X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolCommandsTest.java;h=21f7e19bf5715e8677a5280aec7a95cab2b5d6b6;hb=8d55494f762adc45e799ea38ebb33ec2e3f73b10;hp=211e91827ea78162a8893dda991249014534a709;hpb=42f4227ed213d422a87d3b22fc9e85d14ffaf53f;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index 211e918..21f7e19 100644
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -23,38 +23,36 @@ package jalview.ext.jmol;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.JvOptionPane;
 import jalview.gui.SequenceRenderer;
 import jalview.schemes.JalviewColourScheme;
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommandI;
-import jalview.structure.StructureCommandsI;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 
-import java.awt.Color;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class JmolCommandsTest
 {
+  private JmolCommands testee;
 
   @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
+  public void setUp()
   {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+    testee = new JmolCommands();
   }
 
   @Test(groups = { "Functional" })
@@ -95,7 +93,8 @@ public class JmolCommandsTest
             "B", map, null);
     ssm.addStructureMapping(sm2);
 
-    String[] commands = new JmolCommands().colourBySequence(ssm, files,
+    String[] commands = testee.colourBySequence(ssm,
+            files,
             seqs, sr, af.alignPanel);
     assertEquals(commands.length, 2);
 
@@ -130,7 +129,6 @@ public class JmolCommandsTest
   @Test(groups = "Functional")
   public void testGetAtomSpec()
   {
-    StructureCommandsI testee = new JmolCommands();
     AtomSpecModel model = new AtomSpecModel();
     assertEquals(testee.getAtomSpec(model, false), "");
     model.addRange("1", 2, 4, "A");
@@ -161,7 +159,7 @@ public class JmolCommandsTest
     model.addRange("5", 25, 35, " ");
     assertEquals(testee.getAtomSpec(model, false),
             "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1");
-  
+
   }
 
   @Test(groups = { "Functional" })
@@ -180,21 +178,18 @@ public class JmolCommandsTest
 
     // Colours should appear in the Jmol command in the order in which
     // they were added; within colour, by model, by chain, ranges in start order
-    List<StructureCommandI> commands = new JmolCommands()
-            .colourBySequence(map);
-    assertEquals(commands.size(), 3);
+    List<StructureCommandI> commands = testee.colourBySequence(map);
+    assertEquals(commands.size(), 1);
     String expected1 = "select 2-5:A/1.1|9-23:A/1.1|7:B/1.1|1:A/2.1|4-7:B/2.1;color[0,0,255]";
     String expected2 = "select 3-5:A/2.1|8:A/2.1;color[255,255,0]";
     String expected3 = "select 3-9:A/1.1;color[255,0,0]";
-    assertEquals(commands.get(0).getCommand(), expected1);
-    assertEquals(commands.get(1).getCommand(), expected2);
-    assertEquals(commands.get(2).getCommand(), expected3);
+    assertEquals(commands.get(0).getCommand(),
+            expected1 + ";" + expected2 + ";" + expected3);
   }
 
   @Test(groups = { "Functional" })
   public void testSuperposeStructures()
   {
-    StructureCommandsI testee = new JmolCommands();
     AtomSpecModel ref = new AtomSpecModel();
     ref.addRange("1", 12, 14, "A");
     ref.addRange("1", 18, 18, "B");
@@ -217,7 +212,75 @@ public class JmolCommandsTest
   @Test(groups = "Functional")
   public void testGetModelStartNo()
   {
-    StructureCommandsI testee = new JmolCommands();
     assertEquals(testee.getModelStartNo(), 1);
   }
+
+  @Test(groups = "Functional")
+  public void testColourByChain()
+  {
+    StructureCommandI cmd = testee.colourByChain();
+    assertEquals(cmd.getCommand(), "select *;color chain");
+  }
+
+  @Test(groups = "Functional")
+  public void testColourByCharge()
+  {
+    List<StructureCommandI> cmds = testee.colourByCharge();
+    assertEquals(cmds.size(), 1);
+    assertEquals(cmds.get(0).getCommand(),
+            "select *;color white;select ASP,GLU;color red;"
+                    + "select LYS,ARG;color blue;select CYS;color yellow");
+  }
+
+  @Test(groups = "Functional")
+  public void testSetBackgroundColour()
+  {
+    StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
+    assertEquals(cmd.getCommand(), "background [255,175,175]");
+  }
+
+  @Test(groups = "Functional")
+  public void testFocusView()
+  {
+    StructureCommandI cmd = testee.focusView();
+    assertEquals(cmd.getCommand(), "zoom 0");
+  }
+
+  @Test(groups = "Functional")
+  public void testSaveSession()
+  {
+    StructureCommandI cmd = testee.saveSession("/some/filepath");
+    assertEquals(cmd.getCommand(), "write STATE \"/some/filepath\"");
+  }
+
+  @Test(groups = "Functional")
+  public void testShowBackbone()
+  {
+    List<StructureCommandI> cmds = testee.showBackbone();
+    assertEquals(cmds.size(), 1);
+    assertEquals(cmds.get(0).getCommand(),
+            "select *; cartoons off; backbone");
+  }
+
+  @Test(groups = "Functional")
+  public void testLoadFile()
+  {
+    StructureCommandI cmd = testee.loadFile("/some/filepath");
+    assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
+
+    // single backslash gets escaped to double
+    cmd = testee.loadFile("\\some\\filepath");
+    assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
+  }
+
+  @Test(groups = "Functional")
+  public void testOpenSession()
+  {
+    StructureCommandI cmd = testee.openSession("/some/filepath");
+    assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
+
+    // single backslash gets escaped to double
+    cmd = testee.openSession("\\some\\filepath");
+    assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
+  }
 }