From 5dd25c264e226a73f2b0d9123daa7f88b6003224 Mon Sep 17 00:00:00 2001
From: Moritz Heckmann <moritz.heckmann@datavisyn.io>
Date: Tue, 12 Nov 2024 10:04:14 +0100
Subject: [PATCH] remove GenomeNavigation

---
 src/utils/GenomeNavigation.ts | 183 ----------------------------------
 src/utils/index.ts            |   1 -
 2 files changed, 184 deletions(-)
 delete mode 100644 src/utils/GenomeNavigation.ts

diff --git a/src/utils/GenomeNavigation.ts b/src/utils/GenomeNavigation.ts
deleted file mode 100644
index 43ccd41ae..000000000
--- a/src/utils/GenomeNavigation.ts
+++ /dev/null
@@ -1,183 +0,0 @@
-/**
- * HG38 intervals from gosling.js 'computeChromSizes' function
- */
-function computeForAssembly(assembly?: 'hg38') {
-  if (assembly === 'hg38') {
-    return {
-      interval: {
-        chr1: [0, 248956422],
-        chr2: [248956422, 491149951],
-        chr3: [491149951, 689445510],
-        chr4: [689445510, 879660065],
-        chr5: [879660065, 1061198324],
-        chr6: [1061198324, 1232004303],
-        chr7: [1232004303, 1391350276],
-        chr8: [1391350276, 1536488912],
-        chr9: [1536488912, 1674883629],
-        chr10: [1674883629, 1808681051],
-        chr11: [1808681051, 1943767673],
-        chr12: [1943767673, 2077042982],
-        chr13: [2077042982, 2191407310],
-        chr14: [2191407310, 2298451028],
-        chr15: [2298451028, 2400442217],
-        chr16: [2400442217, 2490780562],
-        chr17: [2490780562, 2574038003],
-        chr18: [2574038003, 2654411288],
-        chr19: [2654411288, 2713028904],
-        chr20: [2713028904, 2777473071],
-        chr21: [2777473071, 2824183054],
-        chr22: [2824183054, 2875001522],
-        chrX: [2875001522, 3031042417],
-        chrY: [3031042417, 3088269832],
-      },
-      size: {
-        chr1: 248956422,
-        chr2: 242193529,
-        chr3: 198295559,
-        chr4: 190214555,
-        chr5: 181538259,
-        chr6: 170805979,
-        chr7: 159345973,
-        chr8: 145138636,
-        chr9: 138394717,
-        chr10: 133797422,
-        chr11: 135086622,
-        chr12: 133275309,
-        chr13: 114364328,
-        chr14: 107043718,
-        chr15: 101991189,
-        chr16: 90338345,
-        chr17: 83257441,
-        chr18: 80373285,
-        chr19: 58617616,
-        chr20: 64444167,
-        chr21: 46709983,
-        chr22: 50818468,
-        chrX: 156040895,
-        chrY: 57227415,
-      },
-      total: 3088269832,
-    };
-  }
-
-  throw new Error('Assembly not supported');
-}
-
-export type ChromKey =
-  | 'chr1'
-  | 'chr2'
-  | 'chr3'
-  | 'chr4'
-  | 'chr5'
-  | 'chr6'
-  | 'chr7'
-  | 'chr8'
-  | 'chr9'
-  | 'chr10'
-  | 'chr11'
-  | 'chr12'
-  | 'chr13'
-  | 'chr14'
-  | 'chr15'
-  | 'chr16'
-  | 'chr17'
-  | 'chr18'
-  | 'chr19'
-  | 'chr20'
-  | 'chr21'
-  | 'chr22'
-  | 'chrX'
-  | 'chrY';
-
-/**
- * Utility class to convert different types of genomic positions.
- * The data is taken from gosling.js for hg38 and works similar to `computeChromSizes` in [gosling.js](https://github.com/gosling-lang/gosling.js).
- *
- * ### Use cases
- * - Drawing genome axis
- * - Working with tile fetchers in gosling
- * - Fetching transcripts from our backend
- * - ...
- *
- * ### Usage
- *
- * ```ts
- * const nav = new GenomeNavigation('hg38');
- * const absolutePosition = nav.relativeToAbsolutePosition('chr1', 100);
- * ```
- */
-export class GenomeNavigation {
-  private chromosomesInOrder = [...Array.from({ length: 22 }, (_, i) => `chr${i + 1}`), 'chrX', 'chrY'] as ChromKey[];
-
-  private chromosomeSizes: Record<string, number> = {};
-
-  private totalSize = 0;
-
-  private averageSize = 0;
-
-  private interval: Record<ChromKey, [number, number]>;
-
-  constructor(assembly: 'hg38' = 'hg38') {
-    const stats = computeForAssembly(assembly);
-
-    this.chromosomeSizes = stats.size;
-    this.totalSize = stats.total;
-
-    this.interval = stats.interval as Record<ChromKey, [number, number]>;
-
-    this.averageSize = this.totalSize / this.chromosomesInOrder.length;
-  }
-
-  getStartOfChromosome(chrom: string) {
-    return this.interval[chrom as ChromKey]![0];
-  }
-
-  getEndOfChromosome(chrom: string) {
-    return this.interval[chrom as ChromKey]![1];
-  }
-
-  getTotalGenomeSize() {
-    return this.totalSize;
-  }
-
-  relativeToAbsolutePosition(chrom: string, pos: number) {
-    return this.interval[chrom as ChromKey]![0] + pos;
-  }
-
-  getFirstRelativePosition() {
-    return {
-      chromosome: this.chromosomesInOrder[0],
-      position: 0,
-    };
-  }
-
-  getLastRelativePosition() {
-    return {
-      chromosome: this.chromosomesInOrder[this.chromosomesInOrder.length - 1],
-      position: this.chromosomeSizes[this.chromosomesInOrder[this.chromosomesInOrder.length - 1]!]! - 1,
-    };
-  }
-
-  absoluteToRelativePosition(pos: number) {
-    if (pos <= 0) {
-      return this.getFirstRelativePosition();
-    }
-    if (pos >= this.totalSize) {
-      return this.getLastRelativePosition();
-    }
-
-    // Replace with binary search for faster lookup
-    for (let i = 0; i < this.chromosomesInOrder.length; i++) {
-      const chromosome = this.chromosomesInOrder[i]!;
-
-      if (this.interval[chromosome]![0] <= pos && pos < this.interval[chromosome]![1]) {
-        return {
-          chromosome,
-          position: pos - this.interval[chromosome]![0],
-        };
-      }
-    }
-
-    throw new Error('Could not find the chromosome');
-  }
-}
diff --git a/src/utils/index.ts b/src/utils/index.ts
index ebe0368ba..e717b937c 100644
--- a/src/utils/index.ts
+++ b/src/utils/index.ts
@@ -4,4 +4,3 @@ export * from './initializeLibrary';
 export * from './fromNow';
 export * from './colors';
 export * from './sanitize-filename';
-export * from './GenomeNavigation';