X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=751175d8025f607e7a433933ebb36134bdf0e44c;hb=567c2595554096f10feab130153f97286f3f7d80;hp=90a79522b9038c9510fe5b4f30d1f71fa6ab061c;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 90a7952..751175d 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -20,10 +20,6 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.scoremodels.FeatureScoreModel;
-import jalview.analysis.scoremodels.PIDScoreModel;
-import jalview.api.analysis.ScoreModelI;
-
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -36,8 +32,6 @@ import java.util.Vector;
 
 public class ResidueProperties
 {
-  public static Hashtable<String, ScoreModelI> scoreMatrices = new Hashtable<String, ScoreModelI>();
-
   // Stores residue codes/names and colours and other things
   public static final int[] aaIndex; // aaHash version 2.1.1 and below
 
@@ -222,10 +216,14 @@ 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));
@@ -473,105 +471,6 @@ public class ResidueProperties
 
   // public static final double hydmax = 1.38;
   // public static final double hydmin = -2.53;
-  private static final int[][] BLOSUM62 = {
-      { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
-          -2, 0, -2, -1, 0, -4 },
-      { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3,
-          -2, -3, -1, 0, -1, -4 },
-      { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2,
-          -3, 3, 0, -1, -4 },
-      { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
-          -3, -3, 4, 1, -1, -4 },
-      { 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1,
-          -2, -2, -1, -3, -3, -2, -4 },
-      { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,
-          -2, 0, 3, -1, -4 },
-      { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,
-          -2, 1, 4, -1, -4 },
-      { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
-          -3, -3, -1, -2, -1, -4 },
-      { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2,
-          2, -3, 0, 0, -1, -4 },
-      { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
-          -1, 3, -3, -3, -1, -4 },
-      { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
-          -1, 1, -4, -3, -1, -4 },
-      { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3,
-          -2, -2, 0, 1, -1, -4 },
-      { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
-          -1, 1, -3, -1, -1, -4 },
-      { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1,
-          3, -1, -3, -3, -1, -4 },
-      { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,
-          -4, -3, -2, -2, -1, -2, -4 },
-      { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,
-          -2, 0, 0, 0, -4 },
-      { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
-          -2, 0, -1, -1, 0, -4 },
-      { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,
-          11, 2, -3, -4, -3, -2, -4 },
-      { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2,
-          2, 7, -1, -3, -2, -1, -4 },
-      { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
-          -1, 4, -3, -2, -1, -4 },
-      { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4,
-          -3, -3, 4, 1, -1, -4 },
-      { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,
-          -2, 1, 4, -1, -4 },
-      { 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0,
-          -2, -1, -1, -1, -1, -1, -4 },
-      { -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
-          -4, -4, -4, -4, -4, -4, 1 }, };
-
-  static final int[][] PAM250 = {
-      { 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3,
-          0, 0, 0, 0, -8 },
-      { -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
-          -2, -1, 0, -1, -8 },
-      { 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,
-          2, 1, 0, -8 },
-      { 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4,
-          -2, 3, 3, -1, -8 },
-      { -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,
-          -8, 0, -2, -4, -5, -3, -8 },
-      { 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,
-          -2, 1, 3, -1, -8 },
-      { 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4,
-          -2, 3, 3, -1, -8 },
-      { 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,
-          -1, 0, 0, -1, -8 },
-      { -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,
-          -2, 1, 2, -1, -8 },
-      { -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,
-          -1, 4, -2, -2, -1, -8 },
-      { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,
-          -1, 2, -3, -3, -1, -8 },
-      { -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4,
-          -2, 1, 0, -1, -8 },
-      { -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4,
-          -2, 2, -2, -2, -1, -8 },
-      { -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0,
-          7, -1, -4, -5, -2, -8 },
-      { 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,
-          -1, -1, 0, -1, -8 },
-      { 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3,
-          -1, 0, 0, 0, -8 },
-      { 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3,
-          0, 0, -1, 0, -8 },
-      { -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5,
-          17, 0, -6, -5, -6, -4, -8 },
-      { -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,
-          10, -2, -3, -4, -2, -8 },
-      { 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,
-          -2, 4, -2, -2, -1, -8 },
-      { 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3,
-          -2, 3, 2, -1, -8 },
-      { 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4,
-          -2, 2, 3, -1, -8 },
-      { 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,
-          -2, -1, -1, -1, -1, -8 },
-      { -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
-          -8, -8, -8, -8, -8, -8, 1 }, };
 
   // not currently used
   // public static final Map<String, Color> ssHash = new Hashtable<String,
@@ -594,40 +493,6 @@ public class ResidueProperties
    * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
    */
 
