Merge branch 'JAL-1378_jb2.1cli' into RNAalifold

[jalview.git] / src / jalview / analysis / PCA.java

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 4441eeb..109a591 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -46,8 +46,9 @@ public class PCA implements Runnable
   StringBuffer details = new StringBuffer();
 
   /**
-   * Creates a new PCA object.
-   * By default, uses blosum62 matrix to generate sequence similarity matrices
+   * Creates a new PCA object. By default, uses blosum62 matrix to generate
+   * sequence similarity matrices
+   * 
    * @param s
    *          Set of amino acid sequences to perform PCA on
    */
@@ -55,13 +56,16 @@ public class PCA implements Runnable
   {
     this(s, false);
   }
-  
+
   /**
-   * Creates a new PCA object.
-   * By default, uses blosum62 matrix to generate sequence similarity matrices
+   * Creates a new PCA object. By default, uses blosum62 matrix to generate
+   * sequence similarity matrices
+   * 
    * @param s
    *          Set of sequences to perform PCA on
-   *          @param nucleotides if true, uses standard DNA/RNA matrix for sequence similarity calculation.
+   * @param nucleotides
+   *          if true, uses standard DNA/RNA matrix for sequence similarity
+   *          calculation.
    */
   public PCA(String[] s, boolean nucleotides)
   {
@@ -71,7 +75,7 @@ public class PCA implements Runnable
 
     while ((ii < s.length) && (s[ii] != null))
     {
-      bs[ii] = new BinarySequence(s[ii],nucleotides);
+      bs[ii] = new BinarySequence(s[ii], nucleotides);
       bs[ii].encode();
       ii++;
     }
@@ -79,10 +83,10 @@ public class PCA implements Runnable
     BinarySequence[] bs2 = new BinarySequence[s.length];
     ii = 0;
 
-    String sm=nucleotides ? "DNA" : "BLOSUM62";
-    ScoreMatrix smtrx=ResidueProperties.getScoreMatrix(sm);
-    details.append("PCA calculation using "+sm+" sequence similarity matrix\n========\n\n");
-    
+    String sm = nucleotides ? "DNA" : "BLOSUM62";
+    ScoreMatrix smtrx = ResidueProperties.getScoreMatrix(sm);
+    details.append("PCA calculation using " + sm
+            + " sequence similarity matrix\n========\n\n");
     while ((ii < s.length) && (s[ii] != null))
     {
       bs2[ii] = new BinarySequence(s[ii], nucleotides);
@@ -232,7 +236,8 @@ public class PCA implements Runnable
    */
   public void run()
   {
-    details.append("PCA Calculation Mode is "+(jvCalcMode ? "Jalview variant" : "Original SeqSpace")+"\n");
+    details.append("PCA Calculation Mode is "
+            + (jvCalcMode ? "Jalview variant" : "Original SeqSpace") + "\n");
     Matrix mt = m.transpose();
 
     details.append(" --- OrigT * Orig ---- \n");