function returns list instead of modifying parameter

service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java

@@ -152,8 +152,8 @@ public class ColorSchemaReader {
       String[] columns = line.split("\t");
 
       Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<>();
-      List<Pair<MiriamType, Integer>> customIdentifiers = new ArrayList<>();
-      parseColumns(columns, schemaColumns, customIdentifiers, ColorSchemaType.GENETIC_VARIANT);
+      List<Pair<MiriamType, Integer>> customIdentifiers = parseColumns(columns, schemaColumns,
+          ColorSchemaType.GENETIC_VARIANT);
       Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
       Integer contigColumn = schemaColumns.get(ColorSchemaColumn.CONTIG);
       if (contigColumn == null) {
@@ -481,8 +481,7 @@ public class ColorSchemaReader {
       String[] columns = line.split("\t");
 
       Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<>();
-      List<Pair<MiriamType, Integer>> customIdentifiers = new ArrayList<>();
-      parseColumns(columns, schemaColumns, customIdentifiers, ColorSchemaType.GENERIC);
+      List<Pair<MiriamType, Integer>> customIdentifiers = parseColumns(columns, schemaColumns, ColorSchemaType.GENERIC);
 
       Integer valueColumn = schemaColumns.get(ColorSchemaColumn.VALUE);
       Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
@@ -680,8 +679,9 @@ public class ColorSchemaReader {
    * @throws InvalidColorSchemaException
    *           thrown when the list of column headers contain invalid value
    */
-  public void parseColumns(String[] columns, Map<ColorSchemaColumn, Integer> schemaColumns,
-      List<Pair<MiriamType, Integer>> customIdentifiers, ColorSchemaType type) throws InvalidColorSchemaException {
+  public List<Pair<MiriamType, Integer>> parseColumns(String[] columns, Map<ColorSchemaColumn, Integer> schemaColumns,
+      ColorSchemaType type) throws InvalidColorSchemaException {
+    List<Pair<MiriamType, Integer>> result = new ArrayList<>();
     Map<String, MiriamType> acceptableIdentifiers = new HashMap<>();
     Map<String, MiriamType> deprecatedIdentifiers = new HashMap<>();
     for (MiriamType miriamType : MiriamType.values()) {
@@ -701,9 +701,9 @@ public class ColorSchemaReader {
       }
       if (!found) {
         if (acceptableIdentifiers.keySet().contains(columns[i].toLowerCase())) {
-          customIdentifiers.add(new Pair<>(acceptableIdentifiers.get(columns[i].toLowerCase()), i));
+          result.add(new Pair<>(acceptableIdentifiers.get(columns[i].toLowerCase()), i));
         } else if (deprecatedIdentifiers.keySet().contains(columns[i].toLowerCase())) {
-          customIdentifiers.add(new Pair<>(deprecatedIdentifiers.get(columns[i].toLowerCase()), i));
+          result.add(new Pair<>(deprecatedIdentifiers.get(columns[i].toLowerCase()), i));
         } else {
           String columnNames = "";
           for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
@@ -719,6 +719,7 @@ public class ColorSchemaReader {
         }
       }
     }
+    return result;
   }
 
   /**