JAL-3127 always look up sequence ID colour from view when colouring by Sequence ID

[jalview.git] / src / jalview / schemes / ResidueColourScheme.java

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 6aa798e..2f7a5e0 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -62,8 +62,9 @@ public abstract class ResidueColourScheme implements ColourSchemeI
   /**
    * Creates a new ResidueColourScheme object.
    * 
-   * @param final int[] index table into colors (ResidueProperties.naIndex or
-   *        ResidueProperties.aaIndex)
+   * @param final
+   *          int[] index table into colors (ResidueProperties.naIndex or
+   *          ResidueProperties.aaIndex)
    * @param colors
    *          colours for symbols in sequences
    */
@@ -98,8 +99,7 @@ public abstract class ResidueColourScheme implements ColourSchemeI
   {
     Color colour = Color.white;
 
-    if (colors != null && symbolIndex != null
-            && c < symbolIndex.length
+    if (colors != null && symbolIndex != null && c < symbolIndex.length
             && symbolIndex[c] < colors.length)
     {
       colour = colors[symbolIndex[c]];
@@ -208,4 +208,14 @@ public abstract class ResidueColourScheme implements ColourSchemeI
   {
     return true;
   }
+
+  /**
+   * Default method returns false. Override this to return true in colour
+   * schemes that have a colour associated with gap residues.
+   */
+  @Override
+  public boolean hasGapColour()
+  {
+    return false;
+  }
 }