@genome-spy/core 0.34.0 → 0.36.0

package/dist/schema.json

@@ -462,7 +462,7 @@
         "axis": {
           "anyOf": [
             {
-              "$ref": "#/definitions/Axis"
+              "$ref": "#/definitions/GenomeAxis"
             },
             {
               "type": "null"
@@ -1253,6 +1253,52 @@
       ],
       "type": "object"
     },
+    "FlattenParams": {
+      "additionalProperties": false,
+      "properties": {
+        "as": {
+          "anyOf": [
+            {
+              "items": {
+                "type": "string"
+              },
+              "type": "array"
+            },
+            {
+              "type": "string"
+            }
+          ],
+          "description": "The output field name(s) for the flattened field.\n\n**Default:** the input fields."
+        },
+        "fields": {
+          "anyOf": [
+            {
+              "items": {
+                "$ref": "#/definitions/Field"
+              },
+              "type": "array"
+            },
+            {
+              "$ref": "#/definitions/Field"
+            }
+          ],
+          "description": "The field(s) to flatten. If no field is defined, the data object itself is treated as an array to be flattened."
+        },
+        "index": {
+          "description": "The output field name for the zero-based index of the array values. If unspecified, an index field is not added.",
+          "type": "string"
+        },
+        "type": {
+          "const": "flatten",
+          "description": "The type of the transform to be applied",
+          "type": "string"
+        }
+      },
+      "required": [
+        "type"
+      ],
+      "type": "object"
+    },
     "FlattenSequenceParams": {
       "additionalProperties": false,
       "properties": {
@@ -1349,6 +1395,321 @@
     "Generator": {
       "$ref": "#/definitions/SequenceGenerator"
     },
+    "GenomeAxis": {
+      "additionalProperties": false,
+      "properties": {
+        "chromGrid": {
+          "description": "A boolean flag indicating if chromosome grid lines should be included as part of the axis.\n\n__Default value:__ `false`",
+          "type": "boolean"
+        },
+        "chromGridCap": {
+          "description": "The stroke cap for the chromosome grid line's ending style. One of `\"butt\"`, `\"round\"` or `\"square\"`.\n\n__Default value:__ `\"butt\"`",
+          "enum": [
+            "butt",
+            "round",
+            "square"
+          ],
+          "type": "string"
+        },
+        "chromGridColor": {
+          "description": "Color of grid lines.\n\n__Default value:__ `lightgray`",
+          "type": "string"
+        },
+        "chromGridDash": {
+          "description": "An array of alternating [stroke, space] lengths for dashed chromosome grid mark lines.",
+          "items": {
+            "type": "number"
+          },
+          "type": "array"
+        },
+        "chromGridDashOffset": {
+          "description": "The pixel offset at which to start drawing with the chromosome grid mark dash array.",
+          "type": "number"
+        },
+        "chromGridFillEven": {
+          "description": "Fill color of odd chromosomes.\n\n__Default value:__ (none)",
+          "type": "string"
+        },
+        "chromGridFillOdd": {
+          "description": "Fill color of odd chromosomes.\n\n__Default value:__ (none)",
+          "type": "string"
+        },
+        "chromGridOpacity": {
+          "description": "The opacity of the chromosome grid lines.\n\n__Default value:__ `1`",
+          "type": "number"
+        },
+        "chromGridWidth": {
+          "description": "Width of the chromosome grid lines.\n\n__Default value:__ `1`",
+          "type": "number"
+        },
+        "chromLabelAlign": {
+          "$ref": "#/definitions/Align"
+        },
+        "chromLabelColor": {
+          "type": "string"
+        },
+        "chromLabelFont": {
+          "type": "string"
+        },
+        "chromLabelFontSize": {
+          "type": "number"
+        },
+        "chromLabelFontStyle": {
+          "$ref": "#/definitions/FontStyle"
+        },
+        "chromLabelFontWeight": {
+          "$ref": "#/definitions/FontWeight"
