higlass 1.13.5 → 2.0.0

package/app/scripts/utils/type-guards.js

@@ -1,9 +1,11 @@
+/** @import * as t from '../types' */
+
 /**
- * @param {import('../types').TrackConfig} trackConfig
- * @return {trackConfig is import('../types').CombinedTrackConfig}
+ * @param {t.TrackConfig} trackConfig
+ * @return {trackConfig is t.CombinedTrackConfig}
  */
 export function isCombinedTrackConfig(trackConfig) {
-  return trackConfig.type === 'combined';
+  return 'contents' in trackConfig && trackConfig.type === 'combined';
 }
 
 /**
@@ -23,17 +25,24 @@ export function isObject(obj) {
 }
 
 /**
- * @param {import('../types').TilesetInfo | undefined} info
- * @returns {info is import('../types').LegacyTilesetInfo}
+ * @param {t.TilesetInfo | undefined} info
+ * @returns {info is t.LegacyTilesetInfo}
  */
 export function isLegacyTilesetInfo(info) {
   return isObject(info) && 'max_width' in info;
 }
 
 /**
- * @param {import('../types').TilesetInfo | undefined} info
- * @returns {info is import('../types').ResolutionsTilesetInfo}
+ * @param {t.TilesetInfo | undefined | { error: string }} info
+ * @returns {info is t.ResolutionsTilesetInfo}
  */
 export function isResolutionsTilesetInfo(info) {
   return isObject(info) && 'resolutions' in info;
 }
+/**
+ * @param {t.TilesetInfo | undefined | { error: string }} info
+ * @returns {info is t.TilesetInfo}
+ */
+export function isTilesetInfo(info) {
+  return isObject(info) && !('error' in info);
+}

package/app/scripts/utils/visit-positioned-tracks.js

@@ -1,12 +1,17 @@
 import visitTracks from './visit-tracks';
 
-/** @typedef {{ [Key in import('../types').TrackPosition]: import('../types').TrackConfig[] }} PositionedTracks
+/** @import { TrackConfig, TrackPosition, TrackVisitor } from '../types' */
+
+/**
+ * @template [T=TrackConfig]
+ * @typedef {{ [Key in TrackPosition]?: Array<T> }} PositionedTracks
  */
 
 /**
  * Track visitor for positioned tracks, i.e., tracks with a position.
+ *
  * @param {PositionedTracks} positionedTracks - List of all positioned tracks from the view definition.
- * @param {import('../types').TrackVisitor} visitor - Callback function receiving individual tracks.
+ * @param {TrackVisitor} visitor - Callback function receiving individual tracks.
  * @param {boolean} inclCombinedTracks - If `true` recursively visit combined tracks.
  */
 const visitPositionedTracks = (
@@ -14,11 +19,11 @@ const visitPositionedTracks = (
   visitor,
   inclCombinedTracks = true,
 ) => {
-  /** @type {import('../types').TrackConfig[]} */
+  /** @type {Array<TrackConfig>} */
   const allTracks = [];
 
   for (const [stringPosition, tracks] of Object.entries(positionedTracks)) {
-    /** @type {import('../types').TrackPosition} */
+    /** @type {TrackPosition} */
     // @ts-expect-error - Typings for Object#entries don't have strong inference,
     // might change in the future.
     const position = stringPosition;

package/app/styles/AddTrackPositionMenu.module.scss

@@ -65,6 +65,7 @@
   text-align: center;
   outline: none;
   border: 1px solid $gray;
+  position: relative;
 }
 
 .add-track-position-middle-middle:hover {
@@ -72,6 +73,42 @@
   color: $white;
 }
 
