X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FPCA.java;h=9babaee1ea6928a1731b3906c1a4cbada0fa5bee;hb=34d5dfb25731d7d797177cadfce954258ae90991;hp=d978451457e07a51034cd33148c07a75463648fa;hpb=35679161e01fac267b1a58bec4244baae94d7fd2;p=jalview.git

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);
-
   }
 
   /**