higlass 1.13.6 → 2.0.1

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" }
+        }
+      }
+    }
+  }
+}

package/dist/app/scripts/AddTrackDialog.d.ts

@@ -0,0 +1,64 @@
+export class AddTrackDialog extends React.Component<any, any, any> {
+    constructor(props: any);
+    options: {};
+    state: {
+        selectedTilesets: {
+            datatype: string;
+        }[];
+        allTracksSameDatatype: boolean;
+    };
+    handleSubmitBound: (evt: any) => void;
+    handleTilesetPickerDoubleClickBound: (tileset: any) => void;
+    selectedTilesetsChangedBound: (selectedTilesetsIn: any) => void;
+    /**
+     * Get the track available track orientations for the given
+     * track position. Generally "top" or "bottom" equal "1d-horizontal",
+     * "left" or "right" correspond to "1d-vertical" and "center" means "2d".
+     *
+     * Arguments
+     * ---------
+     *  position: string
+     *
+     * Returns
+     * -------
+     *
+     *  A string containing the track orientation.
+     */
+    getOrientation(position: any): string;
+    handleSubmit(evt: any): void;
+    /**
+     * The user double clicked a tileset in the tileset finder dialog.
+     * This means that only one is selected.
+     *
+     * Arguments
+     * ---------
+     *  tileset: { uuid: 'CXCX', filetype: 'cooler' ....}
+     */
+    handleTilesetPickerDoubleClick(tileset: any): void;
+    handleOptionsChanged(newOptions: any): void;
+    handlePlotTypeSelected(newPlotType: any): void;
+    selectedPlotType: any;
+    selectedTilesetsChanged(selectedTilesetsIn: any): void;
+    render(): React.JSX.Element;
+    tilesetFinder: import("./TilesetFinder").TilesetFinder | null | undefined;
+    plotTypeChooser: PlotTypeChooser | null | undefined;
+}
+export namespace AddTrackDialog {
+    namespace defaultProps {
+        let position: string;
+    }
+    namespace propTypes {
+        export let datatype: PropTypes.Requireable<string>;
+        export let extent: PropTypes.Requireable<string>;
+        export let host: PropTypes.Requireable<string>;
+        export let onCancel: PropTypes.Validator<(...args: any[]) => any>;
+        export let onTracksChosen: PropTypes.Validator<(...args: any[]) => any>;
+        let position_1: PropTypes.Requireable<string>;
+        export { position_1 as position };
+        export let trackSourceServers: PropTypes.Validator<any[]>;
+    }
+}
+export default AddTrackDialog;
+import React from 'react';
+import PlotTypeChooser from './PlotTypeChooser';
+import PropTypes from 'prop-types';

package/dist/app/scripts/AddTrackPositionMenu.d.ts

@@ -0,0 +1,5 @@
+declare const _default: typeof React.Component<{
+    theme?: Theme;
+}>;
+export default _default;
+import React from 'react';

package/dist/app/scripts/Annotations1dTrack.d.ts

@@ -0,0 +1,15 @@
+export function rectsAtPoint(track: any, x: any, y: any): [];
+export default Annotations1dTrack;
+declare class Annotations1dTrack extends BedLikeTrack {
+    constructor(context: any, options: any, isVertical: any);
+    /**
+     * @param  {x} x position of the evt relative to the track
+     * @param  {y} y position of the evt relative to the track
+     */
+    click(x: any, y: any): {
+        type: string;
+        event: null;
+        payload: [];
+    };
+}
+import BedLikeTrack from './BedLikeTrack';