From bf64f4d798bf695600cc16cb7e421c77ac8b1da3 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 7 Feb 2017 13:20:31 +0000
Subject: [PATCH] JAL-2379 removed unused commented code

---
 src/jalview/analysis/PCA.java |   52 -----------------------------------------
 1 file changed, 52 deletions(-)

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index d978451..9babaee 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -76,17 +76,6 @@ public class PCA implements Runnable
   {
     this.seqs = s;
 
-    // BinarySequence[] bs = new BinarySequence[s.length];
-    // int ii = 0;
-    //
-    // while ((ii < s.length) && (s[ii] != null))
-    // {
-    // bs[ii] = new BinarySequence(s[ii], nucleotides);
-    // bs[ii].encode();
-    // ii++;
-    // }
-    //
-    // BinarySequence[] bs2 = new BinarySequence[s.length];
     scoreMatrix = null;
     String sm = s_m;
     if (sm != null)
@@ -102,47 +91,6 @@ public class PCA implements Runnable
     }
     details.append("PCA calculation using " + sm
             + " sequence similarity matrix\n========\n\n");
-    // ii = 0;
-    // while ((ii < s.length) && (s[ii] != null))
-    // {
-    // bs2[ii] = new BinarySequence(s[ii], nucleotides);
-    // if (scoreMatrix != null)
-    // {
-    // try
-    // {
-    // bs2[ii].matrixEncode(scoreMatrix);
-    // } catch (InvalidSequenceTypeException x)
-    // {
-    // details.append("Unexpected mismatch of sequence type and score matrix. Calculation will not be valid!\n\n");
-    // }
-    // }
-    // ii++;
-    // }
-    //
-    // int count = 0;
-    // while ((count < bs.length) && (bs[count] != null))
-    // {
-    // count++;
-    // }
-    //
-    // double[][] seqmat = new double[count][];
-    // double[][] seqmat2 = new double[count][];
-    //
-    // int i = 0;
-    // while (i < count)
-    // {
-    // seqmat[i] = bs[i].getDBinary();
-    // seqmat2[i] = bs2[i].getDBinary();
-    // i++;
-    // }
-    //
-    // /*
-    // * using a SparseMatrix to hold the encoded sequences matrix
-    // * greatly speeds up matrix multiplication as these are mostly zero
-    // */
-    // m = new SparseMatrix(seqmat);
-    // m2 = new Matrix(seqmat2);
-
   }
 
   /**
-- 
1.7.10.2