npm - @rcsb/rcsb-saguaro-app - Versions diffs - 6.2.5-dev-js-seqcoord.2 → 6.2.6 - Mend

@rcsb/rcsb-saguaro-app 6.2.5-dev-js-seqcoord.2 → 6.2.6

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 (521) hide show

package/lib/RcsbGraphQL/RcsbQueryMultipleEntriesProperties.js CHANGED Viewed

@@ -19,4 +19,3 @@ export class RcsbQueryMultipleEntriesProperties {
         });
     }
 }
-//# sourceMappingURL=RcsbQueryMultipleEntriesProperties.js.map

package/lib/RcsbGraphQL/RcsbQueryMultipleInstanceSequences.js CHANGED Viewed

@@ -19,4 +19,3 @@ export class RcsbQueryMultipleInstanceSequences {
         });
     }
 }
-//# sourceMappingURL=RcsbQueryMultipleInstanceSequences.js.map

package/lib/RcsbGroupWeb/RcsbGroupBuilder.js CHANGED Viewed

@@ -26,4 +26,3 @@ export const searchQueryContextManager = {
         return SearchQueryContextManager.subscribe(f);
     }
 };
-//# sourceMappingURL=RcsbGroupBuilder.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartAdditionalProperties.js CHANGED Viewed

	@@ -1,2 +1 @@
1 1	export {};
2	- //# sourceMappingURL=GroupChartAdditionalProperties.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartEvents.js CHANGED Viewed

@@ -126,4 +126,3 @@ export var GroupChartEvents;
         }
     }
 })(GroupChartEvents || (GroupChartEvents = {}));
-//# sourceMappingURL=GroupChartEvents.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartLayout.js CHANGED Viewed

@@ -32,4 +32,3 @@ function histogramChart(attributeName, chart) {
 function barChart(attributeName, chart) {
     return (_jsx("div", { id: `chart:${chart[0].attributeName}`, children: _jsx(BarChartComponent, { data: chart.map(c => c.data), chartConfig: chart[0].chartConfig, attributeName: attributeName }) }));
 }
-//# sourceMappingURL=GroupChartLayout.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/GroupChartTools.js CHANGED Viewed

@@ -89,4 +89,3 @@ export var GroupChartMap;
         });
     }
 })(GroupChartMap || (GroupChartMap = {}));
-//# sourceMappingURL=GroupChartTools.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbGroupChartComponent.js CHANGED Viewed

@@ -47,4 +47,3 @@ function applyLayoutConfig(layout, chartMap, layoutConfig) {
         }
     });
 }
-//# sourceMappingURL=RcsbGroupChartComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupChart/RcsbStatsChartComponent.js CHANGED Viewed

@@ -34,4 +34,3 @@ export class RcsbStatsChartComponent extends React.Component {
         });
     }
 }
-//# sourceMappingURL=RcsbStatsChartComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupContent/RcsbGroupContentComponent.js CHANGED Viewed

@@ -74,4 +74,3 @@ export class RcsbGroupContentComponent extends React.Component {
         };
     }
 }
-//# sourceMappingURL=RcsbGroupContentComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupDisplay.js CHANGED Viewed

@@ -39,4 +39,3 @@ export class RcsbGroupDisplay {
         createRoot(e).render(_jsx(RcsbResidueChartComponent, { granularity: granularity, rcsbId: rcsbId, facetLayoutGrid: facetLayoutGrid, chartDisplayConfig: chartDisplayConfig }));
     }
 }
-//# sourceMappingURL=RcsbGroupDisplay.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/Components/Slider.js CHANGED Viewed

@@ -17,4 +17,3 @@ export class Slider extends React.Component {
 export function actionIcon(action) {
     return (_jsx("span", { style: { cursor: "pointer" }, className: "h1 user-select-none", children: action == "prev" ? "❮" : "❯" }));
 }
-//# sourceMappingURL=Slider.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMemberItem.js CHANGED Viewed

@@ -67,4 +67,3 @@ function imageIcon(ei) {
                     transform: "translate(-50%, -50%)"
                 }, className: `fa ${isExperimental ? "fa-flask" : "fa-desktop"}` }) }) }));
 }
-//# sourceMappingURL=GroupMemberItem.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMembersGrid.js CHANGED Viewed

@@ -96,4 +96,3 @@ function parseItems(groupProvenanceId, propsList) {
         :
             propsList.map((o) => (o.instances)).flat().map((o) => (Object.assign(Object.assign({}, o), { molecularWeight: o.entityMolecularWeight })));
 }
-//# sourceMappingURL=GroupMembersGrid.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/RcsbGroupMembersComponent.js CHANGED Viewed

@@ -90,4 +90,3 @@ function mod(n, p) {
     const r = n % p;
     return r < 0 ? p + r : r;
 }
-//# sourceMappingURL=RcsbGroupMembersComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/RcsbGroupSeacrhQueryComponent.js CHANGED Viewed

