From ac5827eb3ea6f1c671dc2c952ed632b2aabe7e45 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Wed, 1 Nov 2017 16:13:18 +0000
Subject: [PATCH] JAL-2795 Sequence[] references now as SequenceI[] & deleted
 double class

---
 .../archaeopteryx/ArchaeopteryxTreeConverter.java  |    7 ++-
 .../ext/archaeopteryx/MatrixConversionFactory.java |   66 --------------------
 src/jalview/ext/archaeopteryx/MatrixConverter.java |    4 +-
 src/jalview/ext/forester/ForesterMatrix.java       |    9 ++-
 4 files changed, 10 insertions(+), 76 deletions(-)
 delete mode 100644 src/jalview/ext/archaeopteryx/MatrixConversionFactory.java

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
index 689d5cd..9542397 100644
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
@@ -2,9 +2,9 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
-import jalview.math.MatrixI;
 import jalview.util.MessageManager;
 
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 
@@ -16,7 +16,7 @@ public class ArchaeopteryxTreeConverter
 
   private PhylogenyNode rootNode;
 
-  protected MatrixI distances;
+  protected DistanceMatrix distances;
   
   protected TreeBuilder jalviewTree;
   
@@ -28,7 +28,8 @@ public class ArchaeopteryxTreeConverter
   {
     this.jalviewTree = calculatedTree;
     this.sequences = jalviewTree.getSequences();
-    this.distances = jalviewTree.getDistances();
+    this.distances = MatrixConverter.convertJalviewToForester(
+            jalviewTree.getDistances(), jalviewTree.getSequences());
 
   }
 
diff --git a/src/jalview/ext/archaeopteryx/MatrixConversionFactory.java b/src/jalview/ext/archaeopteryx/MatrixConversionFactory.java
deleted file mode 100644
index 19409e0..0000000
--- a/src/jalview/ext/archaeopteryx/MatrixConversionFactory.java
+++ /dev/null
@@ -1,66 +0,0 @@
-package jalview.ext.archaeopteryx;
-
-import jalview.math.MatrixI;
-
-import org.forester.evoinference.matrix.distance.DistanceMatrix;
-
-public class MatrixConversionFactory
-{
-  DistanceMatrix foresterMatrix;
-
-  MatrixI jalviewMatrix;
-
-  public static MatrixConversionFactory createConverter(
-          DistanceMatrix foresterInputMatrix)
-  {
-    MatrixConversionFactory converter = new MatrixConversionFactory();
-    converter.convertForesterToJalview(foresterInputMatrix);
-    return converter;
-
-  }
-
-  public static MatrixConversionFactory createConverter(MatrixI jalviewInputMatrix)
-  {
-    MatrixConversionFactory converter = new MatrixConversionFactory();
-    converter.convertJalviewToForester(jalviewInputMatrix);
-    return converter;
-
-  }
-
-  private DistanceMatrix convertJalviewToForester(
-          MatrixI jalviewMatrix)
-  {
-    this.jalviewMatrix = jalviewMatrix;
-    return foresterMatrix;
-
-  }
-
-  private MatrixI convertForesterToJalview(
-          DistanceMatrix foresterMatrix)
-  {
-    this.foresterMatrix = foresterMatrix;
-
-    return jalviewMatrix;
-  }
-
-  protected DistanceMatrix getForesterMatrix()
-  {
-    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/archaeopteryx/MatrixConverter.java b/src/jalview/ext/archaeopteryx/MatrixConverter.java
index 9eaece8..ef44030 100644
--- a/src/jalview/ext/archaeopteryx/MatrixConverter.java
+++ b/src/jalview/ext/archaeopteryx/MatrixConverter.java
@@ -1,6 +1,6 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 import jalview.ext.forester.ForesterMatrix;
 import jalview.math.MatrixI;
 
@@ -19,7 +19,7 @@ public final class MatrixConverter
 
   public static DistanceMatrix convertJalviewToForester(
           final MatrixI jalviewInputMatrix,
-          final Sequence[] matrixSequences)
+          final SequenceI[] matrixSequences)
   {
     if (jalviewInputMatrix.width() != jalviewInputMatrix.height())
     {
diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java
index e48ee27..e0f2994 100644
--- a/src/jalview/ext/forester/ForesterMatrix.java
+++ b/src/jalview/ext/forester/ForesterMatrix.java
@@ -1,6 +1,6 @@
 package jalview.ext.forester;
 
-import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 import jalview.math.MatrixI;
 import jalview.util.MessageManager;
 
@@ -22,18 +22,17 @@ public class ForesterMatrix implements DistanceMatrix
 
   private final MatrixI jalviewMatrix;
 
-
   private final String[] identifiers;
 
   public ForesterMatrix(final MatrixI jalviewInputMatrix,
-          final Sequence[] matrixSequences)
+          final SequenceI[] matrixSequences)
   {
     this.jalviewMatrix = jalviewInputMatrix;
     this.identifiers = new String[matrixSequences.length];
 
     int i = 0;
 
-    for (Sequence sequence : matrixSequences)
+    for (SequenceI sequence : matrixSequences)
     {
       identifiers[i] = sequence.getName();
       i++;
@@ -52,7 +51,7 @@ public class ForesterMatrix implements DistanceMatrix
   @Override
   public String getIdentifier(final int i)
   {
-    return identifiers[i];
+    return identifiers[i]; // add handling if index is out of bounds
   }
 
 
-- 
1.7.10.2