From 2b418afe4a7d013647076b26ebdd2523b2079922 Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Thu, 19 Oct 2023 09:44:52 -0700
Subject: [PATCH] Use indexes wherever possible

---
 js/bam/bamReader.js   | 42 +++++++++++++++++++++++-------------------
 js/bigwig/bwReader.js | 36 +++++-------------------------------
 js/browser.js         |  5 +----
 js/ucsc/ucscHub.js    |  6 ++++--
 4 files changed, 33 insertions(+), 56 deletions(-)

diff --git a/js/bam/bamReader.js b/js/bam/bamReader.js
index fdcdb03bc..8f023da3a 100644
--- a/js/bam/bamReader.js
+++ b/js/bam/bamReader.js
@@ -26,25 +26,7 @@ class BamReader {
     }
 
     async readAlignments(chr, bpStart, bpEnd) {
-
-        const chrToIndex = await this.getChrIndex()
-
-        if(!this.chrAliasTable.has(chr)) {
-            const chromosome = this.genome.getChromosome(chr)
-            if(chromosome) {
-                const aliases = chromosome.altNames
-                for(let a of aliases) {
-                    if(this.chrNames.has(a)) {
-                        this.chrAliasTable.set(chr, a)
-                    }
-                }
-            }
-            if(!this.chrAliasTable.has(chr)) this.chrAliasTable.set(chr, chr)
-        }
-
-        const queryChr = this.chrAliasTable.get(chr) || chr
-
-        const chrId = chrToIndex[queryChr]
+        const chrId = await this.#getChrIdx(chr)
         const alignmentContainer = new AlignmentContainer(chr, bpStart, bpEnd, this.config)
 
         if (chrId === undefined) {
@@ -71,6 +53,28 @@ class BamReader {
         }
     }
 
+    async #getChrIdx(chr) {
+        const chrToIndex = await this.getChrIndex()
+
+        if (!this.chrAliasTable.has(chr)) {
+            const chromosome = this.genome.getChromosome(chr)
+            if (chromosome) {
+                const aliases = chromosome.altNames
+                for (let a of aliases) {
+                    if (this.chrNames.has(a)) {
+                        this.chrAliasTable.set(chr, a)
+                    }
+                }
+            }
+            if (!this.chrAliasTable.has(chr)) this.chrAliasTable.set(chr, chr)
+        }
+
+        const queryChr = this.chrAliasTable.get(chr) || chr
+
+        const chrId = chrToIndex[queryChr]
+        return chrId
+    }
+
     async getHeader() {
         if (!this.header) {
             const genome = this.genome
diff --git a/js/bigwig/bwReader.js b/js/bigwig/bwReader.js
index d4046c57b..5be5b0cd1 100644
--- a/js/bigwig/bwReader.js
+++ b/js/bigwig/bwReader.js
@@ -81,36 +81,8 @@ class BWReader {
 
         await this.loadHeader()
 
-        let chrIdx1 = await this.#getIdForChr(chr1) // this.chromTree.nameToId.get(chr1)
-        let chrIdx2 = await this.#getIdForChr(chr2)  // this.chromTree.nameToId.get(chr2)
-
-        // // Try alias
-        // if (chrIdx1 === undefined) {
-        //     const aliasRecord = await this.genome.getAliasRecord(chr1)
-        //     if (aliasRecord) {
-        //         const aliases = Object.keys(aliasRecord)
-        //             .filter(k => k !== "start" && k !== "end")
-        //             .map(k => aliasRecord[k])
-        //             .filter(a => this.chromTree.nameToId.has(a))
-        //         if (aliases.length > 0) {
-        //             chrIdx1 = this.chromTree.nameToId.get(aliases[0])
-        //             this.chrAliasTable.set(chr1, aliases[0])
-        //         }
-        //     }
-        // }
-        // if (chrIdx2 === undefined) {
-        //     const aliasRecord = await this.genome.getAliasRecord(chr2)
-        //     if (aliasRecord) {
-        //         const aliases = Object.keys(aliasRecord)
-        //             .filter(k => k !== "start" && k !== "end")
-        //             .map(k => aliasRecord[k])
-        //             .filter(a => this.chromTree.nameToId.has(a))
-        //         if (aliases.length > 0) {
-        //             chrIdx2 = this.chromTree.nameToId.get(aliases[0])
-        //             this.chrAliasTable.set(chr2, aliases[0])
-        //         }
-        //     }
-        // }
+        let chrIdx1 = await this.#getIdForChr(chr1)
+        let chrIdx2 = await this.#getIdForChr(chr2)
 
         if (chrIdx1 === undefined || chrIdx2 === undefined) {
             return []
@@ -205,16 +177,18 @@ class BWReader {
         // Try alias
         if (chrIdx === undefined) {
             const aliasRecord = await this.genome.getAliasRecord(chr)
+            let alias
             if (aliasRecord) {
                 const aliases = Object.keys(aliasRecord)
                     .filter(k => k !== "start" && k !== "end")
                     .map(k => aliasRecord[k])
                     .filter(a => this.chromTree.nameToId.has(a))
                 if (aliases.length > 0) {
+                    alias = aliases[0]
                     chrIdx = this.chromTree.nameToId.get(aliases[0])
-                    this.chrAliasTable.set(chr, aliases[0])
                 }
             }
+            this.chrAliasTable.set(chr, alias)  // alias may be undefined => no alias exists. Setting prevents repeated attempts
         }
         return chrIdx
     }
diff --git a/js/browser.js b/js/browser.js
index 466b10fc9..33fd95ff4 100755
--- a/js/browser.js
+++ b/js/browser.js
@@ -235,9 +235,6 @@ class Browser {
 
         // chromosome select widget
         this.chromosomeSelectWidget = new ChromosomeSelectWidget(this, $genomicLocation.get(0))
-        if (undefined === config.showChromosomeWidget) {
-            config.showChromosomeWidget = true   // Default to true
-        }
         if (true === config.showChromosomeWidget) {
             this.chromosomeSelectWidget.show()
         } else {
@@ -738,7 +735,7 @@ class Browser {
         let genomeLabel = (genome.id && genome.id.length < 20 ? genome.id : `${genome.id.substring(0,8)}...${genome.id.substring(genome.id.length-8)}`)
         this.$current_genome.text(genomeLabel)
         this.$current_genome.attr('title', genome.description)
-        if(false !== this.config.showChromosomeWidget) {
+        if(this.config.showChromosomeWidget) {
             this.chromosomeSelectWidget.update(genome)
         }
     }
diff --git a/js/ucsc/ucscHub.js b/js/ucsc/ucscHub.js
index a0893e83a..14beca9ba 100644
--- a/js/ucsc/ucscHub.js
+++ b/js/ucsc/ucscHub.js
@@ -31,8 +31,10 @@ class Hub {
     }
 
     static supportedTypes = new Set(["bigBed", "bigWig", "bigGenePred"])
-    static filterTracks = new Set(["cytoBandIdeo", "assembly", "gap", "gapOverlap", "allGaps",
-        "cpgIslandExtUnmasked", "windowMasker"])
+    static filterTracks = new Set(["cytoBandIdeo"])
+
+    //["cytoBandIdeo", "assembly", "gap", "gapOverlap", "allGaps",
+    //         "cpgIslandExtUnmasked", "windowMasker"])
 
     constructor(url, stanzas, groups) {