From 5235e3d065984303def2aeb8cc662223fb2f9c5a Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Mon, 30 Oct 2017 16:29:31 +0000
Subject: [PATCH] JAL-2795 rebuilt MatrixConverter to be purely static

---
 src/jalview/ext/archaeopteryx/MatrixConverter.java |   58 +++++++++++---------
 src/jalview/ext/forester/ForesterMatrix.java       |   14 +----
 2 files changed, 32 insertions(+), 40 deletions(-)

diff --git a/src/jalview/ext/archaeopteryx/MatrixConverter.java b/src/jalview/ext/archaeopteryx/MatrixConverter.java
index 779d7a3..9eaece8 100644
--- a/src/jalview/ext/archaeopteryx/MatrixConverter.java
+++ b/src/jalview/ext/archaeopteryx/MatrixConverter.java
@@ -1,50 +1,54 @@
 package jalview.ext.archaeopteryx;
 
+import jalview.datamodel.Sequence;
+import jalview.ext.forester.ForesterMatrix;
 import jalview.math.MatrixI;
 
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 
-public class MatrixConverter
+public final class MatrixConverter
 {
-  DistanceMatrix foresterMatrix;
-
-  MatrixI jalviewMatrix;
-
-  public static MatrixConverter createConverter(
-          DistanceMatrix foresterInputMatrix)
+  /**
+   * Shouldn't get instantiated
+   */
+  private MatrixConverter()
   {
-    MatrixConverter converter = new MatrixConverter();
-    converter.setForesterMatrix(foresterInputMatrix);
-    return converter;
 
   }
 
-  public static MatrixConverter createConverter(MatrixI jalviewInputMatrix)
+
+  public static DistanceMatrix convertJalviewToForester(
+          final MatrixI jalviewInputMatrix,
+          final Sequence[] matrixSequences)
   {
-    MatrixConverter converter = new MatrixConverter();
-    converter.setJalviewMatrix(jalviewInputMatrix);
-    return converter;
+    if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
+    {
+      // some kind of warning?
+    }
+       DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
+            matrixSequences);
+    return foresterMatrix;
+
 
   }
 
-  protected DistanceMatrix getForesterMatrix()
+  public static DistanceMatrix convertJalviewToForester(
+          final MatrixI jalviewInputMatrix,
+          final String[] matrixIdentifiers)
   {
+    if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
+    {
+      // some kind of warning?
+    }
+
+    DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
+            matrixIdentifiers);
     return foresterMatrix;
-  }
 
-  protected void setForesterMatrix(DistanceMatrix foresterMatrix)
-  {
-    this.foresterMatrix = foresterMatrix;
-  }
 
-  protected MatrixI getJalviewMatrix()
-  {
-    return jalviewMatrix;
   }
 
-  protected void setJalviewMatrix(MatrixI jalviewMatrix)
-  {
-    this.jalviewMatrix = jalviewMatrix;
-  }
+
+
 
 }
diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java
index c58b2a9..4ce3d12 100644
--- a/src/jalview/ext/forester/ForesterMatrix.java
+++ b/src/jalview/ext/forester/ForesterMatrix.java
@@ -22,7 +22,7 @@ public class ForesterMatrix implements DistanceMatrix
 
   private Sequence[] sequences;
 
-  private String[] identifiers;
+  private final String[] identifiers;
 
   public ForesterMatrix(final MatrixI jalviewInputMatrix,
           final Sequence[] matrixSequences)
@@ -31,10 +31,6 @@ public class ForesterMatrix implements DistanceMatrix
     this.sequences = matrixSequences;
     this.identifiers = new String[sequences.length];
 
-    if (jalviewMatrix.width() != jalviewMatrix.height())
-    {
-      // some kind of warning?
-    }
     int i = 0;
 
     for (Sequence sequence : sequences)
@@ -51,14 +47,6 @@ public class ForesterMatrix implements DistanceMatrix
     this.jalviewMatrix = jalviewInputMatrix;
     this.identifiers = matrixIdentifiers;
 
-
-    if (jalviewMatrix.width() != jalviewMatrix.height())
-    {
-      // some kind of warning?
-    }
-
-
-
   }
 
   @Override
-- 
1.7.10.2