Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / test / jalview / datamodel / ContactMatrixTest.java

diff --git a/test/jalview/datamodel/ContactMatrixTest.java b/test/jalview/datamodel/ContactMatrixTest.java
new file mode 100644 (file)
index 0000000..a8fdb8c
--- /dev/null
+++ b/test/jalview/datamodel/ContactMatrixTest.java
@@ -0,0 +1,150 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.gui.JvOptionPane;
+
+public class ContactMatrixTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  /**
+   * standard asserts for ContactMatrixI
+   */
+  public static void testContactMatrixI(ContactMatrixI cm,
+          boolean symmetric)
+  {
+    // assume contact matrix is square for text
+    ContactListI clist = cm.getContactList(1);
+
+    int width = clist.getContactHeight();
+    Double minValue, maxValue;
+    minValue = clist.getContactAt(0);
+    maxValue = minValue;
+
+    for (int p = 0; p < width; p++)
+    {
+      ContactListI pList = cm.getContactList(p);
+      for (int q = p; q < width; q++)
+      {
+        if (q == p)
+        {
+          // compute minMax for pList
+          minMax(minValue, maxValue, pList);
+
+        }
+        ContactListI qList = cm.getContactList(q);
+        if (symmetric)
+        {
+          Assert.assertEquals(qList.getContactAt(p), pList.getContactAt(q),
+                  "Contact matrix not symmetric");
+        }
+        else
+        {
+          Assert.assertNotEquals(qList.getContactAt(p),
+                  pList.getContactAt(q),
+                  "Contact matrix expected to be not symmetric");
+        }
+      }
+    }
+  }
+
+  private static void minMax(Double minValue, Double maxValue,
+          ContactListI pList)
+  {
+    int width = pList.getContactHeight();
+    for (int rowcol = 0; rowcol < width; rowcol++)
+    {
+      double v = pList.getContactAt(rowcol);
+      if (minValue > v)
+      {
+        minValue = v;
+      }
+      if (maxValue < v)
+      {
+        maxValue = v;
+      }
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testminMaxCalc()
+  {
+    ContactListI clist = new ContactListImpl(new ContactListProviderI()
+    {
+      double[] val = { 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7 };
+
+      @Override
+      public int getPosition()
+      {
+        return 0;
+      }
+
+      @Override
+      public int getContactHeight()
+      {
+        return val.length;
+      }
+
+      @Override
+      public double getContactAt(int column)
+      {
+        if (column < 0 || column >= val.length)
+        {
+          return Double.NaN;
+        }
+        return val[column];
+      }
+
+    });
+    // TODO - write test !
+  }
+
+  /**
+   * test construction and accessors for asymmetric contact matrix
+   */
+  @Test(groups = { "Functional" })
+  public void testAsymmetricContactMatrix()
+  {
+    // TODO - write test !
+
+  }
+
+  /**
+   * test construction and accessors for symmetric contact matrix
+   */
+  @Test(groups = { "Functional" })
+  public void testSymmetricContactMatrix()
+  {
+    // TODO - write test !
+
+  }
+
+}