fixed mutation type filter counts

Signed-off-by: Onur Sumer <s.onur.sumer@gmail.com>

package.json

@@ -192,7 +192,7 @@
     "react-markdown": "^3.4.1",
     "react-mfb": "^0.6.0",
     "react-motion": "^0.4.7",
-    "react-mutation-mapper": "^0.3.0-beta.5",
+    "react-mutation-mapper": "^0.3.0-beta.11",
     "react-overlays": "0.7.4",
     "react-portal": "^4.2.0",
     "react-rangeslider": "^2.1.0",

src/shared/components/mutationMapper/MutationMapperDataStore.ts

@@ -2,6 +2,7 @@ import * as _ from 'lodash';
 import {action, computed, observable} from "mobx";
 import autobind from "autobind-decorator";
 import {
+    applyDataFiltersOnDatum,
     DataFilter,
     DataFilterType,
     DataStore,
@@ -43,7 +44,7 @@ export default class MutationMapperDataStore
 
     @computed
     public get sortedFilteredGroupedData(): GroupedData {
-        return groupDataByGroupFilters(this.groupFilters, this, this.applyFilter);
+        return groupDataByGroupFilters(this.groupFilters, this.sortedFilteredData, this.applyFilter);
     }
 
     @computed
@@ -105,15 +106,15 @@ export default class MutationMapperDataStore
     {
         super.setFilter((d:Mutation[], filterString?:string, filterStringUpper?:string, filterStringLower?:string) =>
             (!fn || fn(d, filterString, filterStringUpper, filterStringLower)) &&
-            (this.dataFilters.length === 0 || this.dataMainFilter(d[0]))
+            (this.dataFilters.length === 0 || this.dataMainFilter(d))
         );
     }
 
     // override the parent method to always keep the default main filter
     @action
     public resetFilter() {
         super.resetFilter();
-        this.dataFilter = (d:Mutation[]) => (this.dataFilters.length === 0 || this.dataMainFilter(d[0]));
+        this.dataFilter = (d:Mutation[]) => (this.dataFilters.length === 0 || this.dataMainFilter(d));
     }
 
     @action
@@ -160,41 +161,28 @@ export default class MutationMapperDataStore
     }
 
     @autobind
-    public dataMainFilter(mutation: Mutation): boolean
+    public dataMainFilter(d: Mutation[]): boolean
     {
-        return (
-            this.dataFilters.length > 0 &&
-            !this.dataFilters
-                .map(dataFilter => this.applyFilter(dataFilter, mutation))
-                .includes(false)
-        );
+        return applyDataFiltersOnDatum(d, this.dataFilters, this.applyFilter);
     }
 
     @autobind
     public dataSelectFilter(d: Mutation[]): boolean
     {
-        return (
-            this.selectionFilters.length > 0 &&
-            !this.selectionFilters
-                .map(dataFilter => this.applyFilter(dataFilter, d[0]))
-                .includes(false)
-        );
+        return applyDataFiltersOnDatum(d, this.selectionFilters, this.applyFilter);
     }
 
     @autobind
     public dataHighlightFilter(d: Mutation[]): boolean
     {
-        return (
-            this.highlightFilters.length > 0 &&
-            !this.highlightFilters
-                .map(dataFilter => this.applyFilter(dataFilter, d[0]))
-                .includes(false)
-        );
+        return applyDataFiltersOnDatum(d, this.highlightFilters, this.applyFilter);
     }
 
     @autobind
-    public applyFilter(filter: DataFilter, mutation: Mutation): boolean
+    public applyFilter(filter: DataFilter, d: Mutation | Mutation[]): boolean
     {
+        const mutation = _.flatten([d])[0];
+
         if (this.customFilterApplier) {
             // let the custom filter applier decide how to apply the given filter
             return this.customFilterApplier.applyFilter(filter, mutation);
@@ -204,4 +192,11 @@ export default class MutationMapperDataStore
             return filter.type !== DataFilterType.POSITION || filter.values.includes(mutation.proteinPosStart);
         }
     }
+
+    @autobind
+    public applyLazyMobXTableFilter(d: Mutation | Mutation[]): boolean
+    {
+        return !this.filterString || this.dataFilter(
+            [_.flatten([d])[0]], this.filterString.toLowerCase(), this.filterString.toUpperCase());
+    }
 }

src/shared/components/mutationMapper/MutationMapperStore.ts

@@ -3,12 +3,14 @@ import {computed} from "mobx";
 import MobxPromise, {cached, labelMobxPromises} from "mobxpromise";
 
 import {
-    DataFilter, defaultHotspotFilter,
+    applyDataFilters,
+    DataFilterType,
     DefaultMutationMapperDataFetcher,
-    DefaultMutationMapperStore, defaultOncoKbFilter,
+    DefaultMutationMapperStore,
     getMutationsToTranscriptId,
+    groupDataByProteinImpactType,
     groupOncoKbIndicatorDataByMutations,
-    IHotspotIndex, isHotspot
+    IHotspotIndex
 } from "react-mutation-mapper";
 
 import genomeNexusClient from "shared/api/genomeNexusClientInstance";
@@ -153,6 +155,23 @@ export default class MutationMapperStore extends DefaultMutationMapperStore
         }
     }
 
