JAL-2403 removed remaining jvCalcMode references from PCA

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 5d2e7e7..11c73c1 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -35,8 +35,6 @@ import java.io.PrintStream;
  */
 public class PCA implements Runnable
 {
-  boolean jvCalcMode = true;
-
   MatrixI symm;
 
   double[] eigenvalue;
@@ -174,10 +172,6 @@ public class PCA implements Runnable
     // long now = System.currentTimeMillis();
     try
     {
-      details.append("PCA Calculation Mode is "
-              + (jvCalcMode ? "Jalview variant" : "Original SeqSpace")
-              + "\n");
-
       eigenvector = computeSimilarity(seqs);
 
       details.append(" --- OrigT * Orig ---- \n");
@@ -264,11 +258,6 @@ public class PCA implements Runnable
     return result;
   }
 
-  public void setJvCalcMode(boolean calcMode)
-  {
-    this.jvCalcMode = calcMode;
-  }
-
   /**
    * Answers the N dimensions of the NxN PCA matrix. This is the number of
    * sequences involved in the pairwise score calculation.

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index f216009..0121e5c 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -73,15 +73,9 @@ public class PCAModel
     similarityParams = params;
   }
 
-  public boolean isJvCalcMode()
-  {
-    return jvCalcMode;
-  }
-
   public void run()
   {
     pca = new PCA(seqstrings, scoreModel, similarityParams);
-    pca.setJvCalcMode(jvCalcMode);
     pca.run();
 
     // Now find the component coordinates