Add AugmentedAlignment interface #530

lphy-base/src/main/java/lphy/base/evolution/alignment/AugmentedAlignment.java

@@ -0,0 +1,16 @@
+package lphy.base.evolution.alignment;
+
+/**
+ * Guide to create an alignment containing the internal node sequences.
+ */
+public interface AugmentedAlignment<T> extends TaxaCharacterMatrix<T> {
+
+    /**
+     * @param sequenceId the index of sequences, tips are from 0 to (ntaxa - 1),
+     *                   internal nodes are the rest, and root index is the last.
+     * @param position   the site position.
+     * @return  the integer state at the given coordinate of this alignment.
+     */
+    T getState(int sequenceId, int position);
+
+}