npm - jbrowse-plugin-msaview - Versions diffs - 2.2.7 → 2.2.11 - Mend

jbrowse-plugin-msaview 2.2.7 → 2.2.11

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (65) hide show

package/dist/LaunchMsaView/util.d.ts CHANGED Viewed

@@ -5,6 +5,8 @@ export declare function getTranscriptLength(feature: Feature): {
     mod: number;
 };
 export declare function getId(val?: Feature): string;
+export declare function getMatchableIds(val?: Feature): string[];
+export declare function featureMatchesId(feature: Feature, id: string): boolean;
 export declare function getTranscriptDisplayName(val?: Feature): string;
 export declare function getGeneDisplayName(val?: Feature): string;
 export declare function getSortedTranscriptFeatures(feature: Feature): Feature[];

package/dist/LaunchMsaView/util.js CHANGED Viewed

@@ -25,7 +25,22 @@ export function getTranscriptLength(feature) {
     };
 }
 export function getId(val) {
-    return val?.get('name') ?? val?.get('id') ?? '';
+    return val?.id() ?? '';
+}
+export function getMatchableIds(val) {
+    if (!val) {
+        return [];
+    }
+    const ids = [
+        val.id(),
+        val.get('name'),
+        val.get('id'),
+        val.get('transcript_id'),
+    ].filter((id) => !!id);
+    return [...new Set(ids)];
+}
+export function featureMatchesId(feature, id) {
+    return getMatchableIds(feature).includes(id);
 }
 export function getTranscriptDisplayName(val) {
     return val === undefined
@@ -43,7 +58,8 @@ export function getGeneDisplayName(val) {
             .join(' ');
 }
 export function getSortedTranscriptFeatures(feature) {
-    return getTranscriptFeatures(feature).toSorted((a, b) => getTranscriptLength(b).len - getTranscriptLength(a).len);
+    const transcripts = getTranscriptFeatures(feature);
+    return transcripts.toSorted((a, b) => getTranscriptLength(b).len - getTranscriptLength(a).len);
 }
 export function cleanProteinSequence(seq) {
     return seq.replaceAll('*', '').replaceAll('&', '');

package/dist/LaunchMsaView/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MsaViewPanel/doLaunchBlast.js CHANGED Viewed

@@ -2,23 +2,41 @@ import { makeId, strip } from '../LaunchMsaView/components/util';
 import { cleanProteinSequence } from '../LaunchMsaView/util';
 import { saveBlastResult } from '../utils/blastCache';
 import { launchMSA } from '../utils/msa';
-import { queryBlast } from '../utils/ncbiBlast';
+import { queryBlast, queryBlastFromRid } from '../utils/ncbiBlast';
 import { fetchTaxonomyInfo } from '../utils/taxonomyNames';
 export async function doLaunchBlast({ self, }) {
-    const { baseUrl, blastDatabase, blastProgram, msaAlgorithm, proteinSequence, selectedTranscript, } = self.blastParams;
+    const { baseUrl, blastDatabase, blastProgram, msaAlgorithm, proteinSequence, selectedTranscript, rid: existingRid, } = self.blastParams;
     const cleanedSeq = cleanProteinSequence(proteinSequence);
-    const { hits, rid } = await queryBlast({
-        query: cleanedSeq,
-        blastDatabase,
-        blastProgram,
-        baseUrl,
-        onProgress: arg => {
-            self.setProgress(arg);
-        },
-        onRid: r => {
-            self.setRid(r);
-        },
-    });
+    let hits;
+    let rid;
+    if (existingRid) {
+        self.setRid(existingRid);
+        const result = await queryBlastFromRid({
+            rid: existingRid,
+            baseUrl,
+            onProgress: arg => {
+                self.setProgress(arg);
+            },
+        });
+        hits = result.hits;
+        rid = result.rid;
+    }
+    else {
+        const result = await queryBlast({
+            query: cleanedSeq,
+            blastDatabase,
+            blastProgram,
+            baseUrl,
+            onProgress: arg => {
+                self.setProgress(arg);
+            },
+            onRid: r => {
+                self.setRid(r);
+            },
+        });
+        hits = result.hits;
+        rid = result.rid;
+    }
     self.setProgress('Fetching species taxonomy info...');
     const taxids = hits
         .map(h => h.description[0]?.taxid)
@@ -54,7 +72,10 @@ export async function doLaunchBlast({ self, }) {
         treeMetadata: treeMetadataJson,
         rid,
         geneId: selectedTranscript?.get('parentId'),
-        transcriptId: selectedTranscript?.get('id'),
+        transcriptId: selectedTranscript?.id(),
+        transcriptName: selectedTranscript?.get('name') ?? selectedTranscript?.get('id'),
+        geneName: selectedTranscript?.get('gene_name') ??
+            selectedTranscript?.get('parentId'),
     });
     return {
         ...result,

