X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=0b1b7cc943ba6d14aacdb10310d6108bfd004cb1;hb=a45b4529c64901e9e4b53b6c74ee804370c91002;hp=4d46279ba34d53b63fe75e00b2bc8f82be8bacd6;hpb=a0559d1b4aa6c156f413cde0e7ae5c877cb3cbdb;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 4d46279..0b1b7cc 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
 
@@ -477,7 +471,7 @@ 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 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,
@@ -527,7 +521,7 @@ 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 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,
@@ -603,7 +597,8 @@ 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 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
       { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // T
@@ -620,18 +615,11 @@ 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 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";
@@ -1251,15 +1239,6 @@ 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()
@@ -1286,39 +1265,16 @@ public class ResidueProperties
     return aa3Hash;
   }
 
-  public static int[][] 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)
-  {
-    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());
@@ -1329,49 +1285,12 @@ 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)
+  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;
   }