Revert "trackline logic bug -- all header lines were treated as a tra…

…ck line, not just likes beginning with "track"" This reverts commit fddefa7.
igvteam · Dec 14, 2021 · cce9115 · cce9115
1 parent fddefa7
commit cce9115
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Showing 9 changed files with 15 additions and 120 deletions.
diff --git a/dev/misc/igv-paper.html b/dev/misc/igv-paper.html
diff --git a/js/feature/featureParser.js b/js/feature/featureParser.js
@@ -94,7 +94,8 @@ class FeatureParser {
         let line
         while ((line = await dataWrapper.nextLine()) !== undefined) {
             if (line.startsWith("track") || line.startsWith("#track")) {
-                header.trackLineProperties = parseTrackLine(line)
+                let h = parseTrackLine(line)
+                Object.assign(header, h)
             } else if (line.startsWith("browser")) {
                 // UCSC line, currently ignored
             } else if (line.startsWith("#columns")) {

diff --git a/js/feature/featureTrack.js b/js/feature/featureTrack.js
@@ -117,8 +117,8 @@ class FeatureTrack extends TrackBase {
         }
 
         // Set properties from track line
-        if (this.header && this.header.trackLineProperties) {
-            this.setTrackProperties(this.header.trackLineProperties)
+        if (this.header) {
+            this.setTrackProperties(this.header)
         }
 
         if (this.visibilityWindow === undefined && typeof this.featureSource.defaultVisibilityWindow === 'function') {

diff --git a/js/feature/interactionTrack.js b/js/feature/interactionTrack.js
@@ -87,8 +87,8 @@ class InteractionTrack extends TrackBase {
         }
 
         // Set properties from track line
-        if (this.header && this.header.trackLineProperties) {
-            this.setTrackProperties(this.header.trackLineProperties)
+        if (this.header) {
+            this.setTrackProperties(this.header)
         }
 
         if (this.visibilityWindow === undefined && typeof this.featureSource.defaultVisibilityWindow === 'function') {

diff --git a/js/feature/segTrack.js b/js/feature/segTrack.js
@@ -107,8 +107,8 @@ class SegTrack extends TrackBase {
             this.header = await this.featureSource.getHeader()
         }
         // Set properties from track line
-        if (this.header && this.header.trackLineProperties) {
-            this.setTrackProperties(this.header.trackLineProperties)
+        if (this.header) {
+            this.setTrackProperties(this.header)
         }
     }
 

diff --git a/js/feature/spliceJunctionTrack.js b/js/feature/spliceJunctionTrack.js
@@ -82,8 +82,8 @@ class SpliceJunctionTrack extends TrackBase {
         }
 
         // Set properties from track line
-        if (this.header && this.header.trackLineProperties) {
-            this.setTrackProperties(this.header.trackLineProperties)
+        if (this.header) {
+            this.setTrackProperties(this.header)
         }
 
         if (this.visibilityWindow === undefined && typeof this.featureSource.defaultVisibilityWindow === 'function') {

diff --git a/js/feature/wigTrack.js b/js/feature/wigTrack.js
@@ -73,9 +73,7 @@ class WigTrack extends TrackBase {
 
     async postInit() {
         const header = await this.getHeader()
-        if (header && header.trackLineProperties) {
-            this.setTrackProperties(header.trackLineProperties)
-        }
+        if (header) this.setTrackProperties(header)
     }
 
     async getFeatures(chr, start, end, bpPerPixel) {

diff --git a/js/gcnv/gcnvTrack.js b/js/gcnv/gcnvTrack.js
@@ -49,9 +49,8 @@ class GCNVTrack extends TrackBase {
             this.sampleNames = this.header.columnNames.slice(3)
 
             // Set generic properties from track line
-            if (this.header && this.header.trackLineProperties) {
-                this.setTrackProperties(this.header.trackLineProperties)
-            }
+            this.setTrackProperties(this.header)   // setTrackProperties defined in TrackBase
+
             // set option to highlight sample track line on click
             if (this.header.hasOwnProperty("clickToHighlight")) {
                 let colour = this.header["clickToHighlight"]

diff --git a/js/gwas/gwasTrack.js b/js/gwas/gwasTrack.js
@@ -79,8 +79,8 @@ class GWASTrack extends TrackBase {
         }
 
         // Set properties from track line
-        if (this.header && this.header.trackLineProperties) {
-            this.setTrackProperties(this.header.trackLineProperties)
+        if (this.header) {
+            this.setTrackProperties(this.header)   // setTrackProperties defined in TrackBase
         }
 
         // Set initial range if specfied, unless autoscale == true