@@ -84,4 +84,3 @@ class RcsbGroupSearchQueryComponent extends React.Component {
         ]);
     }
 }
-//# sourceMappingURL=RcsbGroupSeacrhQueryComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupSeacrhQuery/SearchQueryContextManager.js CHANGED Viewed

@@ -89,4 +89,3 @@ SearchQueryContextManager.attributeList = [];
 SearchQueryContextManager.currentSearchQuery = new DataContainer();
 SearchQueryContextManager.groupProvenanceId = new DataContainer();
 SearchQueryContextManager.groupId = new DataContainer();
-//# sourceMappingURL=SearchQueryContextManager.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/RcsbResidueChartComponent.js CHANGED Viewed

@@ -30,4 +30,3 @@ export class RcsbResidueChartComponent extends React.Component {
         });
     }
 }
-//# sourceMappingURL=RcsbResidueChartComponent.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/DistributionChartFactoryImpl/DistributionChartFactory.js CHANGED Viewed

@@ -32,4 +32,3 @@ export class DistributionChartFactory {
         };
     }
 }
-//# sourceMappingURL=DistributionChartFactory.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/MultipleTrackDistributionFactory.js CHANGED Viewed

@@ -30,4 +30,3 @@ export class MultipleTrackDistributionFactory {
         };
     }
 }
-//# sourceMappingURL=MultipleTrackDistributionFactory.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/NumericalTrackDistributionFactory.js CHANGED Viewed

@@ -35,4 +35,3 @@ export class NumericalTrackDistributionFactory {
         };
     }
 }
-//# sourceMappingURL=NumericalTrackDistributionFactory.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryImpl/TrackDistributionFactory.js CHANGED Viewed

@@ -19,4 +19,3 @@ export class TrackDistributionFactory {
         }
     }
 }
-//# sourceMappingURL=TrackDistributionFactory.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/ResidueDistributionFactoryInterface.js CHANGED Viewed

	@@ -1,2 +1 @@
1 1	export {};
2	- //# sourceMappingURL=ResidueDistributionFactoryInterface.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartFactories/TrackBlockFactoryImpl/TrackBlockFactory.js CHANGED Viewed

@@ -17,4 +17,3 @@ export class TrackBlockFactory {
         return Array.from(trackMap.entries()).map(e => ({ blockType: e[0], tracks: e[1] }));
     }
 }
-//# sourceMappingURL=TrackBlockFactory.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/Helper.js CHANGED Viewed

@@ -20,4 +20,3 @@ export var Helper;
         });
     }
 })(Helper || (Helper = {}));
-//# sourceMappingURL=Helper.js.map

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbResidueChart/ResidueChartTools/ResidueChartTools.js CHANGED Viewed

@@ -1,6 +1,6 @@
 import { __awaiter } from "tslib";
 import { AnnotationCollector } from "../../../../RcsbCollectTools/AnnotationCollector/AnnotationCollector";
-import { SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { filter, interfaceAnnotations } from "../../../../RcsbFvWeb/RcsbFvModule/RcsbFvInterface";
 import * as rcm from "../../../../RcsbAnnotationConfig/RcsbResidueConfig.ac.json";
 import { AnnotationBlockManager } from "../../../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager";
@@ -53,7 +53,7 @@ export var ResidueChartTools;
             const annotationsRequestContext = {
                 queryId: instanceId,
                 reference: SequenceReference.PdbInstance,
-                sources: [AnnotationReference.PdbEntity, AnnotationReference.PdbInstance, AnnotationReference.Uniprot, AnnotationReference.PdbInterface],
+                sources: [Source.PdbEntity, Source.PdbInstance, Source.Uniprot, Source.PdbInterface],
                 annotationGenerator: interfaceAnnotations,
                 annotationFilter: filter
             };
@@ -85,4 +85,3 @@ export var ResidueChartTools;
     const annotationCollector = new AnnotationCollector();
     const alignmentCollector = new AlignmentCollector();
 })(ResidueChartTools || (ResidueChartTools = {}));
-//# sourceMappingURL=ResidueChartTools.js.map

package/lib/RcsbQueries/Borrego/.graphqlconfig ADDED Viewed

@@ -0,0 +1,15 @@
+{
+  "name": "Untitled GraphQL Schema",
+  "schemaPath": "schema.graphql",
+  "extensions": {
+    "endpoints": {
+      "Default GraphQL Endpoint": {
+        "url": "https://1d-coordinates.rcsb.org/graphql",
+        "headers": {
+          "user-agent": "JS GraphQL"
+        },
+        "introspect": false
+      }
+    }
+  }
+}

