From d8ae9323e25bd1d55b1252c7130b6ce382d0471c Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Fri, 11 Oct 2024 08:15:57 -0700
Subject: [PATCH] Add "visibility window" to wig track.   Useful when using
 "none" for summarization with large bigwig files.

---
 js/feature/wigTrack.js |  7 ++++++-
 js/ui/menuUtils.js     | 11 +++++++----
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/js/feature/wigTrack.js b/js/feature/wigTrack.js
index 58ee4e17b..cc44205ca 100755
--- a/js/feature/wigTrack.js
+++ b/js/feature/wigTrack.js
@@ -23,7 +23,8 @@ class WigTrack extends TrackBase {
         scaleFactor: undefined,
         overflowColor: `rgb(255, 32, 255)`,
         baselineColor: 'lightGray',
-        summarize: true
+        summarize: true,
+        visibilityWindow: undefined
     }
 
     constructor(config, browser) {
@@ -69,6 +70,10 @@ class WigTrack extends TrackBase {
         if (header) this.setTrackProperties(header)
     }
 
+    supportsWholeGenome() {
+        return this.visibilityWindow === undefined || this.visibilityWindow < 0
+    }
+
     async getFeatures(chr, start, end, bpPerPixel) {
 
         const windowFunction = this.windowFunction
diff --git a/js/ui/menuUtils.js b/js/ui/menuUtils.js
index 17dad9aa3..98feb1cb3 100644
--- a/js/ui/menuUtils.js
+++ b/js/ui/menuUtils.js
@@ -6,7 +6,7 @@ import {colorPalettes} from "../util/colorPalletes.js"
 
 const colorPickerTrackTypeSet = new Set(['bedtype', 'alignment', 'annotation', 'variant', 'wig', 'interact'])
 
-const vizWindowTypes = new Set(['alignment', 'annotation', 'variant', 'eqtl', 'qtl', 'snp', 'shoebox'])
+const vizWindowTypes = new Set(['alignment', 'annotation', 'variant', 'eqtl', 'qtl', 'snp', 'shoebox', 'wig'])
 
 const multiTrackSelectExclusionTypes = new Set(['sequence', 'ruler', 'ideogram'])
 
@@ -83,7 +83,7 @@ class MenuUtils {
 
         if (isVisibilityWindowType(trackView)) {
             list.push('<hr/>')
-            list.push(visibilityWindowMenuItem())
+            list.push(visibilityWindowMenuItem(trackView.track.type))
         }
 
         return list
@@ -166,7 +166,7 @@ function groupAutoScaleMenuItem() {
 }
 
 
-function visibilityWindowMenuItem() {
+function visibilityWindowMenuItem(trackType) {
 
     const object = $('<div>')
     object.text('Set visibility window')
@@ -184,9 +184,12 @@ function visibilityWindowMenuItem() {
             this.trackView.updateViews()
         }
 
+        const label = 'wig' === trackType ?
+            'Visibility window (bp). Enter 0 for whole chromosome, -1 for whole genome.' :
+            'Visibility window (bp). Enter 0 for whole chromosome.'
         const config =
             {
-                label: 'Visibility Window',
+                label,
                 value: this.visibilityWindow,
                 callback
             }