From eb0d71ed66dcd7d8519eae1f084b76d60b374142 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 23 Mar 2017 16:39:46 +0000
Subject: [PATCH] JAL-2397 scale PCA by PID to alignment width to match
 SeqSpace

---
 src/jalview/analysis/PCA.java     |    9 +++++++++
 src/jalview/math/Matrix.java      |   19 +++++++++++++++++++
 src/jalview/math/MatrixI.java     |    7 +++++++
 test/jalview/math/MatrixTest.java |   12 ++++++++++++
 4 files changed, 47 insertions(+)

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index b481e89..5d2e7e7 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.PIDModel;
 import jalview.api.analysis.DistanceScoreModelI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
@@ -235,6 +236,14 @@ public class PCA implements Runnable
     {
       result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av,
               similarityParams);
+      if (scoreModel instanceof PIDModel)
+      {
+        /*
+         * scale % identities to width of alignment for backwards
+         * compatibility with Jalview 2.10.1 SeqSpace PCA calculation 
+         */
+        result.multiply(av.getWidth() / 100d);
+      }
     }
     else if (scoreModel instanceof DistanceScoreModelI)
     {
diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index aaeb8da..821fc66 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -957,4 +957,23 @@ public class Matrix implements MatrixI
       }
     }
   }
+
+  /**
+   * Multiply every entry in the matrix by the given value. This method is not
+   * thread-safe.
+   */
+  @Override
+  public void multiply(double d)
+  {
+    for (double[] row : value)
+    {
+      if (row != null)
+      {
+        for (int i = 0; i < row.length; i++)
+        {
+          row[i] *= d;
+        }
+      }
+    }
+  }
 }
diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index f0603dd..94b9333 100644
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.java
@@ -87,4 +87,11 @@ public interface MatrixI
    * @param maxToZero
    */
   void reverseRange(boolean maxToZero);
+
+  /**
+   * Multiply all entries by the given value
+   * 
+   * @param d
+   */
+  void multiply(double d);
 }
diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java
index 61b98f3..bd4108c 100644
--- a/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@ -502,4 +502,16 @@ public class MatrixTest
     assertEquals(m1.getValue(1, 2), 15d, DELTA);
   }
 
+  @Test(groups = "Functional")
+  public void testMultiply()
+  {
+    Matrix m = new Matrix(new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+    m.multiply(2d);
+    assertEquals(m.getValue(0, 0), 4d, DELTA);
+    assertEquals(m.getValue(0, 1), 7d, DELTA);
+    assertEquals(m.getValue(0, 2), 8d, DELTA);
+    assertEquals(m.getValue(1, 0), -6.8d, DELTA);
+    assertEquals(m.getValue(1, 1), 8d, DELTA);
+    assertEquals(m.getValue(1, 2), 30d, DELTA);
+  }
 }
-- 
1.7.10.2