+.add-track-position-middle-middle-full {
+  height: 80px;
+  display: flex;
+  flex-direction: column;
+  justify-content: center;
+  align-items: center;
+}
+
+.add-track-position-middle-middle-upper-right {
+  width: 0;
+  height: 0;
+  border-top: 30px solid $gray;
+  border-left: 30px solid transparent;
+  position: absolute;
+  top: 0;
+  right: 0;
+}
+
+.add-track-position-middle-middle-upper-right:hover {
+  border-top: 30px solid $active;
+}
+
+.add-track-position-middle-middle-lower-left {
+  width: 0;
+  height: 0;
+  border-bottom: 30px solid $gray;
+  border-right: 30px solid transparent;
+  position: absolute;
+  bottom: 0;
+  left: 0;
+}
+
+.add-track-position-middle-middle-lower-left:hover {
+  border-bottom: 30px solid $active;
+}
+
 .add-track-position-bottom-middle {
   min-height: 20px;
   text-align: center;

package/app/styles/HiGlass.module.scss

@@ -28,11 +28,11 @@
 .higlass-canvas {
   position: absolute;
   width: 100%;
-  height: 100%;
 }
 
 .higlass-drawing-surface {
   position: relative;
+  width: 100%
 }
 
 .higlass-svg {
@@ -47,6 +47,8 @@
 .tiled-area {
   display: flex;
   flex-direction: column;
+  width: 100%;
+  height: 100%;
 }
 
 .track-mouseover-menu {

package/app/styles/d3-context-menu.css

@@ -24,7 +24,6 @@
 
 	-webkit-touch-callout: none; /* iOS Safari */
 	-webkit-user-select: none;   /* Chrome/Safari/Opera */
-	-khtml-user-select: none;    /* Konqueror */
 	-moz-user-select: none;      /* Firefox */
 	-ms-user-select: none;       /* Internet Explorer/Edge */
 	user-select: none;

package/app/styles/prism.css

@@ -45,6 +45,7 @@ pre[class*="language-"] {
 }
 
 :not(pre) > code[class*="language-"],
+/* biome-ignore lint/suspicious/noEmptyBlock: vendored */
 pre[class*="language-"] {
 }
 

