Change preference hierarchy behavior -- user settings for generic alignment tracks ("Alignments" tab) will now cascade down to RNA and 3rd gen alignments if there is no specific user setting for those types. Fixes igvteam#760.

Author: jrobinso

src/main/java/org/broad/igv/prefs/IGVPreferences.java

@@ -86,16 +86,15 @@ public IGVPreferences(Map<String, String> userPreferences,
     public String get(String key) {
         key = key.trim();
 
-        if(userPreferences.containsKey(key)) {
+        if (userPreferences.containsKey(key)) {
             return userPreferences.get(key);
-        }
-        else if(defaults != null && defaults.containsKey(key)) {
+        } else if (parent != null && parent.userPreferences.containsKey(key)) {
+            return parent.userPreferences.get(key);
+        } else if (defaults != null && defaults.containsKey(key)) {
             return defaults.get(key);
-        }
-        else if(parent != null) {
+        } else if (parent != null) {
             return parent.get(key);
-        }
-        else {
+        } else {
             return null;
         }
     }
@@ -104,6 +103,7 @@ else if(parent != null) {
     /**
      * Return preference with given key and specified default value.  If key is not present defaultValue is returned,
      * no search through defaults or hierarchy is performed.
+     *
      * @param key
      * @param defaultValue
      * @return
@@ -115,7 +115,6 @@ public String get(String key, String defaultValue) {
     }
 
 
-
     /**
      * Return the preference as a boolean value.
      *
@@ -243,10 +242,9 @@ public void addOverrides(Map<String, String> newPrefs) {
 
     public boolean getAntiAliasing() {
 
-        if(userPreferences.containsKey(Constants.ENABLE_ANTIALISING) || Globals.IS_LINUX == false) {
+        if (userPreferences.containsKey(Constants.ENABLE_ANTIALISING) || Globals.IS_LINUX == false) {
             return getAsBoolean(Constants.ENABLE_ANTIALISING);
-        }
-        else {
+        } else {
             // Linux with no explicit setting
             return false;
         }
@@ -792,7 +790,7 @@ private PaletteColorTable getLegacyMutationColorScheme() {
     }
 
     static String getMutationColorKey(String type) {
-        switch(type) {
+        switch (type) {
             case "Indel":
                 return MUTATION_INDEL_COLOR_KEY;
             case "Missense":
@@ -934,6 +932,6 @@ public void print(PrintWriter pw) {
             pw.println(entry.getValue());
         }
     }
-    
+
 
 }

src/main/resources/org/broad/igv/prefs/preferences.tab

@@ -62,6 +62,7 @@ CN_FREQ.AMP_THRESHOLD	CN freq amplification threshold	float	0.1
 CN_FREQ.DEL_THRESHOLD	CN freq deletion threshold	float	-0.1
 
 #Alignments
+info	Settings for alignment tracks.  See the RNA or Third Gen tabs to override for specific types.
 
 ##Track Display
 SAM.SHOW_ALIGNMENT_TRACK	Show alignment track	boolean	TRUE