X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2FMCview%2FPDBChainTest.java;h=713293934ad2eaf604ab83aa0d8ef0c02f21092d;hb=92e39eb6a3ab1a0e3ab45cef49a64a1c7a7007b6;hp=193d294357b639417927e248147b98b9c14bfb86;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git

diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index 193d294..7132939 100644
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -1,33 +1,76 @@
+/*
+ * 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 MCview;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import java.awt.Color;
-import java.util.Vector;
 
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.TaylorColourScheme;
+import jalview.structure.StructureImportSettings;
+
+import java.awt.Color;
+import java.util.Vector;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class PDBChainTest
 {
-  PDBChain c = new PDBChain("1GAQ", "A");
-  Atom a1 = new Atom(1f, 2f, 3f);
 
-  Atom a2 = new Atom(5f, 6f, 4f);
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  PDBChain c;
+
+  final Atom a1 = new Atom(1f, 2f, 3f);
+
+  final Atom a2 = new Atom(5f, 6f, 4f);
 
-  Atom a3 = new Atom(2f, 5f, 6f);
+  final Atom a3 = new Atom(2f, 5f, 6f);
 
-  Atom a4 = new Atom(2f, 1f, 7f);
+  final Atom a4 = new Atom(2f, 1f, 7f);
 
-  @Test
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    System.out.println("setup");
+    StructureImportSettings.setShowSeqFeatures(true);
+    c = new PDBChain("1GAQ", "A");
+  }
+
+  @Test(groups = { "Functional" })
   public void testGetNewlineString()
   {
     assertEquals(System.lineSeparator(), c.getNewlineString());
@@ -35,7 +78,7 @@ public class PDBChainTest
     assertEquals("gaga", c.getNewlineString());
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testPrint()
   {
     c.offset = 7;
@@ -63,7 +106,7 @@ public class PDBChainTest
    * Test the method that constructs a Bond between two atoms and adds it to the
    * chain's list of bonds
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testMakeBond()
   {
     /*
@@ -98,7 +141,7 @@ public class PDBChainTest
     assertEquals(3f, b2.end[2], 0.0001f);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testSetChainColours_colour()
   {
     c.makeBond(a1, a2);
@@ -115,7 +158,7 @@ public class PDBChainTest
    * Test setting bond start/end colours based on a colour scheme i.e. colour by
    * residue
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testSetChainColours_colourScheme()
   {
     Color alaColour = new Color(204, 255, 0);
@@ -143,7 +186,7 @@ public class PDBChainTest
     assertEquals(Color.gray, b.endCol);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testGetChargeColour()
   {
     assertEquals(Color.red, PDBChain.getChargeColour("ASP"));
@@ -158,7 +201,7 @@ public class PDBChainTest
   /**
    * Test the method that sets bond start/end colours by residue charge property
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testSetChargeColours()
   {
     a1.resName = "ASP"; // red
@@ -187,7 +230,7 @@ public class PDBChainTest
   /**
    * Test the method that converts the raw list of atoms to a list of residues
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testMakeResidueList_noAnnotation()
   {
     Vector<Atom> atoms = new Vector<Atom>();
@@ -245,35 +288,35 @@ public class PDBChainTest
    * Test the method that converts the raw list of atoms to a list of residues,
    * including parsing of tempFactor to an alignment annotation
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testMakeResidueList_withTempFactor()
   {
     Vector<Atom> atoms = new Vector<Atom>();
     c.atoms = atoms;
     atoms.add(makeAtom(4, "N", "MET"));
-    atoms.get(atoms.size()-1).tfactor = 1f;
+    atoms.get(atoms.size() - 1).tfactor = 1f;
     atoms.add(makeAtom(4, "CA", "MET"));
-    atoms.get(atoms.size()-1).tfactor = 2f;
+    atoms.get(atoms.size() - 1).tfactor = 2f;
     atoms.add(makeAtom(4, "C", "MET"));
-    atoms.get(atoms.size()-1).tfactor = 3f;
+    atoms.get(atoms.size() - 1).tfactor = 3f;
     atoms.add(makeAtom(5, "O", "LYS"));
-    atoms.get(atoms.size()-1).tfactor = 7f;
+    atoms.get(atoms.size() - 1).tfactor = 7f;
     atoms.add(makeAtom(5, "N", "LYS"));
-    atoms.get(atoms.size()-1).tfactor = 8f;
+    atoms.get(atoms.size() - 1).tfactor = 8f;
     atoms.add(makeAtom(5, "CA", "LYS"));
-    atoms.get(atoms.size()-1).tfactor = 9f;
+    atoms.get(atoms.size() - 1).tfactor = 9f;
     atoms.add(makeAtom(6, "O", "LEU"));
-    atoms.get(atoms.size()-1).tfactor = 4f;
+    atoms.get(atoms.size() - 1).tfactor = 4f;
     atoms.add(makeAtom(6, "N", "LEU"));
-    atoms.get(atoms.size()-1).tfactor = 5f;
+    atoms.get(atoms.size() - 1).tfactor = 5f;
     atoms.add(makeAtom(6, "CA", "LEU"));
-    atoms.get(atoms.size()-1).tfactor = 6f;
-  
+    atoms.get(atoms.size() - 1).tfactor = 6f;
+
     /*
      * make residues including temp factor annotation
      */
     c.makeResidueList(true);
-    
+
     /*
      * Verify annotations; note the tempFactor is read from the first atom in
      * each residue i.e. we expect values 1, 7, 4 for the residues
@@ -296,7 +339,7 @@ public class PDBChainTest
    * Test the method that constructs bonds between successive residues' CA or P
    * atoms
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testMakeCaBondList()
   {
     c.isNa = true;
@@ -327,7 +370,7 @@ public class PDBChainTest
     assertTrue(c.isNa);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testMakeCaBondList_nucleotide()
   {
     c.isNa = false;
@@ -359,7 +402,7 @@ public class PDBChainTest
   /**
    * Test the method that updates atoms with their alignment positions
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testMakeExactMapping()
   {
     Vector<Atom> atoms = new Vector<Atom>();