@jbrowse/plugin-linear-genome-view 1.6.9 → 1.7.3

package/dist/LinearGenomeView/util.d.ts

@@ -1,14 +1,14 @@
-/**
- * Given a scale ( bp/px ) and minimum distances (px) between major and minor
- * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
- * the gridline pitches to use.
- */
-export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
-    majorPitch: number;
-    minorPitch: number;
-};
-export declare function makeTicks(start: number, end: number, bpPerPx: number, emitMajor?: boolean, emitMinor?: boolean): {
-    type: string;
-    base: number;
-    index: number;
-}[];
+/**
+ * Given a scale ( bp/px ) and minimum distances (px) between major and minor
+ * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
+ * the gridline pitches to use.
+ */
+export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
+    majorPitch: number;
+    minorPitch: number;
+};
+export declare function makeTicks(start: number, end: number, bpPerPx: number, emitMajor?: boolean, emitMinor?: boolean): {
+    type: string;
+    base: number;
+    index: number;
+}[];

package/dist/LinearGenomeView/util.js

@@ -0,0 +1,93 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.chooseGridPitch = chooseGridPitch;
+exports.makeTicks = makeTicks;
+
+/**
+ * Given a scale ( bp/px ) and minimum distances (px) between major and minor
+ * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
+ * the gridline pitches to use.
+ */
+function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
+  scale = Math.abs(scale);
+  var minMajorPitchBp = minMajorPitchPx * scale;
+  var majorMagnitude = parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+  var majorPitch = Math.pow(10, majorMagnitude);
+
+  while (majorPitch < minMajorPitchBp) {
+    majorPitch *= 2;
+
+    if (majorPitch >= minMajorPitchBp) {
+      break;
+    }
+
+    majorPitch *= 2.5;
+  }
+
+  majorPitch = Math.max(majorPitch, 5);
+  var majorPitchPx = majorPitch / scale;
+  var minorPitch = 0;
+
+  if (!(majorPitch % 10) && majorPitchPx / 10 >= minMinorPitchPx) {
+    minorPitch = majorPitch / 10;
+  } else if (!(majorPitch % 5) && majorPitchPx / 5 >= minMinorPitchPx) {
+    minorPitch = majorPitch / 5;
+  } else if (!(majorPitch % 2) && majorPitchPx / 2 >= minMinorPitchPx) {
+    minorPitch = majorPitch / 2;
+  }
+
+  return {
+    majorPitch: majorPitch,
+    minorPitch: minorPitch
+  };
+}
+
+function makeTicks(start, end, bpPerPx) {
+  var emitMajor = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : true;
+  var emitMinor = arguments.length > 4 && arguments[4] !== undefined ? arguments[4] : true;
+  var gridPitch = chooseGridPitch(bpPerPx, 60, 15);
+  var minBase = start;
+  var maxBase = end;
+
+  if (minBase === null || maxBase === null) {
+    return [];
+  }
+
+  if (bpPerPx < 0) {
+    ;
+    var _ref = [maxBase, minBase];
+    minBase = _ref[0];
+    maxBase = _ref[1];
+  } // add 20px additional on the right and left to allow us to draw the ends
+  // of labels that lie a little outside our region
+
+
+  minBase -= Math.abs(20 * bpPerPx) - 1;
+  maxBase += Math.abs(20 * bpPerPx) + 1;
+  var iterPitch = gridPitch.minorPitch || gridPitch.majorPitch;
+  var index = 0;
+  var ticks = [];
+
+  for (var base = Math.ceil(minBase / iterPitch) * iterPitch; base < maxBase; base += iterPitch) {
+    if (emitMinor && base % (gridPitch.majorPitch * 2)) {
+      ticks.push({
+        type: 'minor',
+        base: base - 1,
+        index: index
+      });
+      index += 1;
+    } else if (emitMajor && !(base % (gridPitch.majorPitch * 2))) {
+      ticks.push({
+        type: 'major',
+        base: base - 1,
+        index: index
+      });
+      index += 1;
+    }
+  }
+
+  return ticks;
+}

package/dist/LinearGenomeView/util.test.js

@@ -0,0 +1,78 @@
+"use strict";
+
+var _util = require("./util");
+
+describe('tick calculation', function () {
+  test('one', function () {
+    var result = Array.from((0, _util.makeTicks)(0, 10, 0.05));
+    expect(result).toEqual([{
+      type: 'major',
+      base: -1,
+      index: 0
+    }, {
+      type: 'minor',
+      base: 0,
+      index: 1
+    }, {
+      type: 'minor',
+      base: 1,
+      index: 2
+    }, {
+      type: 'minor',
+      base: 2,
+      index: 3
+    }, {
+      type: 'minor',
+      base: 3,
+      index: 4
+    }, {
+      type: 'minor',
+      base: 4,
+      index: 5
+    }, {
+      type: 'minor',
+      base: 5,
+      index: 6
+    }, {
+      type: 'minor',
+      base: 6,
+      index: 7
+    }, {
+      type: 'minor',
+      base: 7,
+      index: 8
+    }, {
+      type: 'minor',
+      base: 8,
+      index: 9
+    }, {
+      type: 'major',
+      base: 9,
+      index: 10
+    }, {
+      type: 'minor',
+      base: 10,
+      index: 11
+    }]);
+  });
+  test('two', function () {
+    var result = Array.from((0, _util.makeTicks)(0, 50, 1));
+    expect(result).toEqual([{
+      type: 'major',
+      base: -1,
+      index: 0
+    }, {
+      type: 'minor',
+      base: 19,
+      index: 1
+    }, {
+      type: 'minor',
+      base: 39,
+      index: 2
+    }, {
+      type: 'minor',
+      base: 59,
+      index: 3
+    }]);
+  });
+});