@genome-spy/core 0.18.0 → 0.19.1

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 (71) hide show
  1. package/dist/index.js +44 -117
  2. package/dist/schema.json +0 -4
  3. package/package.json +3 -2
  4. package/src/data/collector.js +9 -4
  5. package/src/data/collector.test.js +2 -0
  6. package/src/data/dataFlow.test.js +2 -0
  7. package/src/data/flow.test.js +1 -0
  8. package/src/data/flowNode.test.js +1 -0
  9. package/src/data/flowOptimizer.js +6 -0
  10. package/src/data/flowOptimizer.test.js +1 -0
  11. package/src/data/formats/fasta.test.js +1 -0
  12. package/src/data/sources/inlineSource.test.js +1 -0
  13. package/src/data/sources/sequenceSource.test.js +1 -0
  14. package/src/data/transforms/clone.test.js +1 -0
  15. package/src/data/transforms/coverage.test.js +1 -0
  16. package/src/data/transforms/filter.test.js +1 -0
  17. package/src/data/transforms/flattenDelimited.test.js +1 -0
  18. package/src/data/transforms/flattenSequence.test.js +1 -0
  19. package/src/data/transforms/formula.test.js +1 -0
  20. package/src/data/transforms/identifier.test.js +1 -0
  21. package/src/data/transforms/pileup.test.js +1 -0
  22. package/src/data/transforms/project.test.js +1 -0
  23. package/src/data/transforms/regexExtract.test.js +1 -0
  24. package/src/data/transforms/regexFold.test.js +1 -0
  25. package/src/data/transforms/sample.test.js +1 -0
  26. package/src/data/transforms/stack.test.js +1 -0
  27. package/src/encoder/accessor.test.js +1 -0
  28. package/src/encoder/encoder.test.js +1 -0
  29. package/src/genome/genome.js +14 -2
  30. package/src/genome/genome.test.js +36 -0
  31. package/src/genome/scaleIndex.js +3 -2
  32. package/src/genome/scaleIndex.test.js +23 -6
  33. package/src/genome/scaleLocus.test.js +1 -0
  34. package/src/gl/dataToVertices.js +9 -6
  35. package/src/gl/includes/common.glsl +3 -3
  36. package/src/gl/includes/scales.glsl +33 -2
  37. package/src/gl/point.vertex.glsl +0 -2
  38. package/src/gl/rule.vertex.glsl +1 -1
  39. package/src/gl/webGLHelper.js +0 -3
  40. package/src/marks/mark.js +10 -13
  41. package/src/scale/glslScaleGenerator.js +56 -17
  42. package/src/scale/scale.test.js +1 -0
  43. package/src/scale/ticks.test.js +1 -0
  44. package/src/spec/scale.d.ts +0 -9
  45. package/src/utils/addBaseUrl.test.js +1 -0
  46. package/src/utils/cloner.test.js +1 -0
  47. package/src/utils/coalesce.test.js +1 -0
  48. package/src/utils/concatIterables.test.js +1 -0
  49. package/src/utils/domainArray.test.js +1 -0
  50. package/src/utils/indexer.test.js +1 -0
  51. package/src/utils/iterateNestedMaps.test.js +1 -0
  52. package/src/utils/kWayMerge.test.js +1 -0
  53. package/src/utils/layout/flexLayout.test.js +1 -0
  54. package/src/utils/layout/rectangle.test.js +1 -0
  55. package/src/utils/mergeObjects.test.js +1 -0
  56. package/src/utils/numberExtractor.test.js +1 -0
  57. package/src/utils/propertyCacher.test.js +1 -0
  58. package/src/utils/propertyCoalescer.test.js +1 -0
  59. package/src/utils/reservationMap.test.js +1 -0
  60. package/src/utils/topK.test.js +1 -0
  61. package/src/utils/variableTools.test.js +1 -0
  62. package/src/view/axisResolution.test.js +1 -0
  63. package/src/view/flowBuilder.test.js +1 -0
  64. package/src/view/scaleResolution.js +5 -11
  65. package/src/view/scaleResolution.test.js +1 -0
  66. package/src/view/unitView.js +8 -4
  67. package/src/view/view.test.js +1 -0
  68. package/src/view/viewFactory.test.js +1 -0
  69. package/src/gl/includes/fp64-arithmetic.glsl +0 -187
  70. package/src/gl/includes/fp64-utils.js +0 -142
  71. package/src/gl/includes/scales_fp64.glsl +0 -30
@@ -1,142 +0,0 @@
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- // Adapted from luma.gl - https://github.com/visgl/luma.gl
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-
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- // Copyright (c) 2015 - 2017 Uber Technologies, Inc.
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- //
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- // Permission is hereby granted, free of charge, to any person obtaining a copy
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- // of this software and associated documentation files (the "Software"), to deal
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- // in the Software without restriction, including without limitation the rights
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- // to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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- // copies of the Software, and to permit persons to whom the Software is
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- // furnished to do so, subject to the following conditions:
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- //
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- // The above copyright notice and this permission notice shall be included in
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- // all copies or substantial portions of the Software.
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- //
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- // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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- // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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- // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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- // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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- // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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- // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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- // THE SOFTWARE.
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-
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- /**
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- * Calculate WebGL 64 bit float
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- *
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- * @param {number} a the input float number
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- * @param {number[]} [out] the output array. If not supplied, a new array is created.
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- * @param {number} [startIndex] the index in the output array to fill from. Default 0.
