From 251bd6bbc7324e2235bb663b1b255317817957b1 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 1 Nov 2016 16:13:52 +0000
Subject: [PATCH] JAL-98 use Integer constants; tests added for propHash
 values

---
 src/jalview/schemes/ResidueProperties.java      |  452 ++++++++++++-----------
 test/jalview/schemes/ResiduePropertiesTest.java |   59 +++
 2 files changed, 287 insertions(+), 224 deletions(-)

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 90a7952..f855fde 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -222,10 +222,14 @@ public class ResidueProperties
     purinepyrimidineIndex['n'] = 2;
   }
 
+  private static final Integer ONE = Integer.valueOf(1);
+
+  private static final Integer ZERO = Integer.valueOf(0);
+
   static
   {
-    aa3Hash.put("ALA", Integer.valueOf(0));
-    aa3Hash.put("ARG", Integer.valueOf(1));
+    aa3Hash.put("ALA", ZERO);
+    aa3Hash.put("ARG", ONE);
     aa3Hash.put("ASN", Integer.valueOf(2));
     aa3Hash.put("ASP", Integer.valueOf(3)); // D
     aa3Hash.put("CYS", Integer.valueOf(4));
@@ -910,267 +914,267 @@ public class ResidueProperties
 
   static
   {
-    hydrophobic.put("I", Integer.valueOf(1));
-    hydrophobic.put("L", Integer.valueOf(1));
-    hydrophobic.put("V", Integer.valueOf(1));
-    hydrophobic.put("C", Integer.valueOf(1));
-    hydrophobic.put("A", Integer.valueOf(1));
-    hydrophobic.put("G", Integer.valueOf(1));
-    hydrophobic.put("M", Integer.valueOf(1));
-    hydrophobic.put("F", Integer.valueOf(1));
-    hydrophobic.put("Y", Integer.valueOf(1));
-    hydrophobic.put("W", Integer.valueOf(1));
-    hydrophobic.put("H", Integer.valueOf(1));
-    hydrophobic.put("K", Integer.valueOf(1));
-    hydrophobic.put("X", Integer.valueOf(1));
-    hydrophobic.put("-", Integer.valueOf(1));
-    hydrophobic.put("*", Integer.valueOf(1));
-    hydrophobic.put("R", Integer.valueOf(0));
-    hydrophobic.put("E", Integer.valueOf(0));
-    hydrophobic.put("Q", Integer.valueOf(0));
-    hydrophobic.put("D", Integer.valueOf(0));
-    hydrophobic.put("N", Integer.valueOf(0));
-    hydrophobic.put("S", Integer.valueOf(0));
-    hydrophobic.put("T", Integer.valueOf(0));
-    hydrophobic.put("P", Integer.valueOf(0));
+    hydrophobic.put("I", ONE);
+    hydrophobic.put("L", ONE);
+    hydrophobic.put("V", ONE);
+    hydrophobic.put("C", ONE);
+    hydrophobic.put("A", ONE);
+    hydrophobic.put("G", ONE);
+    hydrophobic.put("M", ONE);
+    hydrophobic.put("F", ONE);
+    hydrophobic.put("Y", ONE);
+    hydrophobic.put("W", ONE);
+    hydrophobic.put("H", ONE);
+    hydrophobic.put("K", ONE);
+    hydrophobic.put("X", ONE);
+    hydrophobic.put("-", ONE);
+    hydrophobic.put("*", ONE);
+    hydrophobic.put("R", ZERO);
+    hydrophobic.put("E", ZERO);
+    hydrophobic.put("Q", ZERO);
+    hydrophobic.put("D", ZERO);
+    hydrophobic.put("N", ZERO);
+    hydrophobic.put("S", ZERO);
+    hydrophobic.put("T", ZERO);
+    hydrophobic.put("P", ZERO);
   }
 
