Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index d51f00e..5cc81a8 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -22,7 +22,7 @@ package jalview.analysis;
 
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Point;
 import jalview.math.MatrixI;
@@ -60,7 +60,8 @@ public class PCA implements Runnable
    * @param sm
    * @param options
    */
-  public PCA(AlignmentView sequences, ScoreModelI sm, SimilarityParamsI options)
+  public PCA(AlignmentView sequences, ScoreModelI sm,
+          SimilarityParamsI options)
   {
     this.seqs = sequences;
     this.scoreModel = sm;
@@ -164,13 +165,13 @@ public class PCA implements Runnable
     sb.append("PCA calculation using ").append(scoreModel.getName())
             .append(" sequence similarity matrix\n========\n\n");
     PrintStream ps = wrapOutputBuffer(sb);
-    
+
     /*
      * pairwise similarity scores
      */
     sb.append(" --- OrigT * Orig ---- \n");
     pairwiseScores.print(ps, "%8.2f");
-    
+
     /*
      * tridiagonal matrix, with D and E vectors
      */
@@ -181,7 +182,7 @@ public class PCA implements Runnable
     sb.append("--- E vector ---\n");
     tridiagonal.printE(ps, "%15.4e");
     ps.println();
-    
+
     /*
      * eigenvalues matrix, with D vector
      */
@@ -190,7 +191,7 @@ public class PCA implements Runnable
     sb.append(" --- Eigenvalues ---\n");
     eigenMatrix.printD(ps, "%15.4e");
     ps.println();
-    
+
     return sb.toString();
   }
 
@@ -220,7 +221,7 @@ public class PCA implements Runnable
       eigenMatrix.tqli();
     } catch (Exception q)
     {
-      Cache.log.error("Error computing PCA:  " + q.getMessage());
+      Console.error("Error computing PCA:  " + q.getMessage());
       q.printStackTrace();
     }
   }