X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommandsTest.java;h=bf4889a4ab5cafa824aa78b443bf961fb15d4990;hb=55ebdfcc6bd979605c9bb2b4092a422b035bc27e;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..bf4889a 100644
--- 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.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");
@@ -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...
@@ -184,12 +184,13 @@ public class ChimeraCommandsTest
     SequenceRenderer sr = new SequenceRenderer(af.getViewport());
     SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
     String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
-    StructureSelectionManager ssm = new StructureSelectionManager();
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(null);
 
     /*
      * 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) });
@@ -202,8 +203,7 @@ 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 +211,7 @@ 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"));