JAL-1632 first cut of Tree chooser dialog and ScoreModels singleton

[jalview.git] / src / jalview / schemes / ResidueProperties.java

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 406814a..c774ebf 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -22,6 +22,7 @@ package jalview.schemes;
 
 import jalview.analysis.scoremodels.FeatureScoreModel;
 import jalview.analysis.scoremodels.PIDScoreModel;
+import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.api.analysis.ScoreModelI;
 
 import java.awt.Color;
@@ -477,7 +478,7 @@ public class ResidueProperties
 
   // public static final double hydmax = 1.38;
   // public static final double hydmin = -2.53;
-  private static final int[][] BLOSUM62 = {
+  public 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,
@@ -527,7 +528,7 @@ public class ResidueProperties
       { -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 = {
+  public 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,
@@ -603,7 +604,8 @@ public class ResidueProperties
   // 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
+  public 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
@@ -1252,7 +1254,8 @@ public class ResidueProperties
     // scoreMatrices.put("Conservation EnhPos", new
     // ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
     scoreMatrices.put("PID", new PIDScoreModel());
-    scoreMatrices.put("Displayed Features", new FeatureScoreModel());
+    scoreMatrices.put("Sequence Feature Similarity",
+            new FeatureScoreModel());
   }
 
   private ResidueProperties()