From 5cdc53bb8a76f6bd364188254e873437d7ac2c7f Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Thu, 2 Nov 2017 12:11:33 +0000
Subject: [PATCH] JAL-2795 moved matrix conversion to the ForesterMatrix class

---
 src/jalview/ext/archaeopteryx/MatrixConverter.java |   54 --------------------
 src/jalview/ext/forester/ForesterMatrix.java       |   29 +++++++++++
 2 files changed, 29 insertions(+), 54 deletions(-)
 delete mode 100644 src/jalview/ext/archaeopteryx/MatrixConverter.java

diff --git a/src/jalview/ext/archaeopteryx/MatrixConverter.java b/src/jalview/ext/archaeopteryx/MatrixConverter.java
deleted file mode 100644
index ef44030..0000000
--- a/src/jalview/ext/archaeopteryx/MatrixConverter.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package jalview.ext.archaeopteryx;
-
-import jalview.datamodel.SequenceI;
-import jalview.ext.forester.ForesterMatrix;
-import jalview.math.MatrixI;
-
-import org.forester.evoinference.matrix.distance.DistanceMatrix;
-
-public final class MatrixConverter
-{
-  /**
-   * Shouldn't get instantiated
-   */
-  private MatrixConverter()
-  {
-
-  }
-
-
-  public static DistanceMatrix convertJalviewToForester(
-          final MatrixI jalviewInputMatrix,
-          final SequenceI[] matrixSequences)
-  {
-    if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
-    {
-      // some kind of warning?
-    }
-       DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
-            matrixSequences);
-    return foresterMatrix;
-
-
-  }
-
-  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;
-
-
-  }
-
-
-
-
-}
diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java
index e0f2994..a1381be 100644
--- a/src/jalview/ext/forester/ForesterMatrix.java
+++ b/src/jalview/ext/forester/ForesterMatrix.java
@@ -163,5 +163,34 @@ public class ForesterMatrix implements DistanceMatrix
 
   }
 
+  public static DistanceMatrix convertJalviewToForester(
+          final MatrixI jalviewInputMatrix,
+          final SequenceI[] matrixSequences)
+  {
+    if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
+    {
+      // some kind of warning?
+    }
+    DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
+            matrixSequences);
+    return foresterMatrix;
+
+  }
+
+  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;
+
+  }
+
 
 }
\ No newline at end of file
-- 
1.7.10.2