JAL-1632 JAL-2416 load score matrices from file, as float[][]

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index c774ebf..b4b5452 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -478,7 +478,7 @@ public class ResidueProperties
 
   // public static final double hydmax = 1.38;
   // public static final double hydmin = -2.53;
-  public static final int[][] BLOSUM62 = {
+  public static final float[][] 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,
@@ -528,7 +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 }, };
 
-  public static final int[][] PAM250 = {
+  public static final float[][] 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,
@@ -604,7 +604,7 @@ public class ResidueProperties
   // treats T and U identically. R and Y weak equivalence with AG and CTU.
   // N matches any other base weakly
   //
-  public static final int[][] DNA = {
+  public static final float[][] 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
@@ -622,9 +622,9 @@ public class ResidueProperties
    */
   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));
+    // scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62));
+    // scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250));
+    // scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA));
   }
 
   public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
@@ -1282,24 +1282,24 @@ public class ResidueProperties
     return aa3Hash;
   }
 
-  public static int[][] getDNA()
+  public static float[][] getDNA()
   {
     return ResidueProperties.DNA;
   }
 
-  public static int[][] getBLOSUM62()
+  public static float[][] getBLOSUM62()
   {
     return ResidueProperties.BLOSUM62;
   }
 
-  public static int getPAM250(String A1, String A2)
+  public static float getPAM250(String A1, String A2)
   {
     return getPAM250(A1.charAt(0), A2.charAt(0));
   }
 
-  public static int getBLOSUM62(char c1, char c2)
+  public static float getBLOSUM62(char c1, char c2)
   {
-    int pog = 0;
+    float pog = 0;
 
     try
     {
@@ -1325,12 +1325,12 @@ public class ResidueProperties
     return cdn;
   }
 
-  public static int[][] getDefaultPeptideMatrix()
+  public static float[][] getDefaultPeptideMatrix()
   {
     return ResidueProperties.getBLOSUM62();
   }
 
-  public static int[][] getDefaultDnaMatrix()
+  public static float[][] getDefaultDnaMatrix()
   {
     return ResidueProperties.getDNA();
   }
@@ -1362,12 +1362,12 @@ public class ResidueProperties
     return scoreMatrices.get(pwtype);
   }
 
-  public static int getPAM250(char c, char d)
+  public static float getPAM250(char c, char d)
   {
     int a = aaIndex[c];
     int b = aaIndex[d];
 
-    int pog = ResidueProperties.PAM250[a][b];
+    float pog = ResidueProperties.PAM250[a][b];
 
     return pog;
   }