   static
   {
-    polar.put("Y", Integer.valueOf(1));
-    polar.put("W", Integer.valueOf(1));
-    polar.put("H", Integer.valueOf(1));
-    polar.put("K", Integer.valueOf(1));
-    polar.put("R", Integer.valueOf(1));
-    polar.put("E", Integer.valueOf(1));
-    polar.put("Q", Integer.valueOf(1));
-    polar.put("D", Integer.valueOf(1));
-    polar.put("N", Integer.valueOf(1));
-    polar.put("S", Integer.valueOf(1));
-    polar.put("T", Integer.valueOf(1));
-    polar.put("X", Integer.valueOf(1));
-    polar.put("-", Integer.valueOf(1));
-    polar.put("*", Integer.valueOf(1));
-    polar.put("I", Integer.valueOf(0));
-    polar.put("L", Integer.valueOf(0));
-    polar.put("V", Integer.valueOf(0));
-    polar.put("C", Integer.valueOf(0));
-    polar.put("A", Integer.valueOf(0));
-    polar.put("G", Integer.valueOf(0));
-    polar.put("M", Integer.valueOf(0));
-    polar.put("F", Integer.valueOf(0));
-    polar.put("P", Integer.valueOf(0));
+    polar.put("Y", ONE);
+    polar.put("W", ONE);
+    polar.put("H", ONE);
+    polar.put("K", ONE);
+    polar.put("R", ONE);
+    polar.put("E", ONE);
+    polar.put("Q", ONE);
+    polar.put("D", ONE);
+    polar.put("N", ONE);
+    polar.put("S", ONE);
+    polar.put("T", ONE);
+    polar.put("X", ONE);
+    polar.put("-", ONE);
+    polar.put("*", ONE);
+    polar.put("I", ZERO);
+    polar.put("L", ZERO);
+    polar.put("V", ZERO);
+    polar.put("C", ZERO);
+    polar.put("A", ZERO);
+    polar.put("G", ZERO);
+    polar.put("M", ZERO);
+    polar.put("F", ZERO);
+    polar.put("P", ZERO);
   }
 
   static
   {
-    small.put("I", Integer.valueOf(0));
-    small.put("L", Integer.valueOf(0));
-    small.put("V", Integer.valueOf(1));
-    small.put("C", Integer.valueOf(1));
-    small.put("A", Integer.valueOf(1));
-    small.put("G", Integer.valueOf(1));
-    small.put("M", Integer.valueOf(0));
-    small.put("F", Integer.valueOf(0));
-    small.put("Y", Integer.valueOf(0));
-    small.put("W", Integer.valueOf(0));
-    small.put("H", Integer.valueOf(0));
-    small.put("K", Integer.valueOf(0));
-    small.put("R", Integer.valueOf(0));
-    small.put("E", Integer.valueOf(0));
-    small.put("Q", Integer.valueOf(0));
-    small.put("D", Integer.valueOf(1));
-    small.put("N", Integer.valueOf(1));
-    small.put("S", Integer.valueOf(1));
-    small.put("T", Integer.valueOf(1));
-    small.put("P", Integer.valueOf(1));
-    small.put("-", Integer.valueOf(1));
-    small.put("*", Integer.valueOf(1));
+    small.put("I", ZERO);
+    small.put("L", ZERO);
+    small.put("V", ONE);
+    small.put("C", ONE);
+    small.put("A", ONE);
+    small.put("G", ONE);
+    small.put("M", ZERO);
+    small.put("F", ZERO);
+    small.put("Y", ZERO);
+    small.put("W", ZERO);
+    small.put("H", ZERO);
+    small.put("K", ZERO);
+    small.put("R", ZERO);
+    small.put("E", ZERO);
+    small.put("Q", ZERO);
+    small.put("D", ONE);
+    small.put("N", ONE);
+    small.put("S", ONE);
+    small.put("T", ONE);
+    small.put("P", ONE);
+    small.put("-", ONE);
+    small.put("*", ONE);
   }
 
