From 3e49bcba7b477c8f016f5b073a0cd2808739a944 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 10 Apr 2017 16:21:35 +0100
Subject: [PATCH] JAL-2403 removed remaining jvCalcMode references from PCA

---
 src/jalview/analysis/PCA.java       |   11 -----------
 src/jalview/viewmodel/PCAModel.java |    6 ------
 2 files changed, 17 deletions(-)

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 5d2e7e7..11c73c1 100755
--- 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
--- 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
-- 
1.7.10.2