From 560fb10bab46bb2bc9f2af28d71fdc0b6e386ad7 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Fri, 27 Oct 2017 16:42:09 +0100
Subject: [PATCH] JAL-2795 start of Jalview's Matrix conversion

---
 forester                                           |    2 +-
 .../ext/archaeopteryx/MatrixConversionFactory.java |   66 ++++++++++++++++++++
 src/jalview/ext/archaeopteryx/MergedMatrix.java    |   64 +++++++++++++++++++
 3 files changed, 131 insertions(+), 1 deletion(-)
 create mode 100644 src/jalview/ext/archaeopteryx/MatrixConversionFactory.java
 create mode 100644 src/jalview/ext/archaeopteryx/MergedMatrix.java

diff --git a/forester b/forester
index 25c731f..26d8d47 160000
--- a/forester
+++ b/forester
@@ -1 +1 @@
-Subproject commit 25c731fbc8a993c2084d364e6c6c8ca9e662ad73
+Subproject commit 26d8d47ed32a0eb9bd43c409d0e26ff13570b246
diff --git a/src/jalview/ext/archaeopteryx/MatrixConversionFactory.java b/src/jalview/ext/archaeopteryx/MatrixConversionFactory.java
new file mode 100644
index 0000000..19409e0
--- /dev/null
+++ b/src/jalview/ext/archaeopteryx/MatrixConversionFactory.java
@@ -0,0 +1,66 @@
+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/MergedMatrix.java b/src/jalview/ext/archaeopteryx/MergedMatrix.java
new file mode 100644
index 0000000..41855de
--- /dev/null
+++ b/src/jalview/ext/archaeopteryx/MergedMatrix.java
@@ -0,0 +1,64 @@
+package jalview.ext.archaeopteryx;
+
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
+
+public class MergedMatrix implements DistanceMatrix
+{
+
+  @Override
+  public String getIdentifier(int i)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public int getIndex(String identifier)
+  {
+    // TODO Auto-generated method stub
+    return 0;
+  }
+
+  @Override
+  public int getSize()
+  {
+    // TODO Auto-generated method stub
+    return 0;
+  }
+
+  @Override
+  public double getValue(int col, int row)
+  {
+    // TODO Auto-generated method stub
+    return 0;
+  }
+
+  @Override
+  public void setIdentifier(int i, String identifier)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setValue(int col, int row, double distance)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public StringBuffer toStringBuffer(Format format)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public double[][] getValues()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+}
\ No newline at end of file
-- 
1.7.10.2