JAL-2416 scoreMatrices removed from ResidueProperties

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index b4b5452..0b1b7cc 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -20,11 +20,6 @@
  */
 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;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -37,8 +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
 
@@ -1246,16 +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("Sequence Feature Similarity",
-            new FeatureScoreModel());
   }
 
   private ResidueProperties()
@@ -1282,11 +1265,6 @@ public class ResidueProperties
     return aa3Hash;
   }
 
-  public static float[][] getDNA()
-  {
-    return ResidueProperties.DNA;
-  }
-
   public static float[][] getBLOSUM62()
   {
     return ResidueProperties.BLOSUM62;
@@ -1297,24 +1275,6 @@ public class ResidueProperties
     return getPAM250(A1.charAt(0), A2.charAt(0));
   }
 
-  public static float getBLOSUM62(char c1, char c2)
-  {
-    float 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());
@@ -1325,43 +1285,6 @@ public class ResidueProperties
     return cdn;
   }
 
-  public static float[][] getDefaultPeptideMatrix()
-  {
-    return ResidueProperties.getBLOSUM62();
-  }
-
-  public static float[][] 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 float getPAM250(char c, char d)
   {
     int a = aaIndex[c];