JAL-2422 basic proof of concept of ChimeraX opened/coloured by Jalview

[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 06a09df..8e68d86 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -59,7 +59,7 @@ public class ChimeraCommandsTest
   public void testBuildColourCommands()
   {
 
-    Map<Object, AtomSpecModel> map = new LinkedHashMap<Object, AtomSpecModel>();
+    Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
     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");
@@ -72,7 +72,7 @@ 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).get(0);
+    String command = ChimeraCommands.buildColourCommands(map, false).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");
@@ -84,8 +84,8 @@ public class ChimeraCommandsTest
     /*
      * make a map of { featureType, {featureValue, {residue range specification } } }
      */
-    Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
-    Map<Object, AtomSpecModel> featureValues = new HashMap<Object, AtomSpecModel>();
+    Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
+    Map<Object, AtomSpecModel> featureValues = new HashMap<>();
     
     /*
      * start with just one feature/value...
@@ -94,7 +94,7 @@ public class ChimeraCommandsTest
     ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
   
     List<String> commands = ChimeraCommands
-            .buildSetAttributeCommands(featuresMap);
+            .buildSetAttributeCommands(featuresMap, false);
     assertEquals(1, commands.size());
 
     /*
@@ -107,7 +107,8 @@ public class ChimeraCommandsTest
     ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
     // same feature value, contiguous range
     ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
-    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
+            false);
     assertEquals(1, commands.size());
     assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
 
@@ -115,14 +116,16 @@ public class ChimeraCommandsTest
     ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
     // same feature value and chain, different model
     ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
-    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
+            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");
 
     // same feature, different value
     ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
-    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
+            false);
     assertEquals(2, commands.size());
     // commands are ordered by feature type but not by value
     // so use contains to test for the expected command:
@@ -138,7 +141,8 @@ public class ChimeraCommandsTest
             "A");
     // feature names are sanitised to change non-alphanumeric to underscore
     // feature values are sanitised to encode single quote characters
-    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    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"));
   }
@@ -189,7 +193,7 @@ public class ChimeraCommandsTest
     /*
      * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
      */
-    HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
+    HashMap<Integer, int[]> map = new HashMap<>();
     for (int pos = 1; pos <= seq1.getLength(); pos++)
     {
       map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
@@ -202,7 +206,8 @@ public class ChimeraCommandsTest
     ssm.addStructureMapping(sm2);
 
     StructureMappingcommandSet[] commands = ChimeraCommands
-            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel,
+                    false);
     assertEquals(1, commands.length);
     assertEquals(1, commands[0].commands.length);
     String theCommand = commands[0].commands[0];