Add basemod colors for 3 chebi codes. See #1563 (#1566)

igvteam · Sep 10, 2024 · 5a9c3ec · 5a9c3ec
1 parent 97dd56d
commit 5a9c3ec
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Showing 3 changed files with 12 additions and 1 deletion.
diff --git a/src/main/java/org/broad/igv/prefs/Constants.java b/src/main/java/org/broad/igv/prefs/Constants.java
@@ -197,13 +197,18 @@ private Constants() {
     public static final String BASEMOD_B_COLOR = "BASEMOD.B_COLOR";
     public static final String BASEMOD_A_COLOR = "BASEMOD.A_COLOR";
     public static final String BASEMOD_O_COLOR = "BASEMOD.O_COLOR";
+    public static final String BASEMOD_17082_COLOR = "BASEMOD.17082_COLOR";
+    public static final String BASEMOD_17596_COLOR = "BASEMOD.17596_COLOR";
+    public static final String BASEMOD_21839_COLOR = "BASEMOD.21839_COLOR";
     public static final String BASEMOD_OTHER_COLOR = "BASEMOD.OTHER_COLOR";
 
     public static final String BASEMOD_NONE_A_COLOR = "BASEMOD.NONE_A_COLOR";
     public static final String BASEMOD_NONE_C_COLOR = "BASEMOD.NONE_C_COLOR";
     public static final String BASEMOD_NONE_T_COLOR = "BASEMOD.NONE_T_COLOR";
     public static final String BASEMOD_NONE_G_COLOR = "BASEMOD.NONE_G_COLOR";
     public static final String BASEMOD_NONE_N_COLOR = "BASEMOD.NONE_N_COLOR";
+
+
     public static final String BASEMOD_GROUP_BY_STRAND = "BASEMOD.GROUP_BY_STRAND";
     public static final String BASEMOD_SKIPPED_BASES = "BASEMOD.SKIPPED_BASES";
     public static final String SMRT_KINETICS_SHOW_OPTIONS = "SMRT_KINETICS.SHOW_OPTIONS";
@@ -300,7 +305,6 @@ private Constants() {
     public static final String CIRC_VIEW_HOST = "CIRC_VIEW_HOST";
 
 
-
     /**
      * List of keys that affect the alignments loaded.  This list is used to trigger a reload, if required.
      * Not all alignment preferences need trigger a reload, this is a subset.

diff --git a/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java b/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java
@@ -43,6 +43,10 @@ public static void updateColors() {
         colors.put("e", preferences.getAsColor(BASEMOD_E_COLOR));
         colors.put("b", preferences.getAsColor(BASEMOD_B_COLOR));
         colors.put("a", preferences.getAsColor(BASEMOD_A_COLOR));
+        colors.put("17082", preferences.getAsColor(BASEMOD_17082_COLOR));
+        colors.put("17596", preferences.getAsColor(BASEMOD_17596_COLOR));
+        colors.put("21839", preferences.getAsColor(BASEMOD_21839_COLOR));
+
         colors.put("other", preferences.getAsColor(BASEMOD_OTHER_COLOR));
         colors.put("NONE_A", preferences.getAsColor(BASEMOD_NONE_A_COLOR));
         colors.put("NONE_C", preferences.getAsColor(BASEMOD_NONE_C_COLOR));

diff --git a/src/main/resources/org/broad/igv/prefs/preferences.tab b/src/main/resources/org/broad/igv/prefs/preferences.tab
@@ -236,6 +236,9 @@ BASEMOD.E_COLOR	5fU	color	141,221,208
 BASEMOD.B_COLOR	5caU	color	0,100,47
 BASEMOD.A_COLOR	6mA	color	51,0,111
 BASEMOD.O_COLOR	8oxoG	color	111,78,129
+BASEMOD.17082_COLOR	pseU	color	51,153,255
+BASEMOD.17596_COLOR	inosine	color	102,153,0
+BASEMOD.21839_COLOR	4mC	color	153,0,153
 BASEMOD.OTHER_COLOR	Other	color	132,178,158
 
 ## Unomdified base colors (2-color option)