JAL-3390 first pass refactoring for JalviewJmolBinding.showStructures

[jalview.git] / test / jalview / ext / rbvi / chimera / ChimeraCommandsTest.java

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index 24ca6e9..6dd5cc7 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -38,7 +38,6 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.JalviewColourScheme;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 
@@ -95,8 +94,8 @@ public class ChimeraCommandsTest
     }
 
     @Override
-    protected StructureMappingcommandSet[] getColourBySequenceCommands(
-            String[] files, AlignmentViewPanel avp)
+    protected String[] getColourBySequenceCommands(String[] files,
+            AlignmentViewPanel avp)
     {
       return null;
     }
@@ -109,8 +108,7 @@ public class ChimeraCommandsTest
     }
 
     @Override
-    protected void colourBySequence(
-            StructureMappingcommandSet[] colourBySequenceCommands)
+    protected void colourBySequence(String[] colourBySequenceCommands)
     {
     }
 
@@ -155,15 +153,15 @@ public class ChimeraCommandsTest
   {
 
     Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
-    ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A");
-    ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B");
-    ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A");
-    ChimeraCommands.addColourRange(map, Color.blue, 1, 1, 1, "A");
-    ChimeraCommands.addColourRange(map, Color.blue, 1, 4, 7, "B");
-    ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A");
-    ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A");
-    ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A");
-    ChimeraCommands.addColourRange(map, Color.red, 0, 6, 9, "A");
+    ChimeraCommands.addMapRange(map, Color.blue, 0, 2, 5, "A");
+    ChimeraCommands.addMapRange(map, Color.blue, 0, 7, 7, "B");
+    ChimeraCommands.addMapRange(map, Color.blue, 0, 9, 23, "A");
+    ChimeraCommands.addMapRange(map, Color.blue, 1, 1, 1, "A");
+    ChimeraCommands.addMapRange(map, Color.blue, 1, 4, 7, "B");
+    ChimeraCommands.addMapRange(map, Color.yellow, 1, 8, 8, "A");
+    ChimeraCommands.addMapRange(map, Color.yellow, 1, 3, 5, "A");
+    ChimeraCommands.addMapRange(map, Color.red, 0, 3, 5, "A");
+    ChimeraCommands.addMapRange(map, Color.red, 0, 6, 9, "A");
 
     // 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
@@ -188,7 +186,7 @@ public class ChimeraCommandsTest
      * start with just one feature/value...
      */
     featuresMap.put("chain", featureValues);
-    ChimeraCommands.addColourRange(featureValues, "X", 0, 8, 20, "A");
+    ChimeraCommands.addMapRange(featureValues, "X", 0, 8, 20, "A");
   
     List<String> commands = ChimeraCommands
             .buildSetAttributeCommands(featuresMap, mockBinding);
@@ -201,18 +199,18 @@ public class ChimeraCommandsTest
     assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:8-20.A");
 
     // add same feature value, overlapping range
-    ChimeraCommands.addColourRange(featureValues, "X", 0, 3, 9, "A");
+    ChimeraCommands.addMapRange(featureValues, "X", 0, 3, 9, "A");
     // same feature value, contiguous range
-    ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "A");
+    ChimeraCommands.addMapRange(featureValues, "X", 0, 21, 25, "A");
     commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
             mockBinding);
     assertEquals(1, commands.size());
     assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
 
     // same feature value and model, different chain
-    ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "B");
+    ChimeraCommands.addMapRange(featureValues, "X", 0, 21, 25, "B");
     // same feature value and chain, different model
-    ChimeraCommands.addColourRange(featureValues, "X", 1, 26, 30, "A");
+    ChimeraCommands.addMapRange(featureValues, "X", 1, 26, 30, "A");
     commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
             mockBinding);
     assertEquals(1, commands.size());
@@ -220,7 +218,7 @@ public class ChimeraCommandsTest
             "setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
 
     // same feature, different value
-    ChimeraCommands.addColourRange(featureValues, "Y", 0, 40, 50, "A");
+    ChimeraCommands.addMapRange(featureValues, "Y", 0, 40, 50, "A");
     commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
             mockBinding);
     assertEquals(2, commands.size());
@@ -233,7 +231,7 @@ public class ChimeraCommandsTest
     featuresMap.clear();
     featureValues.clear();
     featuresMap.put("side-chain binding!", featureValues);
-    ChimeraCommands.addColourRange(featureValues,
+    ChimeraCommands.addMapRange(featureValues,
             "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
             "A");
     // feature names are sanitised to change non-alphanumeric to underscore
@@ -308,11 +306,10 @@ public class ChimeraCommandsTest
     PA.setValue(mockBinding, "ssm", ssm);
     PA.setValue(mockBinding, "sequence", seqs);
 
-    StructureMappingcommandSet[] commands = ChimeraCommands
+    String[] commands = ChimeraCommands
             .getColourBySequenceCommand(files, af.alignPanel, mockBinding);
     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