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- * @returns {number[]} the fp64 representation of the input number
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- */
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- export function fp64ify(a, out = [], startIndex = 0) {
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- const hiPart = Math.fround(a);
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- out[startIndex] = hiPart;
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- out[startIndex + 1] = isFinite(hiPart) ? a - hiPart : 0;
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- return out;
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- }
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-
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- /**
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- * Calculate the low part of a WebGL 64 bit float
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- *
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- * @param {number} a the input float number
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- * @returns {number} the lower 32 bit of the number
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- */
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- export function fp64LowPart(a) {
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- return a - Math.fround(a);
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- }
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-
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- /**
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- * @param {WebGLRenderingContext | WebGL2RenderingContext} gl
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- */
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- export function getPlatformShaderDefines(gl) {
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- const debugInfo = getContextInfo(gl);
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-
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- switch (debugInfo.gpuVendor.toLowerCase()) {
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- case "nvidia":
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- return `\
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- #define NVIDIA_GPU
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- // Nvidia optimizes away the calculation necessary for emulated fp64
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- #define LUMA_FP64_CODE_ELIMINATION_WORKAROUND 1
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- `;
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-
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- case "intel":
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- return `\
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- #define INTEL_GPU
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- // Intel optimizes away the calculation necessary for emulated fp64
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- #define LUMA_FP64_CODE_ELIMINATION_WORKAROUND 1
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- // Intel's built-in 'tan' function doesn't have acceptable precision
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- #define LUMA_FP32_TAN_PRECISION_WORKAROUND 1
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- // Intel GPU doesn't have full 32 bits precision in same cases, causes overflow
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- #define LUMA_FP64_HIGH_BITS_OVERFLOW_WORKAROUND 1
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- `;
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-
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- case "amd":
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- // AMD Does not eliminate fp64 code
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- return `\
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- #define AMD_GPU
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- `;
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-
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- default:
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- // We don't know what GPU it is, could be that the GPU driver or
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- // browser is not implementing UNMASKED_RENDERER constant and not
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- // reporting a correct name
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- return `\
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- #define DEFAULT_GPU
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- // Prevent driver from optimizing away the calculation necessary for emulated fp64
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- #define LUMA_FP64_CODE_ELIMINATION_WORKAROUND 1
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- // Intel's built-in 'tan' function doesn't have acceptable precision
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- #define LUMA_FP32_TAN_PRECISION_WORKAROUND 1
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- // Intel GPU doesn't have full 32 bits precision in same cases, causes overflow
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- #define LUMA_FP64_HIGH_BITS_OVERFLOW_WORKAROUND 1
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- `;
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- }
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- }
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-
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- const GL_VENDOR = 0x1f00;
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- const GL_RENDERER = 0x1f01;
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- const GL_VERSION = 0x1f02;
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- const GL_SHADING_LANGUAGE_VERSION = 0x8b8c;
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-
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- /**
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- * @param {WebGLRenderingContext | WebGL2RenderingContext} gl
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- */
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- export function getContextInfo(gl) {
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- const info = gl.getExtension("WEBGL_debug_renderer_info");
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- const vendor = gl.getParameter(
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- (info && info.UNMASKED_VENDOR_WEBGL) || GL_VENDOR
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- );
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- const renderer = gl.getParameter(
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- (info && info.UNMASKED_RENDERER_WEBGL) || GL_RENDERER
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- );
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- const gpuVendor = identifyGPUVendor(vendor, renderer);
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- const gpuInfo = {
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- gpuVendor,
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- vendor,
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- renderer,
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- version: gl.getParameter(GL_VERSION),
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- shadingLanguageVersion: gl.getParameter(GL_SHADING_LANGUAGE_VERSION),
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- };
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- return gpuInfo;
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- }
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-
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- /**
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- * @param {string} vendor
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- * @param {string} renderer
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- */
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- function identifyGPUVendor(vendor, renderer) {
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- if (vendor.match(/NVIDIA/i) || renderer.match(/NVIDIA/i)) {
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- return "NVIDIA";
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- }
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- if (vendor.match(/INTEL/i) || renderer.match(/INTEL/i)) {
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- return "INTEL";
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- }
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- if (
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- vendor.match(/AMD/i) ||
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- renderer.match(/AMD/i) ||
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- vendor.match(/ATI/i) ||
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- renderer.match(/ATI/i)
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- ) {
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- return "AMD";
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- }
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- return "UNKNOWN GPU";
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- }
@@ -1,30 +0,0 @@
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- float scaleIdentityFp64(vec2 value) {
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- return value[0];
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- }
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-
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- float scaleLinearFp64(vec2 value, vec4 domain, vec2 range) {
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- vec2 domainSpan = sub_fp64(domain.zw, domain.xy);
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- float rangeSpan = range[1] - range[0];
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-
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- float unitValue = div_fp64(sub_fp64(value, domain.xy), domainSpan).x;
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- return unitValue * rangeSpan + range[0];
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- }
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-
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- float scaleBandFp64(vec2 value, vec4 domainExtent, vec2 range,
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- float paddingInner, float paddingOuter,
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- float align, float band) {
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-
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- // TODO: reverse
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- float start = range[0];
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- float stop = range[1];
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-
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- vec2 domainSpan = sub_fp64(domainExtent.zw, domainExtent.xy);
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- float n = domainSpan.x;
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-
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- // Based on: https://github.com/d3/d3-scale/blob/master/src/band.js
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- float step = (stop - start) / max(1.0, n - paddingInner + paddingOuter * 2.0);
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- start += (stop - start - step * (n - paddingInner)) * align;
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- float bandwidth = step * (1.0 - paddingInner);
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-
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- return start + sub_fp64(value, domainExtent.xy).x * step + bandwidth * band;
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- }