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 5e0e52f..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;
@@ -46,19 +58,6 @@ import jalview.structure.AtomSpecModel;
 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;
 
 /**
@@ -286,9 +285,20 @@ public class AAStructureBindingModelTest
         return null;
       }
 
+      /*
+       * for this test, let structure model ids be 0, 1, ...
+       * corresponding to first, second etc pdbfile
+       */
       @Override
-      protected String getModelIdForFile(String chainId)
+      protected String getModelIdForFile(String pdbfile)
       {
+        for (int i = 0; i < this.getPdbCount(); i++)
+        {
+          if (pdbfile.equals(this.getPdbEntry(i).getFile()))
+          {
+            return String.valueOf(i);
+          }
+        }
         return "";
       }
 
@@ -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();
   
     /*