X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;fp=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=1e6142d56a24ca4368ea041cc9c6025f3056cc79;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=90a79522b9038c9510fe5b4f30d1f71fa6ab061c;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 90a7952..1e6142d 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));
@@ -482,7 +486,7 @@ public class ResidueProperties
           -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,
+      { 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 },
@@ -621,13 +625,6 @@ public class ResidueProperties
     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 +907,267 @@ 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