Commented a gotcha (at least, it just got me):

dmyersturnbull · dmyersturnbull · commit fa82bcbe6b65 · 2014-11-19T17:11:24.000-08:00
SimpleGapPenalty penalty = new SimpleGapPenalty();
    penalty.setOpenPenalty((short) 10);
    penalty.getOpenPenalty(); // returns -10, not 10
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleGapPenalty.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleGapPenalty.java
@@ -65,20 +65,26 @@ public SimpleGapPenalty() {
     /**
      * Creates a new set of gap penalties.
      *
-     * @param gop the gap open penalty
-     * @param gep the gap extension penalty
+     * @param gop the gap open penalty; should be nonnegative
+     * @param gep the gap extension penalty; should be nonnegative
      */
     public SimpleGapPenalty(short gop, short gep) {
         this.gop = (short) -Math.abs(gop);
         this.gep = (short) -Math.abs(gep);
         setType();
     }
 
+    /**
+     * <strong>Returns the negative of the extension penalty passed to the constructor.</strong>
+     */
     @Override
     public short getExtensionPenalty() {
         return gep;
     }
 
+    /**
+     * <strong>Returns the negative of the opening penalty passed to the constructor.</strong>
+     */
     @Override
     public short getOpenPenalty() {
         return gop;
@@ -89,12 +95,18 @@ public Type getType() {
         return type;
     }
 
+    /**
+     * @param gep Should be nonnegative
+     */
     @Override
     public void setExtensionPenalty(short gep) {
         this.gep = (short) -Math.abs(gep);
         setType();
     }
 
+    /**
+     * @param gop Should be nonnegative
+     */
     @Override
     public void setOpenPenalty(short gop) {
         this.gop = (short) -Math.abs(gop);
