Merge branch 'features/JAL-845splitPaneMergeDevelop' into develop

[jalview.git] / src / jalview / analysis / CodonComparator.java

diff --git a/src/jalview/analysis/CodonComparator.java b/src/jalview/analysis/CodonComparator.java
new file mode 100644 (file)
index 0000000..fc196de
--- /dev/null
+++ b/src/jalview/analysis/CodonComparator.java
@@ -0,0 +1,91 @@
+package jalview.analysis;
+
+import jalview.datamodel.AlignedCodon;
+
+import java.util.Comparator;
+
+/**
+ * Implements rules for comparing two aligned codons, i.e. determining whether
+ * they should occupy the same position in a translated protein alignment, or
+ * one or the other should 'follow' (by preceded by a gap).
+ * 
+ * @author gmcarstairs
+ *
+ */
+public final class CodonComparator implements Comparator<AlignedCodon>
+{
+
+  @Override
+  public int compare(AlignedCodon ac1, AlignedCodon ac2)
+  {
+    if (ac1 == null || ac2 == null || ac1.equals(ac2))
+    {
+      return 0;
+    }
+
+    /**
+     * <pre>
+     * Case 1: if one starts before the other, and doesn't end after it, then it
+     * precedes. We ignore the middle base position here.
+     * A--GT
+     * -CT-G
+     * </pre>
+     */
+    if (ac1.pos1 < ac2.pos1 && ac1.pos3 <= ac2.pos3)
+    {
+      return -1;
+    }
+    if (ac2.pos1 < ac1.pos1 && ac2.pos3 <= ac1.pos3)
+    {
+      return 1;
+    }
+
+    /**
+     * <pre>
+     * Case 2: if one ends after the other, and doesn't start before it, then it
+     * follows. We ignore the middle base position here.
+     * -TG-A
+     * G-TC
+     * </pre>
+     */
+    if (ac1.pos3 > ac2.pos3 && ac1.pos1 >= ac2.pos1)
+    {
+      return 1;
+    }
+    if (ac2.pos3 > ac1.pos3 && ac2.pos1 >= ac1.pos1)
+    {
+      return -1;
+    }
+
+    /*
+     * Case 3: if start and end match, compare middle base positions.
+     */
+    if (ac1.pos1 == ac2.pos1 && ac1.pos3 == ac2.pos3)
+    {
+      return Integer.compare(ac1.pos2, ac2.pos2);
+    }
+
+    /*
+     * That just leaves the 'enclosing' case - one codon starts after but ends
+     * before the other. If the middle bases don't match, use their comparison
+     * (majority vote).
+     */
+    int compareMiddles = Integer.compare(ac1.pos2, ac2.pos2);
+    if (compareMiddles != 0)
+    {
+      return compareMiddles;
+    }
+
+    /**
+     * <pre>
+     * Finally just leaves overlap with matching middle base, e.g. 
+     * -A-A-A
+     * G--GG 
+     * In this case the choice is arbitrary whether to compare based on
+     * first or last base position. We pick the first. Note this preserves
+     * symmetricality of the comparison.
+     * </pre>
+     */
+    return Integer.compare(ac1.pos1, ac2.pos1);
+  }
+}