X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=c956da114fe7cb5dea102e5cdd4b4ed4b9d3491f;hb=12b5088afc51d015eb9c16f5d79b95918e0e1a5b;hp=0b5840cd796dae7eb53a74d9cdb430d310e13a91;hpb=c4fdef7e109bac9f1da72ec3954a17a931f163df;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 0b5840c..c956da1 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -17,8 +37,8 @@ import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.structure.StructureSelectionManager;
 
-import java.util.LinkedHashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
@@ -28,6 +48,7 @@ public class AlignViewportTest
 {
 
   AlignmentI al;
+
   AlignViewport testee;
 
   @BeforeClass(alwaysRun = true)
@@ -37,41 +58,37 @@ public class AlignViewportTest
         "test/jalview/testProps.jvprops" });
   }
 
- @BeforeMethod(alwaysRun = true)
+  @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
     SequenceI seq1 = new Sequence("Seq1", "ABC");
     SequenceI seq2 = new Sequence("Seq2", "ABC");
     SequenceI seq3 = new Sequence("Seq3", "ABC");
-    SequenceI[] seqs = new SequenceI[]
-    { seq1, seq2, seq3 };
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
     al = new Alignment(seqs);
     al.setDataset(null);
     testee = new AlignViewport(al);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testCollateForPdb()
   {
     /*
      * Set up sequence pdb ids
      */
-    PDBEntry pdb1 = new PDBEntry("1ABC", "A", Type.PDB, "1ABC.pdb");
-    PDBEntry pdb2 = new PDBEntry("2ABC", "A", Type.PDB, "2ABC.pdb");
-    PDBEntry pdb3 = new PDBEntry("3ABC", "A", Type.PDB, "3ABC.pdb");
+    PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb");
+    PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb");
+    PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb");
 
     /*
-     * seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC
+     * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD
      */
     al.getSequenceAt(0).getDatasetSequence()
-            .addPDBId(
-            new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
+            .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
     al.getSequenceAt(2).getDatasetSequence()
-            .addPDBId(
-            new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
+            .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
     al.getSequenceAt(1).getDatasetSequence()
-            .addPDBId(
-            new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
+            .addPDBId(new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
     /*
      * Add a second chain PDB xref to Seq2 - should not result in a duplicate in
      * the results
@@ -87,8 +104,8 @@ public class AlignViewportTest
     /*
      * run method under test
      */
-    SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[]
-    { pdb1, pdb2, pdb3 });
+    SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2,
+        pdb3 });
 
     // seq1 and seq3 refer to PDBEntry[0]
     assertEquals(2, seqs[0].length);
@@ -107,7 +124,7 @@ public class AlignViewportTest
    * Test that a mapping is not deregistered when a second view is closed but
    * the first still holds a reference to the mapping
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testDeregisterMapping_onCloseView()
   {
     /*
@@ -115,40 +132,40 @@ public class AlignViewportTest
      */
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq1\nCAGT\n", FormatAdapter.PASTE);
-  
+
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
-  
-    Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+
+    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
     mappings.add(acf1);
     mappings.add(acf2);
     af1.getViewport().getAlignment().setCodonFrames(mappings);
     af1.newView_actionPerformed(null);
-  
+
     /*
      * Verify that creating the alignment for the new View has registered the
      * mappings
      */
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
-    assertEquals(2, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
-    assertTrue(ssm.seqmappings.contains(acf2));
-  
+    assertEquals(2, ssm.getSequenceMappings().size());
+    assertTrue(ssm.getSequenceMappings().contains(acf1));
+    assertTrue(ssm.getSequenceMappings().contains(acf2));
+
     /*
      * Close the second view. Verify that mappings are not removed as the first
      * view still holds a reference to them.
      */
     af1.closeMenuItem_actionPerformed(false);
-    assertEquals(2, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
-    assertTrue(ssm.seqmappings.contains(acf2));
+    assertEquals(2, ssm.getSequenceMappings().size());
+    assertTrue(ssm.getSequenceMappings().contains(acf1));
+    assertTrue(ssm.getSequenceMappings().contains(acf2));
   }
 
   /**
    * Test that a mapping is deregistered if no alignment holds a reference to it
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testDeregisterMapping_withNoReference()
   {
     Desktop d = Desktop.instance;
@@ -161,25 +178,25 @@ public class AlignViewportTest
             ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq2\nDGEL\n", FormatAdapter.PASTE);
-  
+
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
-  
-    Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
+
+    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
     mappings1.add(acf1);
     af1.getViewport().getAlignment().setCodonFrames(mappings1);
 
-    Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
     mappings2.add(acf2);
     mappings2.add(acf3);
     af2.getViewport().getAlignment().setCodonFrames(mappings2);
-  
+
     /*
      * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
      */
 
-    Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
+    List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
     assertEquals(0, ssmMappings.size());
     ssm.registerMapping(acf1);
     assertEquals(1, ssmMappings.size());
@@ -201,7 +218,7 @@ public class AlignViewportTest
    * Test that a mapping is not deregistered if another alignment holds a
    * reference to it
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testDeregisterMapping_withReference()
   {
     Desktop d = Desktop.instance;
@@ -209,31 +226,31 @@ public class AlignViewportTest
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
     ssm.resetAll();
-  
+
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq2\nDGEL\n", FormatAdapter.PASTE);
-  
+
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
-  
-    Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
+
+    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
     mappings1.add(acf1);
     mappings1.add(acf2);
     af1.getViewport().getAlignment().setCodonFrames(mappings1);
-  
-    Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
+
+    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
     mappings2.add(acf2);
     mappings2.add(acf3);
     af2.getViewport().getAlignment().setCodonFrames(mappings2);
-  
+
     /*
      * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
      */
-  
-    Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
+
+    List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
     assertEquals(0, ssmMappings.size());
     ssm.registerMapping(acf1);
     assertEquals(1, ssmMappings.size());
@@ -241,7 +258,7 @@ public class AlignViewportTest
     assertEquals(2, ssmMappings.size());
     ssm.registerMapping(acf3);
     assertEquals(3, ssmMappings.size());
-  
+
     /*
      * Closing AlignFrame2 should remove mapping acf3 from
      * StructureSelectionManager, but not acf2, since AlignFrame1 still has a