absolute = function (
-    event: MouseEvent | TouchEvent | Touch
+    event: MouseEvent | TouchEvent | Touch,
   ): RawPosition {
@@ -35,0 +35,0 @@ if ((event as TouchEvent).changedTouches !== undefined)

src/workers/conservation.worker.ts

@@ -11,3 +11,3 @@ import { SequencesMSA } from "../types/types";
   sampleSize: number | null = null,
-  isWorker = false
+  isWorker = false,
 ) => {
@@ -14,0 +14,0 @@ const length =

No alert changes

Worsened metrics

Total package byte prevSize

641283

decreased by-0.3%

Number of package files

118

decreased by-1.67%

Lines of code

3555

decreased by-2.68%

Dependency changes

• - Removedd3@7.8.3(transitive)

• Updated@nightingale-elements/nightingale-new-core@^4.3.0-4.4.0-alpha.0.0

• Updatedd3@7.8.5