-  // JBPNote: patch matrix for T/U equivalence when working with DNA or RNA.
-  // Will equate sequences if working with mixed nucleotide sets.
-  // treats T and U identically. R and Y weak equivalence with AG and CTU.
-  // N matches any other base weakly
-  //
-  static final int[][] DNA = { { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A
-      { -8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1 }, // C
-      { -8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1 }, // G
-      { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // T
-      { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // U
-      { 1, 1, 1, 1, 1, 10, 0, 0, 0, 1, 1 }, // I
-      { 1, 1, 1, 1, 1, 0, 10, 0, 0, 1, 1 }, // X
-      { 1, -8, 1, -8, -8, 0, 0, 10, -8, 1, 1 }, // R
-      { -8, 1, -8, 1, 1, 0, 0, -8, 10, 1, 1 }, // Y
-      { 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1 }, // N
-      { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 }, // -
-  };
-  /**
-   * register matrices in list
-   */
-  static
-  {
-    scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62, 0));
-    scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250, 0));
-    scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
-  }
-
-  public static final Color[] pidColours = { midBlue,
-      new Color(153, 153, 255),
-      // Color.lightGray,
-      new Color(204, 204, 255), };
-
-  public static final float[] pidThresholds = { 80, 60, 40, };
-
   public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
 
   public static String START = "ATG";
@@ -910,267 +775,267 @@ 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", ONE);
+    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
@@ -1247,15 +1112,6 @@ public class ResidueProperties
       propMatrixPos[i][i] = maxP;
       propMatrixEpos[i][i] = maxEP;
     }
-    // JAL-1512 comment out physicochemical score matrices for 2.8.1 release
-    // scoreMatrices.put("Conservation Pos", new
-    // ScoreMatrix("Conservation Pos",propMatrixPos,0));
-    // scoreMatrices.put("Conservation Both", new
-    // ScoreMatrix("Conservation Both",propMatrixF,0));
-    // scoreMatrices.put("Conservation EnhPos", new
-    // ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
-    scoreMatrices.put("PID", new PIDScoreModel());
-    scoreMatrices.put("Displayed Features", new FeatureScoreModel());
   }
 
   private ResidueProperties()
@@ -1282,39 +1138,6 @@ public class ResidueProperties
     return aa3Hash;
   }
 
-  public static int[][] getDNA()
-  {
-    return ResidueProperties.DNA;
-  }
-
-  public static int[][] getBLOSUM62()
-  {
-    return ResidueProperties.BLOSUM62;
-  }
-
-  public static int getPAM250(String A1, String A2)
-  {
-    return getPAM250(A1.charAt(0), A2.charAt(0));
-  }
-
-  public static int getBLOSUM62(char c1, char c2)
-  {
-    int pog = 0;
-
-    try
-    {
-      int a = aaIndex[c1];
-      int b = aaIndex[c2];
-
-      pog = ResidueProperties.BLOSUM62[a][b];
-    } catch (Exception e)
-    {
-      // System.out.println("Unknown residue in " + A1 + " " + A2);
-    }
-
-    return pog;
-  }
-
   public static String codonTranslate(String lccodon)
   {
     String cdn = codonHash2.get(lccodon.toUpperCase());
@@ -1325,53 +1148,6 @@ public class ResidueProperties
     return cdn;
   }
 
-  public static int[][] getDefaultPeptideMatrix()
-  {
-    return ResidueProperties.getBLOSUM62();
-  }
-
-  public static int[][] getDefaultDnaMatrix()
-  {
-    return ResidueProperties.getDNA();
-  }
-
-  /**
-   * get a ScoreMatrix based on its string name
-   * 
-   * @param pwtype
-   * @return matrix in scoreMatrices with key pwtype or null
-   */
-  public static ScoreMatrix getScoreMatrix(String pwtype)
-  {
-    Object val = scoreMatrices.get(pwtype);
-    if (val != null && val instanceof ScoreMatrix)
-    {
-      return (ScoreMatrix) val;
-    }
-    return null;
-  }
-
-  /**
-   * get a ScoreModel based on its string name
-   * 
-   * @param pwtype
-   * @return scoremodel of type pwtype or null
-   */
-  public static ScoreModelI getScoreModel(String pwtype)
-  {
-    return scoreMatrices.get(pwtype);
-  }
-
-  public static int getPAM250(char c, char d)
-  {
-    int a = aaIndex[c];
-    int b = aaIndex[d];
-
-    int pog = ResidueProperties.PAM250[a][b];
-
-    return pog;
-  }
-
   public static Hashtable<String, String> toDssp3State;
   static
   {