JAL-2379 commented out code removed

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index ee74b9b..de0bf77 100755 (executable)
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -267,7 +267,6 @@ public class Matrix implements MatrixI
       {
         for (k = 1; k <= l; k++)
         {
-          // double v = Math.abs(value[i - 1][k - 1]);
           double v = Math.abs(getValue(i - 1, k - 1));
           scale += v;
         }
@@ -513,9 +512,6 @@ public class Matrix implements MatrixI
 
             for (k = 1; k <= n; k++)
             {
-              // f = value[k - 1][i];
-              // value[k - 1][i] = (s * value[k - 1][i - 1]) + (c * f);
-              // value[k - 1][i - 1] = (c * value[k - 1][i - 1]) - (s * f);
               f = getValue(k - 1, i);
               setValue(k - 1, i, (s * getValue(k - 1, i - 1)) + (c * f));
               setValue(k - 1, i - 1, (c * getValue(k - 1, i - 1)) - (s * f));

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index cd8eb15..3b6829e 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -82,17 +82,6 @@ public class PCAModel
       ii++;
     }
 
-    // comps is not used - commenting out
-    // double[][] comps = new double[ii][];
-    //
-    // for (int i = 0; i < ii; i++)
-    // {
-    // if (pca.getEigenvalue(i) > 1e-4)
-    // {
-    // comps[i] = pca.component(i);
-    // }
-    // }
-
     top = pca.getM().height() - 1;
 
     points = new Vector<SequencePoint>();