   static
   {
-    positive.put("I", Integer.valueOf(0));
-    positive.put("L", Integer.valueOf(0));
-    positive.put("V", Integer.valueOf(0));
-    positive.put("C", Integer.valueOf(0));
-    positive.put("A", Integer.valueOf(0));
-    positive.put("G", Integer.valueOf(0));
-    positive.put("M", Integer.valueOf(0));
-    positive.put("F", Integer.valueOf(0));
-    positive.put("Y", Integer.valueOf(0));
-    positive.put("W", Integer.valueOf(0));
-    positive.put("H", Integer.valueOf(1));
-    positive.put("K", Integer.valueOf(1));
-    positive.put("R", Integer.valueOf(1));
-    positive.put("E", Integer.valueOf(0));
-    positive.put("Q", Integer.valueOf(0));
-    positive.put("D", Integer.valueOf(0));
-    positive.put("N", Integer.valueOf(0));
-    positive.put("S", Integer.valueOf(0));
-    positive.put("T", Integer.valueOf(0));
-    positive.put("P", Integer.valueOf(0));
-    positive.put("-", Integer.valueOf(1));
-    positive.put("*", Integer.valueOf(1));
+    positive.put("I", ZERO);
+    positive.put("L", ZERO);
+    positive.put("V", ZERO);
+    positive.put("C", ZERO);
+    positive.put("A", ZERO);
+    positive.put("G", ZERO);
+    positive.put("M", ZERO);
+    positive.put("F", ZERO);
+    positive.put("Y", ZERO);
+    positive.put("W", ZERO);
+    positive.put("H", ONE);
+    positive.put("K", ONE);
+    positive.put("R", ONE);
+    positive.put("E", ZERO);
+    positive.put("Q", ZERO);
+    positive.put("D", ZERO);
+    positive.put("N", ZERO);
+    positive.put("S", ZERO);
+    positive.put("T", ZERO);
+    positive.put("P", ZERO);
+    positive.put("-", ONE);
+    positive.put("*", ONE);
   }
 
   static
   {
-    negative.put("I", Integer.valueOf(0));
-    negative.put("L", Integer.valueOf(0));
-    negative.put("V", Integer.valueOf(0));
-    negative.put("C", Integer.valueOf(0));
-    negative.put("A", Integer.valueOf(0));
-    negative.put("G", Integer.valueOf(0));
-    negative.put("M", Integer.valueOf(0));
-    negative.put("F", Integer.valueOf(0));
-    negative.put("Y", Integer.valueOf(0));
-    negative.put("W", Integer.valueOf(0));
-    negative.put("H", Integer.valueOf(0));
-    negative.put("K", Integer.valueOf(0));
-    negative.put("R", Integer.valueOf(0));
-    negative.put("E", Integer.valueOf(1));
-    negative.put("Q", Integer.valueOf(0));
-    negative.put("D", Integer.valueOf(1));
-    negative.put("N", Integer.valueOf(0));
-    negative.put("S", Integer.valueOf(0));
-    negative.put("T", Integer.valueOf(0));
-    negative.put("P", Integer.valueOf(0));
-    negative.put("-", Integer.valueOf(1));
-    negative.put("*", Integer.valueOf(1));
+    negative.put("I", ZERO);
+    negative.put("L", ZERO);
+    negative.put("V", ZERO);
+    negative.put("C", ZERO);
+    negative.put("A", ZERO);
+    negative.put("G", ZERO);
+    negative.put("M", ZERO);
+    negative.put("F", ZERO);
+    negative.put("Y", ZERO);
+    negative.put("W", ZERO);
+    negative.put("H", ZERO);
+    negative.put("K", ZERO);
+    negative.put("R", ZERO);
+    negative.put("E", ONE);
+    negative.put("Q", ZERO);
+    negative.put("D", ONE);
+    negative.put("N", ZERO);
+    negative.put("S", ZERO);
+    negative.put("T", ZERO);
+    negative.put("P", ZERO);
+    negative.put("-", ONE);
+    negative.put("*", ONE);
   }
 