+        },
+        "chromLabelPadding": {
+          "type": "number"
+        },
+        "chromLabels": {
+          "type": "boolean"
+        },
+        "chromTickColor": {
+          "type": "string"
+        },
+        "chromTickDash": {
+          "items": {
+            "type": "number"
+          },
+          "type": "array"
+        },
+        "chromTickDashOffset": {
+          "type": "number"
+        },
+        "chromTickSize": {
+          "type": "number"
+        },
+        "chromTickWidth": {
+          "type": "number"
+        },
+        "chromTicks": {
+          "type": "boolean"
+        },
+        "domain": {
+          "description": "A boolean flag indicating if the domain (the axis baseline) should be included as part of the axis.\n\n__Default value:__ `true`",
+          "type": "boolean"
+        },
+        "domainCap": {
+          "description": "The stroke cap for the domain line's ending style. One of `\"butt\"`, `\"round\"` or `\"square\"`.\n\n__Default value:__ `\"butt\"`",
+          "enum": [
+            "butt",
+            "round",
+            "square"
+          ],
+          "type": "string"
+        },
+        "domainColor": {
+          "description": "Color of axis domain line.\n\n__Default value:__ `\"gray\"`.",
+          "type": "string"
+        },
+        "domainDash": {
+          "description": "An array of alternating [stroke, space] lengths for dashed domain lines.",
+          "items": {
+            "type": "number"
+          },
+          "type": "array"
+        },
+        "domainDashOffset": {
+          "description": "The pixel offset at which to start drawing with the domain dash array.",
+          "type": "number"
+        },
+        "domainWidth": {
+          "description": "Stroke width of axis domain line\n\n__Default value:__ `1`",
+          "type": "number"
+        },
+        "format": {
+          "description": "The format specifier pattern for axis labels. Must be a legal [d3-format](https://github.com/d3/d3-format#locale_format) specifier.",
+          "type": "string"
+        },
+        "grid": {
+          "description": "A boolean flag indicating if grid lines should be included as part of the axis.\n\n__Default value:__ `false`",
+          "type": "boolean"
+        },
+        "gridCap": {
+          "description": "The stroke cap for the grid line's ending style. One of `\"butt\"`, `\"round\"` or `\"square\"`.\n\n__Default value:__ `\"butt\"`",
+          "enum": [
+            "butt",
+            "round",
+            "square"
+          ],
+          "type": "string"
+        },
+        "gridColor": {
+          "description": "Color of grid lines.\n\n__Default value:__ `lightgray`",
+          "type": "string"
+        },
+        "gridDash": {
+          "description": "An array of alternating [stroke, space] lengths for dashed grid mark lines.",
+          "items": {
+            "type": "number"
+          },
+          "type": "array"
+        },
+        "gridDashOffset": {
+          "description": "The pixel offset at which to start drawing with the grid mark dash array.",
+          "type": "number"
+        },
+        "gridOpacity": {
+          "description": "The opacity of the grid lines.\n\n__Default value:__ `1`",
+          "type": "number"
+        },
+        "gridWidth": {
+          "description": "Width of the grid lines.\n\n__Default value:__ `1`",
+          "type": "number"
+        },
+        "labelAlign": {
+          "$ref": "#/definitions/Align",
+          "description": "Horizontal text alignment of axis tick labels, overriding the default setting for the current axis orientation."
+        },
+        "labelAngle": {
+          "description": "The rotation angle of the axis labels.\n\n__Default value:__ `-90` for nominal and ordinal fields; `0` otherwise.",
+          "maximum": 360,
+          "minimum": -360,
+          "type": "number"
+        },
+        "labelBaseline": {
+          "$ref": "#/definitions/Baseline",
+          "description": "Vertical text baseline of axis tick labels, overriding the default setting for the current axis orientation. One of `\"alphabetic\"` (default), `\"top\"`, `\"middle\"`, `\"bottom\"`."
