JAL-2388 Renamed column and row subtraction functions

[jalview.git] / test / jalview / structures / models / AAStructureBindingModelTest.java

diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index 6805bc6..0422537 100644 (file)
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -24,20 +24,29 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.schemes.ColourSchemeI;
 import jalview.structure.AtomSpec;
+import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel.SuperposeData;
 
+import java.awt.Color;
 import java.util.Arrays;
 import java.util.List;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -49,6 +58,14 @@ import org.testng.annotations.Test;
  */
 public class AAStructureBindingModelTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /*
    * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
    */
@@ -104,7 +121,6 @@ public class AAStructureBindingModelTest
     pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
     pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
     pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
-    String[][] chains = new String[3][];
     SequenceI[][] seqs = new SequenceI[3][];
     seqs[0] = new SequenceI[] { seq1a, seq1b };
     seqs[1] = new SequenceI[] { seq2 };
@@ -112,13 +128,13 @@ public class AAStructureBindingModelTest
     StructureSelectionManager ssm = new StructureSelectionManager();
 
     ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
-            AppletFormatAdapter.PASTE);
+            DataSourceType.PASTE);
     ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
-            AppletFormatAdapter.PASTE);
+            DataSourceType.PASTE);
     ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
-            AppletFormatAdapter.PASTE);
+            DataSourceType.PASTE);
 
-    testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null)
+    testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
     {
       @Override
       public String[] getPdbFile()
@@ -140,6 +156,65 @@ public class AAStructureBindingModelTest
       public void highlightAtoms(List<AtomSpec> atoms)
       {
       }
+
+      @Override
+      public List<String> getChainNames()
+      {
+        return null;
+      }
+
+      @Override
+      public void setJalviewColourScheme(ColourSchemeI cs)
+      {
+      }
+
+      @Override
+      public void superposeStructures(AlignmentI[] als, int[] alm,
+              ColumnSelection[] alc)
+      {
+      }
+
+      @Override
+      public void setBackgroundColour(Color col)
+      {
+      }
+
+      @Override
+      protected StructureMappingcommandSet[] getColourBySequenceCommands(
+              String[] files, SequenceRenderer sr, FeatureRenderer fr,
+              AlignmentI alignment)
+      {
+        return null;
+      }
+
+      @Override
+      public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+      {
+        return null;
+      }
+
+      @Override
+      public SequenceRenderer getSequenceRenderer(
+              AlignmentViewPanel alignment)
+      {
+        return null;
+      }
+
+      @Override
+      protected void colourBySequence(
+              StructureMappingcommandSet[] colourBySequenceCommands)
+      {
+      }
+
+      @Override
+      public void colourByChain()
+      {
+      }
+
+      @Override
+      public void colourByCharge()
+      {
+      }
     };
   }
 
@@ -224,4 +299,14 @@ public class AAStructureBindingModelTest
     assertFalse(matched[4]); // superposable, but hidden, column
     assertTrue(matched[5]);
   }
+
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+  {
+    return null;
+  }
+
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+  {
+    return null;
+  }
 }