   static
   {
-    charged.put("I", Integer.valueOf(0));
-    charged.put("L", Integer.valueOf(0));
-    charged.put("V", Integer.valueOf(0));
-    charged.put("C", Integer.valueOf(0));
-    charged.put("A", Integer.valueOf(0));
-    charged.put("G", Integer.valueOf(0));
-    charged.put("M", Integer.valueOf(0));
-    charged.put("F", Integer.valueOf(0));
-    charged.put("Y", Integer.valueOf(0));
-    charged.put("W", Integer.valueOf(0));
-    charged.put("H", Integer.valueOf(1));
-    charged.put("K", Integer.valueOf(1));
-    charged.put("R", Integer.valueOf(1));
-    charged.put("E", Integer.valueOf(1));
-    charged.put("Q", Integer.valueOf(0));
-    charged.put("D", Integer.valueOf(1));
-    charged.put("N", Integer.valueOf(0)); // Asparagine is polar but not
+    charged.put("I", ZERO);
+    charged.put("L", ZERO);
+    charged.put("V", ZERO);
+    charged.put("C", ZERO);
+    charged.put("A", ZERO);
+    charged.put("G", ZERO);
+    charged.put("M", ZERO);
+    charged.put("F", ZERO);
+    charged.put("Y", ZERO);
+    charged.put("W", ZERO);
+    charged.put("H", ONE);
+    charged.put("K", ONE);
+    charged.put("R", ONE);
+    charged.put("E", ONE);
+    charged.put("Q", ZERO);
+    charged.put("D", ONE);
+    charged.put("N", ZERO); // Asparagine is polar but not
                                           // charged.
     // Alternative would be charged and
     // negative (in basic form)?
-    charged.put("S", Integer.valueOf(0));
-    charged.put("T", Integer.valueOf(0));
-    charged.put("P", Integer.valueOf(0));
-    charged.put("-", Integer.valueOf(1));
-    charged.put("*", Integer.valueOf(1));
+    charged.put("S", ZERO);
+    charged.put("T", ZERO);
+    charged.put("P", ZERO);
+    charged.put("-", ONE);
+    charged.put("*", ONE);
   }
 
   static
   {
-    aromatic.put("I", Integer.valueOf(0));
-    aromatic.put("L", Integer.valueOf(0));
-    aromatic.put("V", Integer.valueOf(0));
-    aromatic.put("C", Integer.valueOf(0));
-    aromatic.put("A", Integer.valueOf(0));
-    aromatic.put("G", Integer.valueOf(0));
-    aromatic.put("M", Integer.valueOf(0));
-    aromatic.put("F", Integer.valueOf(1));
-    aromatic.put("Y", Integer.valueOf(1));
-    aromatic.put("W", Integer.valueOf(1));
-    aromatic.put("H", Integer.valueOf(1));
-    aromatic.put("K", Integer.valueOf(0));
-    aromatic.put("R", Integer.valueOf(0));
-    aromatic.put("E", Integer.valueOf(0));
-    aromatic.put("Q", Integer.valueOf(0));
-    aromatic.put("D", Integer.valueOf(0));
-    aromatic.put("N", Integer.valueOf(0));
-    aromatic.put("S", Integer.valueOf(0));
-    aromatic.put("T", Integer.valueOf(0));
-    aromatic.put("P", Integer.valueOf(0));
-    aromatic.put("-", Integer.valueOf(1));
-    aromatic.put("*", Integer.valueOf(1));
+    aromatic.put("I", ZERO);
+    aromatic.put("L", ZERO);
+    aromatic.put("V", ZERO);
+    aromatic.put("C", ZERO);
+    aromatic.put("A", ZERO);
+    aromatic.put("G", ZERO);
+    aromatic.put("M", ZERO);
+    aromatic.put("F", ONE);
+    aromatic.put("Y", ONE);
+    aromatic.put("W", ONE);
+    aromatic.put("H", ONE);
+    aromatic.put("K", ZERO);
+    aromatic.put("R", ZERO);
+    aromatic.put("E", ZERO);
+    aromatic.put("Q", ZERO);
+    aromatic.put("D", ZERO);
+    aromatic.put("N", ZERO);
+    aromatic.put("S", ZERO);
+    aromatic.put("T", ZERO);
+    aromatic.put("P", ZERO);
+    aromatic.put("-", ONE);
+    aromatic.put("*", ONE);
   }
 
