JAL-2499 JAL-2403 push 'configure for view' inside ScoreModels, defer

[jalview.git] / src / jalview / analysis / scoremodels / PIDModel.java

diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java
index d537e33..985918b 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDModel.java
+++ b/src/jalview/analysis/scoremodels/PIDModel.java
@@ -8,15 +8,14 @@ import jalview.math.MatrixI;
 import jalview.util.Comparison;
 
 /**
- * A class to provide sequence pairwise similarity based on residue identity
+ * A class to provide sequence pairwise similarity based on residue identity.
+ * Instances of this class are immutable and thread-safe.
  */
 public class PIDModel extends SimilarityScoreModel implements
         PairwiseScoreModelI
 {
   private static final String NAME = "PID";
 
-  private String description;
-
   /**
    * Constructor
    */
@@ -30,10 +29,14 @@ public class PIDModel extends SimilarityScoreModel implements
     return NAME;
   }
 
+  /**
+   * Answers null for description. If a display name is needed, use getName() or
+   * an internationalized string built from the name.
+   */
   @Override
   public String getDescription()
   {
-    return description;
+    return null;
   }
 
   @Override
@@ -80,7 +83,7 @@ public class PIDModel extends SimilarityScoreModel implements
    * Computes similarity scores based on pairwise percentage identity of
    * sequences. For consistency with Jalview 2.10.1's SeqSpace mode PCA
    * calculation, the percentage scores are rescaled to the width of the
-   * sequences (as if counts of identical residues).
+   * sequences (as if counts of identical residues). This method is thread-safe.
    */
   @Override
   public MatrixI findSimilarities(AlignmentView seqData,
@@ -98,7 +101,8 @@ public class PIDModel extends SimilarityScoreModel implements
   /**
    * A distance score is computed in the usual way (by reversing the range of
    * the similarity score results), and then rescaled to percentage values
-   * (reversing the rescaling to count values done in findSimilarities)
+   * (reversing the rescaling to count values done in findSimilarities). This
+   * method is thread-safe.
    */
   @Override
   public MatrixI findDistances(AlignmentView seqData,