JAL-1503 update version in GPL header

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

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 6498b6d..733e7f9 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
@@ -46,8 +47,9 @@ 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
    */
@@ -55,34 +57,49 @@ 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)
   {
+    this(s, nucleotides, null);
+  }
+  public PCA(String[] s, boolean nucleotides, String s_m)
+  {
 
     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] = new BinarySequence(s[ii], nucleotides);
       bs[ii].encode();
       ii++;
     }
 
     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");
-    
+    ScoreMatrix smtrx = null;
+    String sm=s_m;
+    if (sm!=null)
+    {
+      smtrx = ResidueProperties.getScoreMatrix(sm);
+    }
+    if (smtrx==null)
+    {
+      // either we were given a non-existent score matrix or a scoremodel that isn't based on a pairwise symbol score matrix
+      smtrx = ResidueProperties.getScoreMatrix(sm=(nucleotides ? "DNA" : "BLOSUM62"));
+    }
+    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);
@@ -232,12 +249,6 @@ public class PCA implements Runnable
    */
   public void run()
   {
-    Matrix mt = m.transpose();
-
-    details.append(" --- OrigT * Orig ---- \n");
-    // eigenvector = mt.preMultiply(m); // standard seqspace comparison matrix
-    eigenvector = mt.preMultiply(m2); // jalview variation on seqsmace method
-
     PrintStream ps = new PrintStream(System.out)
     {
       public void print(String x)
@@ -251,6 +262,21 @@ public class PCA implements Runnable
       }
     };
 
+    try {
+    details.append("PCA Calculation Mode is "
+            + (jvCalcMode ? "Jalview variant" : "Original SeqSpace") + "\n");
+    Matrix mt = m.transpose();
+
+    details.append(" --- OrigT * Orig ---- \n");
+    if (!jvCalcMode)
+    {
+      eigenvector = mt.preMultiply(m); // standard seqspace comparison matrix
+    }
+    else
+    {
+      eigenvector = mt.preMultiply(m2); // jalview variation on seqsmace method
+    }
+
     eigenvector.print(ps);
 
     symm = eigenvector.copy();
@@ -267,6 +293,12 @@ public class PCA implements Runnable
 
     // Now produce the diagonalization matrix
     eigenvector.tqli();
+    } catch (Exception q)
+    {
+      q.printStackTrace();
+      details.append("\n*** Unexpected exception when performing PCA ***\n"+q.getLocalizedMessage());
+      details.append("*** Matrices below may not be fully diagonalised. ***\n");
+    }
 
     details.append(" --- New diagonalization matrix ---\n");
     eigenvector.print(ps);
@@ -280,4 +312,11 @@ public class PCA implements Runnable
      * ps.print(","+component(seq, ev)); } ps.println(); }
      */
   }
+
+  boolean jvCalcMode = true;
+
+  public void setJvCalcMode(boolean calcMode)
+  {
+    this.jvCalcMode = calcMode;
+  }
 }