package/dist/MsaViewPanel/doLaunchBlast.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MsaViewPanel/model.d.ts CHANGED Viewed

@@ -17,6 +17,7 @@ export interface BlastParams {
     blastProgram: string;
     selectedTranscript?: Feature;
     proteinSequence: string;
+    rid?: string;
 }
 /**
  * #stateModel MsaViewPlugin
@@ -539,6 +540,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     seqPosToGlobalCol(rowName: string, seqPos: number): number;
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
 } & {
+    readonly hoveredCell: {
+        rowName: string;
+        col: number;
+        base: string | undefined;
+        seqPos: number | undefined;
+    } | undefined;
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
     readonly tidyInterProAnnotationTypes: Map<string, import("react-msaview").Accession>;

package/dist/MsaViewPanel/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/index.d.ts CHANGED Viewed

@@ -5,9 +5,9 @@ export default class MsaViewPlugin extends Plugin {
     version: string;
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;
-    rootConfigurationSchema(pluginManager: PluginManager): {
-        msa: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
-            datasets: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
+    rootConfigurationSchema: (pluginManager: PluginManager) => {
+        msa: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            datasets: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 datasetId: {
                     type: string;
                     defaultValue: string;
@@ -21,7 +21,7 @@ export default class MsaViewPlugin extends Plugin {
                     defaultValue: string;
                 };
                 adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
-            }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>>;
-        }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>>>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     };
 }

package/dist/index.js CHANGED Viewed

@@ -14,6 +14,27 @@ export default class MsaViewPlugin extends Plugin {
         super(...arguments);
         this.name = 'MsaViewPlugin';
         this.version = version;
+        this.rootConfigurationSchema = (pluginManager) => {
+            return {
+                msa: ConfigurationSchema('MSA', {
+                    datasets: types.maybe(types.array(ConfigurationSchema('MSAEntry', {
+                        datasetId: {
+                            type: 'string',
+                            defaultValue: '',
+                        },
+                        description: {
+                            type: 'string',
+                            defaultValue: '',
+                        },
+                        name: {
+                            type: 'string',
+                            defaultValue: '',
+                        },
+                        adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+                    }))),
+                }),
+            };
+        };
     }
     install(pluginManager) {
         MsaViewF(pluginManager);
@@ -33,27 +54,5 @@ export default class MsaViewPlugin extends Plugin {
             });
         }
     }
-    // @ts-expect-error
-    rootConfigurationSchema(pluginManager) {
-        return {
-            msa: ConfigurationSchema('MSA', {
-                datasets: types.maybe(types.array(ConfigurationSchema('MSAEntry', {
-                    datasetId: {
-                        type: 'string',
-                        defaultValue: '',
-                    },
-                    description: {
-                        type: 'string',
-                        defaultValue: '',
-                    },
-                    name: {
-                        type: 'string',
-                        defaultValue: '',
-                    },
-                    adapter: pluginManager.pluggableConfigSchemaType('adapter'),
-                }))),
-            }),
-        };
-    }
 }
 //# sourceMappingURL=index.js.map

package/dist/index.js.map CHANGED Viewed

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