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JAL-2255 Bug fix
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueProperties.java
diff --git
a/src/jalview/schemes/ResidueProperties.java
b/src/jalview/schemes/ResidueProperties.java
index
f855fde
..
1e6142d
100755
(executable)
--- a/
src/jalview/schemes/ResidueProperties.java
+++ b/
src/jalview/schemes/ResidueProperties.java
@@
-486,7
+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 },
-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 },
-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 },
@@
-625,13
+625,6
@@
public class ResidueProperties
scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
}
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";
public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
public static String START = "ATG";
@@
-935,7
+928,7
@@
public class ResidueProperties
hydrophobic.put("D", ZERO);
hydrophobic.put("N", ZERO);
hydrophobic.put("S", ZERO);
hydrophobic.put("D", ZERO);
hydrophobic.put("N", ZERO);
hydrophobic.put("S", ZERO);
- hydrophobic.put("T", ZERO);
+ hydrophobic.put("T", ONE);
hydrophobic.put("P", ZERO);
}
hydrophobic.put("P", ZERO);
}