diff --git a/java/src/org/broadinstitute/sting/secondarybase/SecondaryBaseAnnotator.java b/java/src/org/broadinstitute/sting/secondarybase/SecondaryBaseAnnotator.java
new file mode 100755
index 000000000..24473c0b8
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/secondarybase/SecondaryBaseAnnotator.java
@@ -0,0 +1,55 @@
+package org.broadinstitute.sting.secondarybase;
+
+import org.broadinstitute.sting.utils.containers.BoundedScoringSet;
+import org.broadinstitute.sting.utils.StingException;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+
+public class SecondaryBaseAnnotator {
+    private static final int TRAINING_LIMIT = 10000;
+    private boolean trained;
+    private final BoundedScoringSet<RawRead> trainingAggregator;
+    public BasecallingReadModel model;
+
+    public SecondaryBaseAnnotator() {
+        trained = false;
+        trainingAggregator = new BoundedScoringSet<RawRead>(TRAINING_LIMIT);
+    }
+
+    public void addTrainingRead(RawRead rawRead) { trainingAggregator.add(rawRead); }
+
+    public boolean haveEnoughTrainingReads() { return false; }
+
+    public void doneTraining() {
+        ArrayList<RawRead> trainingData = new ArrayList<RawRead>(trainingAggregator.size());
+
+        trainingData.addAll(Arrays.asList(trainingAggregator.toArray(new RawRead[0])));
+
+        model = new BasecallingReadModel(trainingData);
+
+        trained = true;
+    }
+
+    public FourProbRead getFourProbRead(RawRead rawRead) {
+        return model.call(rawRead);
+    }
+
+    public byte[] getSqTagValue(RawRead rawRead) {
+        if (!trained) {
+            throw new StingException("Model must be trained via addTrainingRead() before getSqTagValue() can be called");
+        }
+
+        FourProbRead fpr = model.call(rawRead);
+
+        return fpr.getSQTag(rawRead);
+    }
+
+    private void train() {}
+
+    private byte[] getSQTag(FourProbRead fourProbRead, RawRead rawRead) { return null; }
+
+    private static boolean isGoodTrainingRead(RawRead rawRead) { return false; }
+
+    private static double getAverageQualityScore(RawRead rawRead) { return 0.0; }
+}