Use specifed nameSet, if specified, for whole genome and pulldown chr…

…omosome names.
igvteam · Aug 16, 2024 · 1ed0fc4 · 1ed0fc4
1 parent b611dbc
commit 1ed0fc4
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/src/main/java/org/broad/igv/ui/commandbar/ChromosomeComboBox.java b/src/main/java/org/broad/igv/ui/commandbar/ChromosomeComboBox.java
@@ -10,6 +10,7 @@
 import java.awt.geom.Rectangle2D;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Collectors;
 
 /**
  * Created by jrobinso on 7/6/17.
@@ -39,7 +40,8 @@ public void updateChromosFromGenome(Genome genome) {
 
         UIUtilities.invokeAndWaitOnEventThread(() -> {
 
-            List<String> allChromosomeNames = genome.getChromosomeNames();
+            List<String> allChromosomeNames = genome.getChromosomeNames().stream().map(chr -> genome.getChromosomeDisplayName(chr)).collect(Collectors.toList());
+
             if (allChromosomeNames.size() > 1) {
                 this.setVisible(true);
 

diff --git a/src/main/java/org/broad/igv/ui/panel/RulerPanel.java b/src/main/java/org/broad/igv/ui/panel/RulerPanel.java
@@ -277,7 +277,7 @@ private void drawChromosomeTicks(Graphics g) {
             if (dw > 5) {
                 int center = x + dw / 2;
 
-                String displayName = chrName;
+                String displayName = genome.getChromosomeDisplayName(chrName);
                 if (chrName.startsWith("gi|")) {
                     displayName = Genome.getNCBIName(chrName);
                 } else if (chrName.length() < 6) {