JAL-2629 add documentation to previous work

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

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index e5b242d..7a8ef94 100644 (file)
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -31,6 +31,7 @@ public class HMMERColourScheme extends ResidueColourScheme
 
   }
 
+
   @Override
   public Color findColour(char symbol, int position, SequenceI seq,
           String consensusResidue, float pid)
@@ -42,7 +43,16 @@ public class HMMERColourScheme extends ResidueColourScheme
     return findColour(symbol, position);
   }
 
-  public Color findColour(char symbol, int position)
+  /**
+   * Returns the colour at a particular symbol at a column in the alignment.
+   * 
+   * @param symbol
+   * @param position
+   * @return Red for an insertion, white for a gap, orange for a negative
+   *         information content, white to blue for increasing information
+   *         content.
+   */
+  private Color findColour(char symbol, int position)
   {
 
     if (Comparison.isGap(symbol))
@@ -145,7 +155,6 @@ public class HMMERColourScheme extends ResidueColourScheme
   @Override
   public boolean isSimple()
   {
-    // TODO Auto-generated method stub
     return false;
   }