JAL-2422 JAL-3551 unit tests updated for code changes

[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 f901cbd..16452a5 100644 (file)
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -25,6 +25,18 @@ import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotNull;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.api.AlignmentViewPanel;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.Alignment;
@@ -43,22 +55,9 @@ import jalview.io.FileFormats;
 import jalview.schemes.JalviewColourScheme;
 import jalview.structure.AtomSpec;
 import jalview.structure.AtomSpecModel;
-import jalview.structure.StructureCommandsI.SuperposeData;
+import jalview.structure.StructureCommandI;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
-
-import java.awt.Color;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.BitSet;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 import junit.extensions.PA;
 
 /**
@@ -172,16 +171,16 @@ public class AAStructureBindingModelTest
       }
 
       @Override
-      protected List<String> executeCommand(String command,
+      protected List<String> executeCommand(StructureCommandI command,
               boolean getReply)
       {
         return null;
       }
 
       @Override
-      protected int getModelNoForFile(String chainId)
+      protected String getModelIdForFile(String chainId)
       {
-        return 0;
+        return "";
       }
 
       @Override
@@ -280,16 +279,27 @@ public class AAStructureBindingModelTest
       }
 
       @Override
-      protected List<String> executeCommand(String command,
+      protected List<String> executeCommand(StructureCommandI command,
               boolean getReply)
       {
         return null;
       }
 
+      /*
+       * for this test, let structure model ids be 0, 1, ...
+       * corresponding to first, second etc pdbfile
+       */
       @Override
-      protected int getModelNoForFile(String chainId)
+      protected String getModelIdForFile(String pdbfile)
       {
-        return 0;
+        for (int i = 0; i < this.getPdbCount(); i++)
+        {
+          if (pdbfile.equals(this.getPdbEntry(i).getFile()))
+          {
+            return String.valueOf(i);
+          }
+        }
+        return "";
       }
 
       @Override
@@ -312,10 +322,10 @@ public class AAStructureBindingModelTest
     /*
      * create a data bean to hold data per structure file
      */
-    SuperposeData[] structs = new SuperposeData[testee.getStructureFiles().length];
+    AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee.getStructureFiles().length];
     for (int i = 0; i < structs.length; i++)
     {
-      structs[i] = new SuperposeData(al.getWidth(), 0);
+      structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), "0");
     }
     /*
      * initialise BitSet of 'superposable columns' to true (would be false for
@@ -360,10 +370,10 @@ public class AAStructureBindingModelTest
   @Test(groups = { "Functional" })
   public void testFindSuperposableResidues_hiddenColumn()
   {
-    SuperposeData[] structs = new SuperposeData[al.getHeight()];
+    AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al.getHeight()];
     for (int i = 0; i < structs.length; i++)
     {
-      structs[i] = new SuperposeData(al.getWidth(), 0);
+      structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), "0");
     }
     /*
      * initialise BitSet of 'superposable columns' to true (would be false for
@@ -415,8 +425,8 @@ public class AAStructureBindingModelTest
     SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
     String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
     PDBEntry[] pdbFiles = new PDBEntry[2];
-    pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "INLINEPDB1");
-    pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "INLINEPDB2");
+    pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
+    pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
     StructureSelectionManager ssm = new StructureSelectionManager();
   
     /*