From d48e1301193cf55e0d47e1649eab21ac170b51db Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Tue, 28 Jan 2025 02:18:23 -0500
Subject: [PATCH] Lint

---
 .../LinearVariantMatrixRenderer.ts             |  1 -
 .../LinearVariantMatrixRendering.tsx           | 18 +++---------------
 .../makeImageData.ts                           |  1 -
 .../MultiVariantRenderer.ts                    | 10 +++++-----
 .../src/MultiLinearVariantRenderer/types.ts    |  1 +
 5 files changed, 9 insertions(+), 22 deletions(-)

diff --git a/plugins/variants/src/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts b/plugins/variants/src/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts
index 28e835d2e8..ac9910431b 100644
--- a/plugins/variants/src/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts
+++ b/plugins/variants/src/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts
@@ -40,7 +40,6 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
       width,
     })
 
-    console.log({ res })
     return {
       ...results,
       ...res,
diff --git a/plugins/variants/src/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx b/plugins/variants/src/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx
index e05ba85cd3..9bfef37753 100644
--- a/plugins/variants/src/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx
+++ b/plugins/variants/src/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx
@@ -1,22 +1,16 @@
+import { useRef } from 'react'
+
 import { PrerenderedCanvas } from '@jbrowse/core/ui'
 import { observer } from 'mobx-react'
-import RBush from 'rbush'
-import { useMemo, useRef } from 'react'
 
 const LinearVariantMatrixRendering = observer(function (props: {
   width: number
   height: number
-  rbush: any
   displayModel: any
   arr: string[]
 }) {
-  const { arr, width, height, displayModel, rbush } = props
-  //const clickMap2 = useMemo(
-  //  () => new RBush<{ genotype: string }>().fromJSON(rbush),
-  //  [rbush],
-  //)
+  const { arr, width, height, displayModel } = props
   const ref = useRef<HTMLDivElement>(null)
-  console.log({ arr })
 
   function getFeatureUnderMouse(eventClientX: number, eventClientY: number) {
     // calculates feature under mouse
@@ -30,12 +24,6 @@ const LinearVariantMatrixRendering = observer(function (props: {
 
     const dimY = arr.length
     const dimX = arr[0]?.length || 0
-    //console.log(arr, {
-    //  w: Math.round((offsetX / width) * dimY),
-    //  h: Math.round((offsetY / height) * dimX),
-    //  dimX,
-    //  dimY,
-    //})
     return arr[Math.floor((offsetX / width) * dimY)]?.[
       Math.floor((offsetY / height) * dimX)
     ]
diff --git a/plugins/variants/src/MultiLinearVariantMatrixRenderer/makeImageData.ts b/plugins/variants/src/MultiLinearVariantMatrixRenderer/makeImageData.ts
index c6923fb3b2..fa42cfd030 100644
--- a/plugins/variants/src/MultiLinearVariantMatrixRenderer/makeImageData.ts
+++ b/plugins/variants/src/MultiLinearVariantMatrixRenderer/makeImageData.ts
@@ -1,4 +1,3 @@
-import RBush from 'rbush'
 import {
   getColorAlleleCount,
   getColorPhased,
diff --git a/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRenderer.ts b/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRenderer.ts
index 67e229a8c2..65457a1776 100644
--- a/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRenderer.ts
+++ b/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRenderer.ts
@@ -1,14 +1,14 @@
 import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
 import { featureSpanPx, renderToAbstractCanvas } from '@jbrowse/core/util'
 
-import { getCol, getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util'
-
-import type { Feature } from '@jbrowse/core/util'
-import type { MultiRenderArgsDeserialized } from './types'
 import {
   getColorAlleleCount,
   getColorPhased,
 } from '../shared/multiVariantColor'
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util'
+
+import type { MultiRenderArgsDeserialized } from './types'
+import type { Feature } from '@jbrowse/core/util'
 
 const fudgeFactor = 0.6
 const f2 = fudgeFactor / 2
@@ -95,7 +95,7 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
       features.values(),
       minorAlleleFrequencyFilter,
     )
-    for (const feature of features.values()) {
+    for (const feature of mafs) {
       const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)
       const w = Math.max(Math.round(rightPx - leftPx), 2)
       const samp = feature.get('genotypes') as Record<string, string>
diff --git a/plugins/variants/src/MultiLinearVariantRenderer/types.ts b/plugins/variants/src/MultiLinearVariantRenderer/types.ts
index cc46600f8a..ab0f83abc4 100644
--- a/plugins/variants/src/MultiLinearVariantRenderer/types.ts
+++ b/plugins/variants/src/MultiLinearVariantRenderer/types.ts
@@ -20,4 +20,5 @@ export interface MultiRenderArgsDeserialized
   sources: Source[]
   rowHeight: number
   scrollTop: number
+  minorAlleleFrequencyFilter: number
 }