JAL-2416 scoreMatrices removed from ResidueProperties

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index fe04156..f623a96 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -21,6 +21,7 @@
 package jalview.analysis;
 
 import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Mapping;
@@ -423,11 +424,11 @@ public class AlignSeq
 
     if (type.equals(AlignSeq.PEP))
     {
-      lookup = ResidueProperties.getDefaultPeptideMatrix();
+      lookup = ScoreModels.getInstance().getDefaultModel(true).getMatrix();
     }
     else if (type.equals(AlignSeq.DNA))
     {
-      lookup = ResidueProperties.getDefaultDnaMatrix();
+      lookup = ScoreModels.getInstance().getDefaultModel(false).getMatrix();
     }
   }
 

diff --git a/src/jalview/analysis/scoremodels/PIDScoreModel.java b/src/jalview/analysis/scoremodels/PIDScoreModel.java
index 0f7a67a..e0e8634 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDScoreModel.java
+++ b/src/jalview/analysis/scoremodels/PIDScoreModel.java
@@ -72,4 +72,9 @@ public class PIDScoreModel implements ScoreModelI
     return true;
   }
 
+  @Override
+  public String toString()
+  {
+    return "Percentage identity of sequences";
+  }
 }

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 377fdef..07840fc 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -14,8 +14,17 @@ import java.util.Map;
  */
 public class ScoreModels
 {
-  private static ScoreModels instance = new ScoreModels();
+  /*
+   * constants for built-in score model names
+   * NB! these have to match names in loaded score matrix files
+   */
+  public static final String BLOSUM62 = "BLOSUM62";
+
+  public static final String PAM250 = "PAM250";
 
+  public static final String DNA = "DNA";
+
+  private static ScoreModels instance = new ScoreModels();
   private Map<String, ScoreModelI> models;
 
   public static ScoreModels getInstance()
@@ -99,4 +108,17 @@ public class ScoreModels
     }
     models.put(sm.getName(), sm);
   }
+
+  /**
+   * Returns the default peptide or nucleotide score model, currently BLOSUM62
+   * or DNA
+   * 
+   * @param forPeptide
+   * @return
+   */
+  public PairwiseSeqScoreModel getDefaultModel(boolean forPeptide)
+  {
+    return (PairwiseSeqScoreModel) (forPeptide ? forName("BLOSUM62")
+            : forName("DNA"));
+  }
 }

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index b4b8ec2..d3e6213 100644 (file)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.analysis.NJTree;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.datamodel.Alignment;
@@ -28,7 +29,6 @@ import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
 import jalview.io.NewickFile;
-import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -69,6 +69,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     return tree;
   }
 
+  @Override
   public void finalize() throws Throwable
   {
     ap = null;
@@ -200,6 +201,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       this.newtree = newtree;
     }
 
+    @Override
     public void run()
     {
       if (newtree != null)
@@ -235,7 +237,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-        ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+        ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
         if (sm instanceof ViewBasedAnalysisI)
         {
           try
@@ -286,6 +288,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == newickOutput)
@@ -302,6 +305,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == fitToWindow)

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index c03c40b..a88f74f 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -20,6 +20,8 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -53,6 +55,9 @@ public class Blosum62ColourScheme extends ResidueColourScheme
   public Color findColour(char res, int j, SequenceI seq,
           String consensusResidue, float pid)
   {
+    PairwiseSeqScoreModel sm = (PairwiseSeqScoreModel) ScoreModels
+            .getInstance().forName(ScoreModels.BLOSUM62);
+
     /*
      * compare as upper case; note consensusResidue is 
      * always computed as uppercase
@@ -79,7 +84,8 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
       for (char consensus : consensusResidue.toCharArray())
       {
-        score += ResidueProperties.getBLOSUM62(consensus, res);
+        score += sm.getPairwiseScore(consensus, res);
+        // score += ResidueProperties.getBLOSUM62(consensus, res);
       }
 
       if (score > 0)

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];

diff --git a/test/jalview/schemes/ScoreMatrixPrinter.java b/test/jalview/schemes/ScoreMatrixPrinter.java
index 4e7755c..b58b56f 100644 (file)
--- a/test/jalview/schemes/ScoreMatrixPrinter.java
+++ b/test/jalview/schemes/ScoreMatrixPrinter.java
@@ -21,11 +21,10 @@
 package jalview.schemes;
 
 import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.analysis.ScoreModelI;
 import jalview.gui.JvOptionPane;
 
-import java.util.Map;
-
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -42,25 +41,22 @@ public class ScoreMatrixPrinter
   @Test(groups = { "Functional" })
   public void printAllMatrices()
   {
-    for (Map.Entry<String, ScoreModelI> sm : ResidueProperties.scoreMatrices
-            .entrySet())
+    for (ScoreModelI sm : ScoreModels.getInstance().getModels())
     {
-      System.out.println("Matrix " + sm.getKey());
-      System.out.println(sm.getValue().toString());
+      System.out.println("Matrix " + sm.getName());
+      System.out.println(sm.toString());
     }
   }
 
   @Test(groups = { "Functional" })
   public void printHTMLMatrices()
   {
-    for (Map.Entry<String, ScoreModelI> _sm : ResidueProperties.scoreMatrices
-            .entrySet())
+    for (ScoreModelI sm : ScoreModels.getInstance().getModels())
     {
-      if (_sm.getValue() instanceof ScoreMatrix)
+      if (sm instanceof ScoreMatrix)
       {
-        ScoreMatrix sm = (ScoreMatrix) _sm.getValue();
-        System.out.println("Matrix " + _sm.getKey());
-        System.out.println(sm.outputMatrix(true));
+        System.out.println("Matrix " + sm.getName());
+        System.out.println(((ScoreMatrix) sm).outputMatrix(true));
       }
     }
   }