+        },
+        "labelColor": {
+          "description": "The color of the tick label, can be in hex color code or regular color name.",
+          "type": "string"
+        },
+        "labelFont": {
+          "description": "The font of the tick label.",
+          "type": "string"
+        },
+        "labelFontSize": {
+          "description": "The font size of the label, in pixels.",
+          "minimum": 0,
+          "type": "number"
+        },
+        "labelFontStyle": {
+          "description": "Font style of the title.",
+          "type": "string"
+        },
+        "labelFontWeight": {
+          "description": "Font weight of axis tick labels.",
+          "type": "string"
+        },
+        "labelLimit": {
+          "description": "Maximum allowed pixel width of axis tick labels.\n\n__Default value:__ `180`",
+          "type": "number"
+        },
+        "labelPadding": {
+          "description": "The padding, in pixels, between axis and text labels.\n\n__Default value:__ `2`",
+          "type": "number"
+        },
+        "labels": {
+          "description": "A boolean flag indicating if labels should be included as part of the axis.\n\n__Default value:__ `true`.",
+          "type": "boolean"
+        },
+        "maxExtent": {
+          "description": "The maximum extent in pixels that axis ticks and labels should use. This determines a maximum offset value for axis titles.\n\n__Default value:__ `undefined`.",
+          "type": "number"
+        },
+        "minExtent": {
+          "description": "The minimum extent in pixels that axis ticks and labels should use. This determines a minimum offset value for axis titles.\n\n__Default value:__ `30` for y-axis; `undefined` for x-axis.",
+          "type": "number"
+        },
+        "offset": {
+          "description": "The orthogonal offset in pixels by which to displace the axis from its position along the edge of the chart.",
+          "type": "number"
+        },
+        "orient": {
+          "$ref": "#/definitions/AxisOrient",
+          "description": "The orientation of the axis. One of `\"top\"`, `\"bottom\"`, `\"left\"` or `\"right\"`. The orientation can be used to further specialize the axis type (e.g., a y axis oriented for the right edge of the chart).\n\n__Default value:__ `\"bottom\"` for x-axes and `\"left\"` for y-axes."
+        },
+        "tickCap": {
+          "description": "The stroke cap for the tick lines' ending style. One of `\"butt\"`, `\"round\"` or `\"square\"`.\n\n__Default value:__ `\"butt\"`",
+          "enum": [
+            "butt",
+            "round",
+            "square"
+          ],
+          "type": "string"
+        },
+        "tickColor": {
+          "description": "The color of the axis's tick.\n\n__Default value:__ `\"gray\"`",
+          "type": "string"
+        },
+        "tickCount": {
+          "description": "A desired number of ticks, for axes visualizing quantitative scales. The resulting number may be different so that values are \"nice\" (multiples of `2`, `5`, `10`) and lie within the underlying scale's range.",
+          "minimum": 0,
+          "type": "number"
+        },
+        "tickDash": {
+          "description": "An array of alternating [stroke, space] lengths for dashed tick mark lines.",
+          "items": {
+            "type": "number"
+          },
+          "type": "array"
+        },
+        "tickDashOffset": {
+          "description": "The pixel offset at which to start drawing with the tick mark dash array.",
+          "type": "number"
+        },
+        "tickMinStep": {
+          "description": "The minimum desired step between axis ticks, in terms of scale domain values. For example, a value of `1` indicates that ticks should not be less than 1 unit apart. If `tickMinStep` is specified, the `tickCount` value will be adjusted, if necessary, to enforce the minimum step value.",
+          "type": "number"
+        },
+        "tickSize": {
+          "description": "The size in pixels of axis ticks.\n\n__Default value:__ `5`",
+          "minimum": 0,
+          "type": "number"
+        },
+        "tickWidth": {
+          "description": "The width, in pixels, of ticks.\n\n__Default value:__ `1`",
+          "minimum": 0,
+          "type": "number"
+        },
+        "ticks": {
+          "description": "Boolean value that determines whether the axis should include ticks.\n\n__Default value:__ `true`",
+          "type": "boolean"
+        },
+        "title": {
+          "description": "A title for the axis (none by default).",
+          "type": "string"
+        },
+        "titleColor": {
+          "description": "Color of the title, can be in hex color code or regular color name.",
+          "type": "string"
+        },
+        "titleFont": {
