JAL-2393 code tidy and comments, PIDDistanceModel deprecated

[jalview.git] / src / jalview / analysis / PCA.java

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);