JAL-629 Added --all arg, [*] linkedId and functionality to apply some args to all...

[jalview.git] / test / jalview / gui / StructureViewerTest.java

diff --git a/test/jalview/gui/StructureViewerTest.java b/test/jalview/gui/StructureViewerTest.java
index f8e9133..ace3c9d 100644 (file)
--- a/test/jalview/gui/StructureViewerTest.java
+++ b/test/jalview/gui/StructureViewerTest.java
@@ -1,19 +1,57 @@
+/*
+ * 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.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
 
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class StructureViewerTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = "Functional")
-  public void testGetUniquePdbFiles()
+  public void testGetSequencesForPdbs()
   {
-    assertNull(StructureViewer.getUniquePdbFiles(null));
+    StructureViewer sv = new StructureViewer(null);
+
+    assertNull(sv.getSequencesForPdbs(null, null));
 
     PDBEntry pdbe1 = new PDBEntry("1A70", "A", Type.PDB, "path1");
     PDBEntry pdbe2 = new PDBEntry("3A6S", "A", Type.PDB, "path2");
@@ -21,13 +59,53 @@ public class StructureViewerTest
     PDBEntry pdbe4 = new PDBEntry("1GAQ", "A", Type.PDB, null);
     PDBEntry pdbe5 = new PDBEntry("3A6S", "B", Type.PDB, "path2");
     PDBEntry pdbe6 = new PDBEntry("1GAQ", "B", Type.PDB, null);
+    PDBEntry pdbe7 = new PDBEntry("1FOO", "Q", Type.PDB, null);
+
+    PDBEntry[] pdbs = new PDBEntry[] { pdbe1, pdbe2, pdbe3, pdbe4, pdbe5,
+        pdbe6, pdbe7 };
 
     /*
-     * pdbe2 and pdbe5 get removed as having a duplicate file path
+     * seq1 ... seq6 associated with pdbe1 ... pdbe6
      */
-    PDBEntry[] uniques = StructureViewer.getUniquePdbFiles(new PDBEntry[] {
-        pdbe1, pdbe2, pdbe3, pdbe4, pdbe5, pdbe6 });
-    assertEquals(uniques,
- new PDBEntry[] { pdbe1, pdbe2, pdbe4, pdbe6 });
+    SequenceI[] seqs = new SequenceI[pdbs.length];
+    for (int i = 0; i < seqs.length; i++)
+    {
+      seqs[i] = new Sequence("Seq" + i, "abc");
+    }
+
+    /*
+     * pdbe3/5/6 should get removed as having a duplicate file path
+     */
+    Map<PDBEntry, SequenceI[]> uniques = sv.getSequencesForPdbs(pdbs, seqs);
+    assertTrue(uniques.containsKey(pdbe1));
+    assertTrue(uniques.containsKey(pdbe2));
+    assertFalse(uniques.containsKey(pdbe3));
+    assertTrue(uniques.containsKey(pdbe4));
+    assertFalse(uniques.containsKey(pdbe5));
+    assertFalse(uniques.containsKey(pdbe6));
+    assertTrue(uniques.containsKey(pdbe7));
+
+    // 1A70 associates with seq1 and seq3
+    SequenceI[] ss = uniques.get(pdbe1);
+    assertEquals(ss.length, 2);
+    assertSame(seqs[0], ss[0]);
+    assertSame(seqs[2], ss[1]);
+
+    // 3A6S has seq2 and seq5
+    ss = uniques.get(pdbe2);
+    assertEquals(ss.length, 2);
+    assertSame(seqs[1], ss[0]);
+    assertSame(seqs[4], ss[1]);
+
+    // 1GAQ has seq4 and seq6
+    ss = uniques.get(pdbe4);
+    assertEquals(ss.length, 2);
+    assertSame(seqs[3], ss[0]);
+    assertSame(seqs[5], ss[1]);
+
+    // 1FOO has seq7
+    ss = uniques.get(pdbe7);
+    assertEquals(ss.length, 1);
+    assertSame(seqs[6], ss[0]);
   }
 }