+    @computed
+    protected get mutationsGroupedByProteinImpactType()
+    {
+        const filtersWithoutProteinImpactTypeFilter =
+            this.dataStore.dataFilters.filter(f => f.type !== DataFilterType.PROTEIN_IMPACT_TYPE);
+
+        // apply filters excluding the protein impact type filters
+        // this prevents number of unchecked protein impact types from being counted as zero
+        let sortedFilteredData = applyDataFilters(
+            this.dataStore.allData, filtersWithoutProteinImpactTypeFilter, this.dataStore.applyFilter);
+
+        // also apply lazy mobx table search filter
+        sortedFilteredData = sortedFilteredData.filter(m => this.dataStore.applyLazyMobXTableFilter(m));
+
+        return groupDataByProteinImpactType(sortedFilteredData);
+    }
+
     @computed get processedMutationData(): Mutation[][] {
         // just convert Mutation[] to Mutation[][]
         return (this.mutationData.result || []).map(mutation => [mutation]);

yarn.lock

@@ -3472,10 +3472,10 @@ caseless@~0.12.0:
   resolved "https://registry.yarnpkg.com/caseless/-/caseless-0.12.0.tgz#1b681c21ff84033c826543090689420d187151dc"
   integrity sha1-G2gcIf+EAzyCZUMJBolCDRhxUdw=
 
-cbioportal-frontend-commons@^0.0.22:
-  version "0.0.22"
-  resolved "https://registry.yarnpkg.com/cbioportal-frontend-commons/-/cbioportal-frontend-commons-0.0.22.tgz#6a547913adadf2ae2de08c2ca31f4d5103a409ed"
-  integrity sha512-ECWVbXvkqF0msXcrcDXN1MmQ1f1cfi6/++IkE4ThpSuxNmK08/BsXbYZCqDof42v70yN1auXEbhs3jWNDjHk1g==
+cbioportal-frontend-commons@^0.0.23:
+  version "0.0.23"
+  resolved "https://registry.yarnpkg.com/cbioportal-frontend-commons/-/cbioportal-frontend-commons-0.0.23.tgz#1bd3f2d2a59f5b9b718eb66e862e9ca374a22cf8"
+  integrity sha512-6jdSgduNDCiJuXW05Of/eC6V3JVrEUcOWtao/tex0PdG6nAV0F5H+QeVIkiQ6GVF21LSrB9Loc+vrVklXOmWXQ==
   dependencies:
     autobind-decorator "^2.1.0"
     babel-polyfill "^6.22.0"
@@ -12623,13 +12623,13 @@ react-motion@^0.5.2:
     prop-types "^15.5.8"
     raf "^3.1.0"
 
-react-mutation-mapper@^0.3.0-beta.5:
-  version "0.3.0-beta.5"
-  resolved "https://registry.yarnpkg.com/react-mutation-mapper/-/react-mutation-mapper-0.3.0-beta.5.tgz#eea4d9a94414a3e43a1251d2b5cbe95c93de5514"
-  integrity sha512-MqcFrFSwCfYcQFjxS581X3D+XKCqSYural4dS1OUVnLPIennmHAUVzx0usZAXX1vh1ykI7ZbEumuWJ17knrRFA==
+react-mutation-mapper@^0.3.0-beta.11:
+  version "0.3.0-beta.11"
+  resolved "https://registry.yarnpkg.com/react-mutation-mapper/-/react-mutation-mapper-0.3.0-beta.11.tgz#7a7f876e574b593943b2e98435b31f0a061c0ef8"
+  integrity sha512-Whx0gJrw3ivs3wYsamvwpSYO4EeLsZXlGQdfNy3Npz7kINcM+Kthzup6JIxDhMs/5PDSyBsVeVWvlgxQ0YEnfQ==
   dependencies:
     autobind-decorator "^2.4.0"
-    cbioportal-frontend-commons "^0.0.21"
+    cbioportal-frontend-commons "^0.0.23"
     classnames "^2.2.6"
     jquery "^3.3.1"
     lodash "^4.17.11"