package/dist/app/schema.json

@@ -0,0 +1,525 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "$id": "https://higlass.io/#viewconf",
+  "title": "HiGlass viewconf",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [],
+  "properties": {
+    "editable": {
+      "type": "boolean",
+      "default": true
+    },
+    "viewEditable": {
+      "type": "boolean",
+      "default": true
+    },
+    "tracksEditable": {
+      "type": "boolean",
+      "default": true
+    },
+    "zoomFixed": { "type": "boolean" },
+    "compactLayout": { "type": "boolean" },
+    "exportViewUrl": { "type": "string" },
+    "trackSourceServers": {
+      "type": "array",
+      "items": { "type": "string" },
+      "minLength": 1
+    },
+    "zoomLocks": { "$ref": "#/definitions/locks/zoomLocks" },
+    "locationLocks": { "$ref": "#/definitions/locks/locationLocks" },
+    "valueScaleLocks": { "$ref": "#/definitions/locks/valueScaleLocks" },
+    "views": {
+      "type": "array",
+      "items": { "$ref": "#/definitions/view" },
+      "minLength": 1
+    },
+    "chromInfoPath": { "type": "string" }
+  },
+  "definitions": {
+    "data": {
+      "type": "object",
+      "properties": {
+        "url": { "type": "string" },
+        "server": { "type": "string" },
+        "filetype": { "type": "string" },
+        "type": { "type": "string" },
+        "tilesetInfo": { "type": "object" },
+        "children": { "type": "array" },
+        "tiles": { "type": "object" }
+      }
+    },
+
+    "locks": {
+      "slug": { "type": "string" },
+
+      "locksByViewUid": {
+        "type": "object",
+        "additionalProperties": false,
+        "patternProperties": {
+          ".": { "$ref": "#/definitions/locks/slug" }
+        }
+      },
+
+      "axisSpecificLocks": {
+        "additionalProperties": false,
+        "properties": {
+          "axis": {
+            "enum": ["x", "y"],
+            "type": "string"
+          },
+          "lock": {
+            "type": "string"
+          }
+        },
+        "required": ["lock", "axis"],
+        "type": "object"
+      },
+
+      "locationLocksByViewUid": {
+        "type": "object",
+        "additionalProperties": false,
+        "patternProperties": {
+          ".": {
+            "anyOf": [
+              {
+                "type": "string"
+              },
+              {
+                "additionalProperties": false,
+                "properties": {
+                  "x": {
+                    "$ref": "#/definitions/locks/axisSpecificLocks"
+                  },
+                  "y": {
+                    "$ref": "#/definitions/locks/axisSpecificLocks"
+                  }
+                },
+                "type": "object"
+              }
+            ]
+          }
+        }
+      },
+
+      "zoomLocks": {
+        "type": "object",
+        "additionalProperties": false,
+        "required": [],
+        "properties": {
+          "locksByViewUid": { "$ref": "#/definitions/locks/locksByViewUid" },
+          "locksDict": {
+            "type": "object",
+            "additionalProperties": false,
+            "patternProperties": {
+              ".": {
+                "type": "object",
+                "additionalProperties": false,
+                "properties": {
+                  "uid": { "$ref": "#/definitions/locks/slug" }
+                },
+                "patternProperties": {
+                  "^(?!uid).": {
+                    "type": "array",
+                    "minLength": 3,
+                    "maxLength": 3,
+                    "items": {
+                      "type": "number"
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+      },
+
+      "locationLocks": {
+        "type": "object",
+        "additionalProperties": false,
+        "required": [],
+        "properties": {
+          "locksByViewUid": {
+            "$ref": "#/definitions/locks/locationLocksByViewUid"
+          },
+          "locksDict": {
+            "type": "object",
+            "additionalProperties": false,
+            "patternProperties": {
+              ".": {
+                "type": "object",
+                "additionalProperties": false,
+                "properties": {
+                  "uid": { "$ref": "#/definitions/locks/slug" }
+                },
+                "patternProperties": {
+                  "^(?!uid).": {
+                    "type": "array",
+                    "minLength": 3,
+                    "maxLength": 3,
+                    "items": {
+                      "type": "number"
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+      },
+
+      "valueScaleLocks": {
+        "type": "object",
+        "additionalProperties": false,
+        "required": ["locksByViewUid", "locksDict"],
+        "properties": {
+          "locksByViewUid": { "$ref": "#/definitions/locks/locksByViewUid" },
+          "locksDict": {
+            "type": "object",
+            "additionalProperties": false,
+            "patternProperties": {
+              ".": {
+                "type": "object",
+                "additionalProperties": false,
+                "properties": {
+                  "uid": { "$ref": "#/definitions/locks/slug" },
+                  "ignoreOffScreenValues": { "type": "boolean" }
+                },
+                "patternProperties": {
+                  "^(?!(uid|ignoreOffScreenValues)).": {
+                    "type": "object",
+                    "additionalProperties": false,
