X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=06a09dff9bb0327ecf8b6cbf855f6fe8221f474b;hb=e42e467b0a21b19e9c39c9395bdac19c322d9ffe;hp=d3511712221152cf361184538647d21616304e01;hpb=799c26111d6936a2e70cb5f1fd7d7312311e6db9;p=jalview.git

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index d351171..06a09df 100644
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -60,15 +60,15 @@ public class ChimeraCommandsTest
   {
 
     Map<Object, AtomSpecModel> map = new LinkedHashMap<Object, AtomSpecModel>();
-    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.addAtomSpecRange(map, Color.blue, 0, 2, 5, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 7, 7, "B");
+    ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 9, 23, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 1, 1, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 4, 7, "B");
+    ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 8, 8, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 3, 5, "A");
+    ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 3, 5, "A");
+    ChimeraCommands.addAtomSpecRange(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
@@ -91,7 +91,7 @@ public class ChimeraCommandsTest
      * start with just one feature/value...
      */
     featuresMap.put("chain", featureValues);
-    ChimeraCommands.addColourRange(featureValues, "X", 0, 8, 20, "A");
+    ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
   
     List<String> commands = ChimeraCommands
             .buildSetAttributeCommands(featuresMap);
@@ -104,24 +104,24 @@ 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.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
     // same feature value, contiguous range
-    ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "A");
+    ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
     commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
     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.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
     // same feature value and chain, different model
-    ChimeraCommands.addColourRange(featureValues, "X", 1, 26, 30, "A");
+    ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
     commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
     assertEquals(1, commands.size());
     assertEquals(commands.get(0),
             "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.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
     commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
     assertEquals(2, commands.size());
     // commands are ordered by feature type but not by value
@@ -133,7 +133,7 @@ public class ChimeraCommandsTest
     featuresMap.clear();
     featureValues.clear();
     featuresMap.put("side-chain binding!", featureValues);
-    ChimeraCommands.addColourRange(featureValues,
+    ChimeraCommands.addAtomSpecRange(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
@@ -202,8 +202,7 @@ public class ChimeraCommandsTest
     ssm.addStructureMapping(sm2);
 
     StructureMappingcommandSet[] commands = ChimeraCommands
-            .getColourBySequenceCommand(ssm, files, seqs, sr, null,
-                    af.getViewport());
+            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
     assertEquals(1, commands.length);
     assertEquals(1, commands[0].commands.length);
     String theCommand = commands[0].commands[0];
@@ -211,7 +210,7 @@ public class ChimeraCommandsTest
     assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B"));
     // H colour is #60609f
     assertTrue(theCommand.contains("color #60609f #0:22.A"));
-    // V colour is ##ffff00
+    // V colour is #ffff00
     assertTrue(theCommand.contains("color #ffff00 #1:22.B"));
     // hidden columns are Gray (128, 128, 128)
     assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B"));