+          "description": "Font of the title. (e.g., `\"Helvetica Neue\"`).",
+          "type": "string"
+        },
+        "titleFontSize": {
+          "description": "Font size of the title.",
+          "minimum": 0,
+          "type": "number"
+        },
+        "titleFontStyle": {
+          "description": "Font style of the title.",
+          "type": "string"
+        },
+        "titleFontWeight": {
+          "description": "Font weight of the title. This can be either a string (e.g `\"bold\"`, `\"normal\"`) or a number (`100`, `200`, `300`, ..., `900` where `\"normal\"` = `400` and `\"bold\"` = `700`).",
+          "type": "string"
+        },
+        "titleOpacity": {
+          "description": "Opacity of the axis title.",
+          "type": "number"
+        },
+        "titlePadding": {
+          "description": "The padding, in pixels, between title and axis.",
+          "type": "number"
+        },
+        "values": {
+          "description": "Explicitly set the visible axis tick and label values.",
+          "items": {},
+          "type": "array"
+        }
+      },
+      "type": "object"
+    },
     "GenomeConfig": {
       "additionalProperties": false,
       "properties": {
@@ -1373,6 +1734,40 @@
       ],
       "type": "object"
     },
+    "Gff3Data": {
+      "additionalProperties": false,
+      "properties": {
+        "channel": {
+          "$ref": "#/definitions/PrimaryPositionalChannel",
+          "description": "Which channel's scale domain to monitor.\n\n__Default value:__ `\"x\"`"
+        },
+        "debounceDomainChange": {
+          "description": "The debounce time for domain changes, in milliseconds. Debouncing prevents data fetches while the user is still panning around.\n\n__Default value:__ `200`",
+          "type": "number"
+        },
+        "indexUrl": {
+          "description": "Url of the tabix index file.\n\n__Default value:__ `url` + `\".tbi\"`.",
+          "type": "string"
+        },
+        "type": {
+          "const": "gff3",
+          "type": "string"
+        },
+        "url": {
+          "description": "Url of the bgzip compressed file.",
+          "type": "string"
+        },
+        "windowSize": {
+          "description": "Size of each chunk when fetching the Tabix file. Data is only fetched when the length of the visible domain smaller than the window size.\n\n__Default value:__ `30000000`",
+          "type": "number"
+        }
+      },
+      "required": [
+        "type",
+        "url"
+      ],
+      "type": "object"
+    },
     "HConcatSpec": {
       "additionalProperties": false,
       "properties": {
@@ -1878,6 +2273,9 @@
         },
         {
           "$ref": "#/definitions/BamData"
+        },
+        {
+          "$ref": "#/definitions/Gff3Data"
         }
       ]
     },
@@ -2771,7 +3169,7 @@
         "axis": {
           "anyOf": [
             {
-              "$ref": "#/definitions/Axis"
+              "$ref": "#/definitions/GenomeAxis"
             },
             {
               "type": "null"
@@ -2845,7 +3243,7 @@
         "axis": {
           "anyOf": [
             {
-              "$ref": "#/definitions/Axis"
+              "$ref": "#/definitions/GenomeAxis"
             },
             {
               "type": "null"
@@ -2879,7 +3277,7 @@
         "axis": {
           "anyOf": [
             {
-              "$ref": "#/definitions/Axis"
+              "$ref": "#/definitions/GenomeAxis"
             },
             {
               "type": "null"
@@ -4653,7 +5051,7 @@
         "axis": {
           "anyOf": [
             {
-              "$ref": "#/definitions/Axis"
+              "$ref": "#/definitions/GenomeAxis"
             },
             {
               "type": "null"
@@ -5025,6 +5423,9 @@
         {
           "$ref": "#/definitions/FilterScoredLabelsParams"
         },
+        {
+          "$ref": "#/definitions/FlattenParams"
+        },
         {
           "$ref": "#/definitions/FlattenCompressedExonsParams"
         },

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.34.0",
+  "version": "0.36.0",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "exports": {
@@ -39,7 +39,9 @@
     "@gmod/bam": "^1.1.18",
     "@gmod/bbi": "^4.0.0",
     "@gmod/bed": "^2.1.2",
+    "@gmod/gff": "^1.3.0",
     "@gmod/indexedfasta": "^2.0.4",
+    "@gmod/tabix": "^1.5.10",
     "@types/d3-array": "^3.0.2",
     "@types/d3-dsv": "^3.0.0",
     "@types/d3-ease": "^3.0.0",
@@ -51,6 +53,7 @@
     "d3-color": "^3.0.1",
     "d3-ease": "^3.0.1",
     "d3-format": "^3.0.1",
+    "events": "^3.3.0",
     "flatqueue": "^2.0.3",
     "internmap": "^2.0.3",
     "lit-html": "^2.4.0",
@@ -60,5 +63,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "98fa42af4321cdf388facd721812325533f1d57b"
+  "gitHead": "6f6720382d7d33c9ac9a5b9c392e8a3e5938a862"
 }