JAL-2393 code tidy and comments, PIDDistanceModel deprecated

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 43f2161..b481e89 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -223,8 +223,7 @@ public class PCA implements Runnable
    * Computes a pairwise similarity matrix for the given sequence regions using
    * the configured score model. If the score model is a similarity model, then
    * it computes the result directly. If it is a distance model, then use it to
-   * compute pairwise distances, and convert these to similarity scores by
-   * substracting from the maximum value.
+   * compute pairwise distances, and convert these to similarity scores.
    * 
    * @param av
    * @return
@@ -239,6 +238,10 @@ public class PCA implements Runnable
     }
     else if (scoreModel instanceof DistanceScoreModelI)
     {
+      /*
+       * find distances and convert to similarity scores
+       * reverseRange(false) preserves but reverses the min-max range
+       */
       result = ((DistanceScoreModelI) scoreModel).findDistances(av,
               similarityParams);
       result.reverseRange(false);

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index f28c6bc..6d5b0fe 100644 (file)
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -277,6 +277,7 @@ public abstract class TreeBuilder
     {
       /*
        * compute similarity and invert it to give a distance measure
+       * reverseRange(true) converts maximum similarity to zero distance
        */
       MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
               seqData, scoreOptions);

diff --git a/src/jalview/analysis/scoremodels/PIDDistanceModel.java b/src/jalview/analysis/scoremodels/PIDDistanceModel.java
index 9688037..bb9d834 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/PIDDistanceModel.java
@@ -27,6 +27,10 @@ import jalview.math.Matrix;
 import jalview.math.MatrixI;
 import jalview.util.Comparison;
 
+/**
+ * @deprecated superseded by PIDModel
+ */
+@Deprecated
 public class PIDDistanceModel implements DistanceScoreModelI
 {
 

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 8b7fc42..a4b8343 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -79,21 +79,21 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    * of symbols. The matrix should be square and of the same size as the
    * alphabet, for example 20x20 for a 20 symbol alphabet.
    * 
-   * @param name
+   * @param theName
    *          Unique, human readable name for the matrix
    * @param alphabet
    *          the symbols to which scores apply
-   * @param matrix
+   * @param values
    *          Pairwise scores indexed according to the symbol alphabet
    */
-  public ScoreMatrix(String name, char[] alphabet, float[][] matrix)
+  public ScoreMatrix(String theName, char[] alphabet, float[][] values)
   {
-    if (alphabet.length != matrix.length)
+    if (alphabet.length != values.length)
     {
       throw new IllegalArgumentException(
               "score matrix size must match alphabet size");
     }
-    for (float[] row : matrix)
+    for (float[] row : values)
     {
       if (row.length != alphabet.length)
       {
@@ -102,8 +102,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
       }
     }
 
-    this.matrix = matrix;
-    this.name = name;
+    this.matrix = values;
+    this.name = theName;
     this.symbols = alphabet;
 
     symbolIndex = buildSymbolIndex(alphabet);

diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 193d5f4..494d09f 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -35,10 +35,9 @@ public class ScoreModels
    * <ul>
    * <li>BLOSUM62</li>
    * <li>PAM250</li>
-   * <li>SeqSpace (identity matrix)</li>
+   * <li>PID</li>
    * <li>DNA</li>
    * <li>Sequence Feature Similarity</li>
-   * <li>Percentage Identity</li>
    * </ul>
    */
   private ScoreModels()
@@ -52,7 +51,6 @@ public class ScoreModels
     registerScoreModel(new PIDModel());
     DNA = loadScoreMatrix("scoreModel/dna.scm");
     registerScoreModel(new FeatureDistanceModel());
-    // registerScoreModel(new PIDDistanceModel()); // superseded by PIDModel
   }
 
   /**

diff --git a/src/jalview/api/analysis/ScoreModelI.java b/src/jalview/api/analysis/ScoreModelI.java
index 42f978c..9a633f0 100644 (file)
--- a/src/jalview/api/analysis/ScoreModelI.java
+++ b/src/jalview/api/analysis/ScoreModelI.java
@@ -1,8 +1,5 @@
 package jalview.api.analysis;
 
-import jalview.datamodel.AlignmentView;
-import jalview.math.MatrixI;
-
 public interface ScoreModelI
 {
   /**

diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index d7a1b70..f0603dd 100644 (file)
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.java
@@ -72,13 +72,13 @@ public interface MatrixI
    * <p>
    * If parameter <code>maxToZero</code> is true, then the maximum value becomes
    * zero, i.e. all values are subtracted from the maximum. This is consistent
-   * with converting a similarity score to a distance score - the most similar
-   * (identity) corresponds to zero distance. However note that the operation is
-   * not reversible (unless the original minimum value is zero). For example a
-   * range of 10-40 would become 30-0, which would reverse a second time to
-   * 0-30. Also note that a similarity measure (such as BLOSUM) may give
-   * different identity scores for different sequences, so they cannot all
-   * convert to zero distance.
+   * with converting an identity similarity score to a distance score - the most
+   * similar (identity) corresponds to zero distance. However note that the
+   * operation is not reversible (unless the original minimum value is zero).
+   * For example a range of 10-40 would become 30-0, which would reverse a
+   * second time to 0-30. Also note that a general similarity measure (such as
+   * BLOSUM) may give different 'identity' scores for different sequences, so
+   * they cannot all convert to zero distance.
    * <p>
    * If parameter <code>maxToZero</code> is false, then the values are reflected
    * about the average of {min, max} (effectively swapping min and max). This