   static
   {
-    aliphatic.put("I", Integer.valueOf(1));
-    aliphatic.put("L", Integer.valueOf(1));
-    aliphatic.put("V", Integer.valueOf(1));
-    aliphatic.put("C", Integer.valueOf(0));
-    aliphatic.put("A", Integer.valueOf(0));
-    aliphatic.put("G", Integer.valueOf(0));
-    aliphatic.put("M", Integer.valueOf(0));
-    aliphatic.put("F", Integer.valueOf(0));
-    aliphatic.put("Y", Integer.valueOf(0));
-    aliphatic.put("W", Integer.valueOf(0));
-    aliphatic.put("H", Integer.valueOf(0));
-    aliphatic.put("K", Integer.valueOf(0));
-    aliphatic.put("R", Integer.valueOf(0));
-    aliphatic.put("E", Integer.valueOf(0));
-    aliphatic.put("Q", Integer.valueOf(0));
-    aliphatic.put("D", Integer.valueOf(0));
-    aliphatic.put("N", Integer.valueOf(0));
-    aliphatic.put("S", Integer.valueOf(0));
-    aliphatic.put("T", Integer.valueOf(0));
-    aliphatic.put("P", Integer.valueOf(0));
-    aliphatic.put("-", Integer.valueOf(1));
-    aliphatic.put("*", Integer.valueOf(1));
+    aliphatic.put("I", ONE);
+    aliphatic.put("L", ONE);
+    aliphatic.put("V", ONE);
+    aliphatic.put("C", ZERO);
+    aliphatic.put("A", ZERO);
+    aliphatic.put("G", ZERO);
+    aliphatic.put("M", ZERO);
+    aliphatic.put("F", ZERO);
+    aliphatic.put("Y", ZERO);
+    aliphatic.put("W", ZERO);
+    aliphatic.put("H", ZERO);
+    aliphatic.put("K", ZERO);
+    aliphatic.put("R", ZERO);
+    aliphatic.put("E", ZERO);
+    aliphatic.put("Q", ZERO);
+    aliphatic.put("D", ZERO);
+    aliphatic.put("N", ZERO);
+    aliphatic.put("S", ZERO);
+    aliphatic.put("T", ZERO);
+    aliphatic.put("P", ZERO);
+    aliphatic.put("-", ONE);
+    aliphatic.put("*", ONE);
   }
 
   static
   {
-    tiny.put("I", Integer.valueOf(0));
-    tiny.put("L", Integer.valueOf(0));
-    tiny.put("V", Integer.valueOf(0));
-    tiny.put("C", Integer.valueOf(0));
-    tiny.put("A", Integer.valueOf(1));
-    tiny.put("G", Integer.valueOf(1));
-    tiny.put("M", Integer.valueOf(0));
-    tiny.put("F", Integer.valueOf(0));
-    tiny.put("Y", Integer.valueOf(0));
-    tiny.put("W", Integer.valueOf(0));
-    tiny.put("H", Integer.valueOf(0));
-    tiny.put("K", Integer.valueOf(0));
-    tiny.put("R", Integer.valueOf(0));
-    tiny.put("E", Integer.valueOf(0));
-    tiny.put("Q", Integer.valueOf(0));
-    tiny.put("D", Integer.valueOf(0));
-    tiny.put("N", Integer.valueOf(0));
-    tiny.put("S", Integer.valueOf(1));
-    tiny.put("T", Integer.valueOf(0));
-    tiny.put("P", Integer.valueOf(0));
-    tiny.put("-", Integer.valueOf(1));
-    tiny.put("*", Integer.valueOf(1));
+    tiny.put("I", ZERO);
+    tiny.put("L", ZERO);
+    tiny.put("V", ZERO);
+    tiny.put("C", ZERO);
+    tiny.put("A", ONE);
+    tiny.put("G", ONE);
+    tiny.put("M", ZERO);
+    tiny.put("F", ZERO);
+    tiny.put("Y", ZERO);
+    tiny.put("W", ZERO);
+    tiny.put("H", ZERO);
+    tiny.put("K", ZERO);
+    tiny.put("R", ZERO);
+    tiny.put("E", ZERO);
+    tiny.put("Q", ZERO);
+    tiny.put("D", ZERO);
+    tiny.put("N", ZERO);
+    tiny.put("S", ONE);
+    tiny.put("T", ZERO);
+    tiny.put("P", ZERO);
+    tiny.put("-", ONE);
+    tiny.put("*", ONE);
   }
 