package/lib/RcsbQueries/Borrego/QueryAlignments.graphql CHANGED Viewed

@@ -1,12 +1,12 @@
-query QueryAlignment($queryId: String!, $from: SequenceReference!, $to:SequenceReference!, $range:[Int!]){
-    alignments(
+query QueryAlignment($queryId: String!, $from: SequenceReference, $to:SequenceReference, $range:[Int]){
+    alignment(
         queryId:$queryId
         from:$from
         to:$to
         range:$range
     ){
         query_sequence
-        target_alignments {
+        target_alignment {
             target_id
             orientation
             target_sequence

package/lib/RcsbQueries/Borrego/QueryAnnotations.graphql CHANGED Viewed

@@ -1,10 +1,4 @@
-query QueryAnnotations(
-    $queryId: String!,
-    $reference: SequenceReference!,
-    $sources:[AnnotationReference!]!,
-    $range:[Int!],
-    $filters: [AnnotationFilterInput!]
-){
+query QueryAnnotations($queryId: String!, $reference: SequenceReference, $sources:[Source], $range:[Int], $filters: [FilterInput]){
     annotations(
         queryId:$queryId
         reference:$reference

package/lib/RcsbQueries/Borrego/QueryGroupAlignments.graphql CHANGED Viewed

@@ -1,37 +1,42 @@
-query QueryGroupAlignment(
-    $group: GroupReference!,
-    $groupId: String!,
-    $filter: [String!],
-    $first: Int,
-    $after: Int
-){
-    group_alignments(
+query QueryGroupAlignment($group: GroupReference!, $groupId: String!, $filter: [String], $first: Int!, $after: String){
+    group_alignment(
         group: $group
         groupId: $groupId
         filter: $filter
     ){
         alignment_length
-        alignment_logo {
+        alignment_logo{
             symbol
             value
         }
         query_sequence
-        target_alignments(first: $first, offset: $after) {
-            target_id
-            orientation
-            target_sequence
-            coverage {
-                query_coverage
-                query_length
-                target_coverage
-                target_length
+        target_alignment_subset(first: $first, after: $after) {
+            pageInfo{
+                startCursor
+                endCursor
+                hasNextPage
+                hasPreviousPage
             }
-            aligned_regions {
-                query_begin
-                query_end
-                target_begin
-                target_end
-                exon_shift
+            edges{
+                node{
+                    target_id
+                    orientation
+                    target_sequence
+                    coverage {
+                        query_coverage
+                        query_length
+                        target_coverage
+                        target_length
+                    }
+                    aligned_regions {
+                        query_begin
+                        query_end
+                        target_begin
+                        target_end
+                        exon_shift
+                    }
+                }
+                cursor
             }
         }
     }

package/lib/RcsbQueries/Borrego/QueryGroupAlignmentsNoLogo.graphql CHANGED Viewed

@@ -1,32 +1,38 @@
-query QueryGroupAlignmentNoLogo(
-    $group: GroupReference!,
-    $groupId: String!,
-    $filter: [String!],
-    $first: Int!,
-    $after: Int!){
-    group_alignments(
+query QueryGroupAlignmentNoLogo($group: GroupReference!, $groupId: String!, $filter: [String], $first: Int!, $after: String){
+    group_alignment(
         group: $group
         groupId: $groupId
         filter: $filter
     ){
         alignment_length
         query_sequence
-        target_alignments(first: $first, offset: $after) {
-            target_id
-            orientation
-            target_sequence
-            coverage {
-                query_coverage
-                query_length
-                target_coverage
-                target_length
+        target_alignment_subset(first: $first, after: $after) {
+            pageInfo{
+                startCursor
+                endCursor
+                hasNextPage
+                hasPreviousPage
             }
-            aligned_regions {
-                query_begin
-                query_end
-                target_begin
-                target_end
-                exon_shift
+            edges{
+                node{
+                    target_id
+                    orientation
+                    target_sequence
+                    coverage {
+                        query_coverage
+                        query_length
+                        target_coverage
+                        target_length
+                    }
+                    aligned_regions {
+                        query_begin
+                        query_end
+                        target_begin
+                        target_end
+                        exon_shift
+                    }
+                }
+                cursor
             }
         }
     }

package/lib/RcsbQueries/Borrego/QueryGroupAnnotations.graphql CHANGED Viewed

@@ -1,14 +1,10 @@
-query QueryGroupAnnotations(
-    $group: GroupReference!,
-    $groupId: String!,
-    $sources: [AnnotationReference!]!,
-    $filters: [AnnotationFilterInput!]
-){
+query QueryGroupAnnotations($group: GroupReference!, $groupId: String!, $sources:[Source], $filters: [FilterInput], $histogram:Boolean){
     group_annotations(
         group:$group
         groupId:$groupId
         sources:$sources
         filters:$filters
+        histogram:$histogram
     ){
         source
         target_id