+                    "required": ["view", "track"],
+                    "properties": {
+                      "view": { "type": "string" },
+                      "track": { "$ref": "#/definitions/locks/slug" }
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+
+    "view": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["tracks", "layout"],
+      "properties": {
+        "autocompleteSource": { "type": "string" },
+        "chromInfoPath": { "type": "string" },
+        "genomePositionSearchBox": {
+          "$ref": "#/definitions/viewProperties/genomePositionSearchBox"
+        },
+        "genomePositionSearchBoxVisible": { "type": "boolean" },
+        "initialXDomain": { "$ref": "#/definitions/viewProperties/domain" },
+        "initialYDomain": { "$ref": "#/definitions/viewProperties/domain" },
+        "layout": { "$ref": "#/definitions/viewProperties/layout" },
+        "overlays": {
+          "type": "array",
+          "items": { "$ref": "#/definitions/viewProperties/overlay" }
+        },
+        "selectionView": { "type": "boolean" },
+        "tracks": { "$ref": "#/definitions/viewProperties/tracks_object" },
+        "uid": { "type": "string" },
+        "zoomFixed": { "type": "boolean" },
+        "zoomLimits": {
+          "type": "array",
+          "minLength": 2,
+          "maxLength": 2,
+          "default": [1, null]
+        }
+      }
+    },
+
+    "viewProperties": {
+      "genomePositionSearchBox": {
+        "type": "object",
+        "title": "The Genome Position Search Box Schema",
+        "required": ["chromInfoServer", "chromInfoId"],
+        "properties": {
+          "autocompleteServer": {
+            "type": "string",
+            "title": "The Autocomplete Server URL",
+            "default": "",
+            "examples": ["//higlass.io/api/v1"],
+            "pattern": "^(.*)$"
+          },
+          "autocompleteId": {
+            "type": "string",
+            "title": "The Autocomplete ID",
+            "default": "",
+            "examples": ["OHJakQICQD6gTD7skx4EWA"],
+            "pattern": "^(.*)$"
+          },
+          "chromInfoServer": {
+            "type": "string",
+            "title": "The Chrominfo Server URL",
+            "default": "",
+            "examples": ["//higlass.io/api/v1"],
+            "pattern": "^(.*)$"
+          },
+          "chromInfoId": {
+            "type": "string",
+            "title": "The Chromosome Info ID",
+            "default": "",
+            "examples": ["hg19"],
+            "pattern": "^(.*)$"
+          },
+          "visible": {
+            "type": "boolean",
+            "title": "The Visible Schema",
+            "default": false
+          }
+        }
+      },
+
+      "overlay": {
+        "type": "object",
+        "additionalProperties": false,
+        "properties": {
+          "chromInfoPath": { "type": "string" },
+          "includes": { "type": "array" },
+          "options": {
+            "type": "object",
+            "properties": {
+              "extent": { "type": "array" },
+              "minWidth": { "type": "number" },
+              "fill": { "type": "string" },
+              "fillOpacity": { "type": "number" },
+              "stroke": { "type": "string" },
+              "strokeOpacity": { "type": "number" },
+              "strokeWidth": { "type": "number" },
+              "strokePos": { "type": ["string", "array"] },
+              "outline": { "type": "string" },
+              "outlineOpacity": { "type": "number" },
+              "outlineWidth": { "type": "number" },
+              "outlinePos": { "type": ["string", "array"] }
+            }
+          },
+          "type": { "type": "string" },
+          "uid": { "type": "string" }
+        }
+      },
+
+      "layout": {
+        "type": "object",
+        "additionalProperties": false,
+        "required": ["w", "h", "x", "y"],
+        "properties": {
+          "x": {
+            "type": "integer",
+            "title": "The X Position",
+            "default": 0
+          },
+          "y": {
+            "type": "integer",
+            "title": "The Y Position",
+            "default": 0
+          },
+          "w": {
+            "type": "integer",
+            "title": "Width",
+            "default": 12
+          },
+          "h": {
+            "type": "integer",
+            "title": "Height",
+            "default": 12
+          },
+          "moved": { "type": "boolean" },
+          "static": { "type": "boolean" }
+        }
+      },
+
+      "tracks_object": {
+        "type": "object",
+        "additionalProperties": false,
+        "properties": {
+          "left": { "$ref": "#/definitions/viewProperties/tracks_array" },
+          "right": { "$ref": "#/definitions/viewProperties/tracks_array" },
+          "top": { "$ref": "#/definitions/viewProperties/tracks_array" },
+          "bottom": { "$ref": "#/definitions/viewProperties/tracks_array" },
+          "center": { "$ref": "#/definitions/viewProperties/tracks_array" },
+          "whole": { "$ref": "#/definitions/viewProperties/tracks_array" },
+          "gallery": { "$ref": "#/definitions/viewProperties/tracks_array" }
+        }
+      },
+
+      "tracks_array": {
+        "type": "array",
+        "items": {
+          "oneOf": [
+            { "$ref": "#/definitions/tracks/enum_track" },
+            { "$ref": "#/definitions/tracks/combined_track" },
+            { "$ref": "#/definitions/tracks/heatmap_track" },
