@genspectrum/dashboard-components 0.11.6 → 0.11.7

package/dist/components.d.ts

@@ -481,6 +481,29 @@ export declare class MutationFilterComponent extends PreactLitAdapter {
  *
  * The proportion interval filter can be used to filter the displayed mutations on client side.
  *
+ * #### Jaccard Similarity
+ *
+ * If the `baselineLapisFilter` attribute is set,
+ * the [Jaccard similarity](https://en.wikipedia.org/wiki/Jaccard_index) is computed for each mutation.
+ * It is computed as `variantWithMutationCount / (variantCount + mutationCount - variantWithMutationCount)`,
+ * - `variantCount` is the number of sequences of the variant (i.e. the number of sequences that match the `lapisFilter`),
+ * - `mutationCount` is the number of sequences with the mutation
+ *    (i.e. the number of sequences matching the `baselineLapisFilter` that have the mutation),
+ * - `variantWithMutationCount` is the number of sequences that belong to the variant and have the mutation
+ *    (i.e. the `count` value that is shown in the table).
+ *
+ * Typically, this is useful when you query mutations of a certain "variant"
+ * (i.e. a certain lineage or a certain set of mutations).
+ * Then the `baselineLapisFilter` should be the `lapisFilter` but without the lineage or mutations.
+ *
+ * For example:
+ * You are interested in a certain lineage in a certain country: `lapisFilter={country: 'Switzerland', linage: 'XY.1.2.3'}`.
+ * Then the "baseline" should be the same filter but without the lineage: `baselineLapisFilter={country: 'Switzerland'}`.
+ *
+ * Computing the Jaccard similarity is not always meaningful, because you might not have a "variant"
+ * (e.g. when you only query for a certain country).
+ * In this case you can simply omit the `baselineLapisFilter`.
+ *
  * ### Grid View
  *
  * The grid view shows the proportion of each sequence symbol (nucleotide or amino acid) for each position that has a mutation.
@@ -501,6 +524,17 @@ export declare class MutationsComponent extends PreactLitAdapterWithGridJsStyles
         nucleotideInsertions?: string[];
         aminoAcidInsertions?: string[];
     };
+    /**
+     * LAPIS filter to select the mutation counts that are used to compute the Jaccard similarity.
+     * If not provided, the Jaccard similarity is not computed.
+     * For details, see the [Jaccard Similarity](#jaccard-similarity) section in the component description.
+     */
+    baselineLapisFilter: (Record<string, string | string[] | number | null | boolean | undefined> & {
+        nucleotideMutations?: string[];
+        aminoAcidMutations?: string[];
+        nucleotideInsertions?: string[];
+        aminoAcidInsertions?: string[];
+    }) | undefined;
     /**
      * The type of the sequence for which the mutations should be shown.
      */
@@ -1331,7 +1365,7 @@ declare global {
 
 declare global {
     interface HTMLElementTagNameMap {
-        'gs-mutations-over-time': MutationsOverTimeComponent;
+        'gs-sequences-by-location': SequencesByLocationComponent;
     }
 }
 
@@ -1339,7 +1373,7 @@ declare global {
 declare global {
     namespace JSX {
         interface IntrinsicElements {
-            'gs-mutations-over-time': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
+            'gs-sequences-by-location': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
         }
     }
 }
@@ -1347,7 +1381,7 @@ declare global {
 
 declare global {
     interface HTMLElementTagNameMap {
-        'gs-sequences-by-location': SequencesByLocationComponent;
+        'gs-statistics': StatisticsComponent;
     }
 }
 
@@ -1355,7 +1389,7 @@ declare global {
 declare global {
     namespace JSX {
         interface IntrinsicElements {
-            'gs-sequences-by-location': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
+            'gs-statistics': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
         }
     }
 }
@@ -1363,7 +1397,7 @@ declare global {
 
 declare global {
     interface HTMLElementTagNameMap {
-        'gs-statistics': StatisticsComponent;
+        'gs-mutations-over-time': MutationsOverTimeComponent;
     }
 }
 
@@ -1371,7 +1405,7 @@ declare global {
 declare global {
     namespace JSX {
         interface IntrinsicElements {
-            'gs-statistics': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
+            'gs-mutations-over-time': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
         }
     }
 }
@@ -1379,11 +1413,10 @@ declare global {
 
 declare global {
     interface HTMLElementTagNameMap {
-        'gs-date-range-selector': DateRangeSelectorComponent;
+        'gs-text-input': TextInputComponent;
     }
     interface HTMLElementEventMap {
-        'gs-date-range-filter-changed': CustomEvent<Record<string, string>>;
-        'gs-date-range-option-changed': DateRangeOptionChangedEvent;
+        'gs-text-input-changed': CustomEvent<Record<string, string>>;
     }
 }
 
@@ -1391,7 +1424,7 @@ declare global {
 declare global {
     namespace JSX {
         interface IntrinsicElements {
-            'gs-date-range-selector': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
+            'gs-text-input': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
         }
     }
 }
@@ -1399,10 +1432,11 @@ declare global {
 
 declare global {
     interface HTMLElementTagNameMap {
-        'gs-location-filter': LocationFilterComponent;
+        'gs-date-range-selector': DateRangeSelectorComponent;
     }
     interface HTMLElementEventMap {
-        'gs-location-changed': CustomEvent<Record<string, string>>;
+        'gs-date-range-filter-changed': CustomEvent<Record<string, string>>;
+        'gs-date-range-option-changed': DateRangeOptionChangedEvent;
     }
 }
 
@@ -1410,7 +1444,7 @@ declare global {
 declare global {
     namespace JSX {
         interface IntrinsicElements {
-            'gs-location-filter': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
+            'gs-date-range-selector': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
         }
     }
 }
@@ -1418,10 +1452,10 @@ declare global {
 
 declare global {
     interface HTMLElementTagNameMap {
-        'gs-text-input': TextInputComponent;
+        'gs-location-filter': LocationFilterComponent;
     }
     interface HTMLElementEventMap {
-        'gs-text-input-changed': CustomEvent<Record<string, string>>;
+        'gs-location-changed': CustomEvent<Record<string, string>>;
     }
 }
 
@@ -1429,7 +1463,7 @@ declare global {
 declare global {
     namespace JSX {
         interface IntrinsicElements {
-            'gs-text-input': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
+            'gs-location-filter': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
         }
     }
 }