X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=6a02576840a31de0950bdc2f2f2084268fbb54ad;hb=2ab7b9b152018bb808693218ad88dc3778166492;hp=8e68d866a56e94bd0b7c3acadbe591f5b835f105;hpb=c4ba8c80684447ab6a6e81057d417015ca49a06a;p=jalview.git

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index 8e68d86..6a02576 100644
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -29,11 +29,9 @@ 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.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 
 import java.awt.Color;
@@ -42,19 +40,11 @@ import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class ChimeraCommandsTest
 {
 
-  @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
-  {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-  }
-
   @Test(groups = { "Functional" })
   public void testBuildColourCommands()
   {
@@ -72,7 +62,7 @@ public class ChimeraCommandsTest
 
     // Colours should appear in the Chimera command in the order in which
     // they were added; within colour, by model, by chain, ranges in start order
-    String command = ChimeraCommands.buildColourCommands(map, false).get(0);
+    String command = new ChimeraCommands().buildColourCommands(map).get(0);
     assertEquals(
             command,
             "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:3-5.A,8.A; color #ff0000 #0:3-9.A");
@@ -101,7 +91,7 @@ public class ChimeraCommandsTest
      * feature name gets a jv_ namespace prefix
      * feature value is quoted in case it contains spaces
      */
-    assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:8-20.A");
+    assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:8-20.A");
 
     // add same feature value, overlapping range
     ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
@@ -110,7 +100,7 @@ public class ChimeraCommandsTest
     commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
             false);
     assertEquals(1, commands.size());
-    assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
+    assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:3-25.A");
 
     // same feature value and model, different chain
     ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
@@ -120,7 +110,7 @@ public class ChimeraCommandsTest
             false);
     assertEquals(1, commands.size());
     assertEquals(commands.get(0),
-            "setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
+            "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
 
     // same feature, different value
     ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
@@ -130,8 +120,9 @@ public class ChimeraCommandsTest
     // commands are ordered by feature type but not by value
     // so use contains to test for the expected command:
     assertTrue(commands
-            .contains("setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
-    assertTrue(commands.contains("setattr r jv_chain 'Y' #0:40-50.A"));
+            .contains(
+                    "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
+    assertTrue(commands.contains("setattr res jv_chain 'Y' #0:40-50.A"));
 
     featuresMap.clear();
     featureValues.clear();
@@ -144,7 +135,8 @@ public class ChimeraCommandsTest
     commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
             false);
     assertTrue(commands
-            .contains("setattr r jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!' #0:7-15.A"));
+            .contains(
+                    "setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!' #0:7-15.A"));
   }
 
   /**
@@ -205,12 +197,10 @@ public class ChimeraCommandsTest
             "B", map, null);
     ssm.addStructureMapping(sm2);
 
-    StructureMappingcommandSet[] commands = ChimeraCommands
-            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel,
-                    false);
+    String[] commands = new ChimeraCommands()
+            .colourBySequence(ssm, files, seqs, sr, af.alignPanel);
     assertEquals(1, commands.length);
-    assertEquals(1, commands[0].commands.length);
-    String theCommand = commands[0].commands[0];
+    String theCommand = commands[0];
     // M colour is #82827d (see strand.html help page)
     assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B"));
     // H colour is #60609f