   static
   {
-    proline.put("I", Integer.valueOf(0));
-    proline.put("L", Integer.valueOf(0));
-    proline.put("V", Integer.valueOf(0));
-    proline.put("C", Integer.valueOf(0));
-    proline.put("A", Integer.valueOf(0));
-    proline.put("G", Integer.valueOf(0));
-    proline.put("M", Integer.valueOf(0));
-    proline.put("F", Integer.valueOf(0));
-    proline.put("Y", Integer.valueOf(0));
-    proline.put("W", Integer.valueOf(0));
-    proline.put("H", Integer.valueOf(0));
-    proline.put("K", Integer.valueOf(0));
-    proline.put("R", Integer.valueOf(0));
-    proline.put("E", Integer.valueOf(0));
-    proline.put("Q", Integer.valueOf(0));
-    proline.put("D", Integer.valueOf(0));
-    proline.put("N", Integer.valueOf(0));
-    proline.put("S", Integer.valueOf(0));
-    proline.put("T", Integer.valueOf(0));
-    proline.put("P", Integer.valueOf(1));
-    proline.put("-", Integer.valueOf(1));
-    proline.put("*", Integer.valueOf(1));
+    proline.put("I", ZERO);
+    proline.put("L", ZERO);
+    proline.put("V", ZERO);
+    proline.put("C", ZERO);
+    proline.put("A", ZERO);
+    proline.put("G", ZERO);
+    proline.put("M", ZERO);
+    proline.put("F", ZERO);
+    proline.put("Y", ZERO);
+    proline.put("W", ZERO);
+    proline.put("H", ZERO);
+    proline.put("K", ZERO);
+    proline.put("R", ZERO);
+    proline.put("E", ZERO);
+    proline.put("Q", ZERO);
+    proline.put("D", ZERO);
+    proline.put("N", ZERO);
+    proline.put("S", ZERO);
+    proline.put("T", ZERO);
+    proline.put("P", ONE);
+    proline.put("-", ONE);
+    proline.put("*", ONE);
   }
 
   static
diff --git a/test/jalview/schemes/ResiduePropertiesTest.java b/test/jalview/schemes/ResiduePropertiesTest.java
index b68ca68..41d7448 100644
--- a/test/jalview/schemes/ResiduePropertiesTest.java
+++ b/test/jalview/schemes/ResiduePropertiesTest.java
@@ -25,6 +25,7 @@ import static org.testng.AssertJUnit.assertNull;
 
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
 import org.testng.annotations.Test;
 
@@ -1556,4 +1557,62 @@ public class ResiduePropertiesTest
     assertEquals('Q', ResidueProperties.getSingleCharacterCode("Gln"));
     assertEquals('Q', ResidueProperties.getSingleCharacterCode("gln"));
   }
+
+  @Test(groups = { "Functional" })
+  public void testPhysicoChemicalProperties()
+  {
+    checkProperty("aromatic", "FYWH-*");
+    checkProperty("aliphatic", "IVL-*");
+    checkProperty("tiny", "GAS-*");
+    checkProperty("small", "VCTGACSDNP-*");
+    checkProperty("charged", "HKRDE-*");
+    checkProperty("negative", "DE-*");
+    checkProperty("polar", "YWHRKTSNDEQ-*X");
+    checkProperty("positive", "HKR-*");
+    checkProperty("proline", "P-*");
+    checkProperty("hydrophobic", "MILVFYWHKCGAC-*X");
+  }
+
+  /**
+   * Verify that the residues in the list have the named property, and other
+   * residues do not
+   * 
+   * @param property
+   * @param residues
+   */
+  void checkProperty(String property, String residues)
+  {
+    Map<String, Integer> props = ResidueProperties.propHash.get(property);
+
+    /*
+     * assert residues have the property (value 1 in lookup)
+     */
+    for (char res : residues.toCharArray())
+    {
+      assertEquals(res + " should be " + property, 1,
+              props.get(String.valueOf(res)).intValue());
+    }
+
+    /*
+     * assert other residues do not (value 0 in lookup)
+     */
+    for (String res : ResidueProperties.aa)
+    {
+      if (!residues.contains(res))
+      {
+        Integer propValue = props.get(String.valueOf(res));
+
+        if (propValue != null)
+        {
+          /*
+           * conservation calculation assigns unexpected symbols
+           * the same value as '-'; here we just check those which
+           * explicitly do not have the property
+           */
+          assertEquals(res + " should not be " + property, 0,
+                  propValue.intValue());
+        }
+      }
+    }
+  }
 }
-- 
1.7.10.2