+            {
+              "$ref": "#/definitions/tracks/independent_viewport_projection_track"
+            }
+          ]
+        }
+      },
+
+      "domain": {
+        "type": "array",
+        "items": { "type": "number" },
+        "maxItems": 2,
+        "minItems": 2
+      }
+    },
+
+    "tracks": {
+      "heatmap_track": {
+        "type": "object",
+        "additionalProperties": false,
+        "required": [],
+        "properties": {
+          "uid": { "type": "string" },
+          "type": { "const": "heatmap" },
+          "data": { "$ref": "#/definitions/data" },
+          "height": { "type": "number" },
+          "options": { "type": "object" },
+          "position": { "type": "string" },
+          "server": { "type": "string" },
+          "tilesetUid": { "type": "string" },
+          "width": { "type": "number" },
+          "transforms": { "type": "array" }
+        }
+      },
+
+      "combined_track": {
+        "type": "object",
+        "additionalProperties": false,
+        "required": ["contents"],
+        "properties": {
+          "contents": { "$ref": "#/definitions/viewProperties/tracks_array" },
+          "height": { "type": "number" },
+          "options": {},
+          "position": { "type": "string" },
+          "type": { "const": "combined" },
+          "uid": { "type": "string" },
+          "width": { "type": "number" }
+        }
+      },
+
+      "enum_track": {
+        "type": "object",
+        "additionalProperties": false,
+        "required": ["type"],
+        "properties": {
+          "server": { "type": "string" },
+          "tilesetUid": { "type": "string" },
+          "data": { "$ref": "#/definitions/data" },
+          "uid": { "type": "string" },
+          "type": {
+            "enum": [
+              "multivec",
+              "1d-heatmap",
+              "line",
+              "point",
+              "bar",
+              "divergent-bar",
+              "stacked-interval",
+              "gene-annotations",
+              "linear-2d-rectangle-domains",
+              "chromosome-labels",
+              "linear-heatmap",
+              "1d-value-interval",
+              "2d-annotations",
+              "2d-chromosome-annotations",
+              "2d-chromosome-grid",
+              "2d-chromosome-labels",
+              "2d-rectangle-domains",
+              "2d-tiles",
+              "arrowhead-domains",
+              "bedlike",
+              "cross-rule",
+              "dummy",
+              "horizontal-1d-annotations",
+              "horizontal-1d-heatmap",
+              "horizontal-1d-tiles",
+              "horizontal-1d-value-interval",
+              "horizontal-2d-rectangle-domains",
+              "horizontal-bar",
+              "horizontal-chromosome-grid",
+              "horizontal-chromosome-labels",
+              "horizontal-divergent-bar",
+              "horizontal-gene-annotations",
+              "horizontal-heatmap",
+              "horizontal-line",
+              "horizontal-multivec",
+              "horizontal-point",
+              "horizontal-rule",
+              "horizontal-vector-heatmap",
+              "image-tiles",
+              "left-axis",
+              "left-stacked-interval",
+              "mapbox-tiles",
+              "osm-2d-tile-ids",
+              "osm-tiles",
+              "raster-tiles",
+              "simple-svg",
+              "square-markers",
+              "top-axis",
+              "top-stacked-interval",
+              "vertical-1d-annotations",
+              "vertical-1d-heatmap",
+              "vertical-1d-tiles",
+              "vertical-1d-value-interval",
+              "vertical-2d-rectangle-domains",
+              "vertical-bar",
+              "vertical-bedlike",
+              "vertical-chromosome-grid",
+              "vertical-chromosome-labels",
+              "vertical-gene-annotations",
+              "vertical-heatmap",
+              "vertical-line",
+              "vertical-multivec",
+              "vertical-point",
+              "vertical-rule",
+              "vertical-vector-heatmap",
+              "viewport-projection-center",
+              "viewport-projection-horizontal",
+              "viewport-projection-vertical"
+            ]
+          },
+          "chromInfoPath": { "type": "string" },
+          "fromViewUid": { "type": "string" },
+          "height": { "type": "number" },
+          "options": { "type": "object" },
+          "width": { "type": "number" },
+          "x": { "type": "number" },
+          "y": { "type": "number" }
+        }
+      },
+      "independent_viewport_projection_track": {
+        "type": "object",
+        "additionalProperties": false,
+        "properties": {
+          "uid": { "type": "string" },
+          "type": {
+            "enum": [
+              "viewport-projection-horizontal",
+              "viewport-projection-vertical",
+              "viewport-projection-center"
+            ]
+          },
+          "fromViewUid": { "type": "null" },
+          "projectionXDomain": {
+            "$ref": "#/definitions/viewProperties/domain"
+          },
+          "projectionYDomain": {
+            "$ref": "#/definitions/viewProperties/domain"
+          },
+          "options": { "type": "object" },
+          "transforms": { "type": "array" },
+          "width": { "type": "number" },
+          "x": { "type": "number" },
+          "y": { "type": "number" }
+        }
+      }
+    }
+  }
+}