From c8bb1f07779f5d4c9fc679c35c02a10d6e8dd054 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 4 Dec 2016 10:51:27 +0000
Subject: [PATCH] JAL-2349 dummy contact matrix annotation row

---
 src/jalview/datamodel/ContactMatrixTest.java |   40 ++++++++++++++++++++++++++
 src/jalview/io/FileLoader.java               |    3 ++
 2 files changed, 43 insertions(+)
 create mode 100644 src/jalview/datamodel/ContactMatrixTest.java

diff --git a/src/jalview/datamodel/ContactMatrixTest.java b/src/jalview/datamodel/ContactMatrixTest.java
new file mode 100644
index 0000000..ab76c76
--- /dev/null
+++ b/src/jalview/datamodel/ContactMatrixTest.java
@@ -0,0 +1,40 @@
+package jalview.datamodel;
+
+import java.awt.Color;
+
+public class ContactMatrixTest implements ContactMatrixI
+{
+  private int width = 0;
+
+  public ContactMatrixTest(int width)
+  {
+    this.width = width;
+  }
+  @Override
+  public ContactListI getContactList(final int column)
+  {
+    if (column<0 || column >= width)
+    {
+      return null;
+    }
+    return new ContactListI() {
+      int p = column;
+      @Override
+      public Color getColorForScore(int column)
+      {
+        return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p), 0, Color.white, width, Color.magenta);
+      }
+      @Override
+      public int getColumnWidth()
+      {
+        return 1;
+      }
+      @Override
+      public int getContactHeight()
+      {
+        return width;
+      }
+    };
+  }
+
+}
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3ad74c7..5febda6 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -28,6 +28,7 @@ import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixTest;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -335,6 +336,8 @@ public class FileLoader implements Runnable
 
         if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
         {
+          al.addContactList(new ContactMatrixTest(al.getWidth()));
+
           // construct and register dataset sequences
           for (SequenceI sq : al.getSequences())
           {
-- 
1.7.10.2