X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolCommandsTest.java;h=5846b33771b9decf0853fdd38c947cc4a12444a7;hb=2ab7b9b152018bb808693218ad88dc3778166492;hp=e42b54fa702416da2bd1e1c1d57a73563cc8b23d;hpb=c4ba8c80684447ab6a6e81057d417015ca49a06a;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index e42b54f..5846b33 100644
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -33,7 +33,6 @@ 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.util.HashMap;
@@ -65,8 +64,9 @@ public class JmolCommandsTest
 
     // need some mappings!
 
-    StructureMappingcommandSet[] commands = JmolCommands
-            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+    String[] commands = new JmolCommands().colourBySequence(ssm, files,
+            seqs, sr, af.alignPanel);
+    assertEquals(commands.length, 0);
   }
 
   @Test(groups = { "Functional" })
@@ -91,11 +91,11 @@ public class JmolCommandsTest
     SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
     String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
     StructureSelectionManager ssm = new StructureSelectionManager();
-  
+
     /*
      * 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) });
@@ -106,37 +106,36 @@ public class JmolCommandsTest
     StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
             "B", map, null);
     ssm.addStructureMapping(sm2);
-  
-    StructureMappingcommandSet[] commands = JmolCommands
-            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+
+    String[] commands = new JmolCommands().colourBySequence(ssm, files,
+            seqs, sr, af.alignPanel);
     assertEquals(commands.length, 2);
-    assertEquals(commands[0].commands.length, 1);
 
-    String chainACommand = commands[0].commands[0];
+    String chainACommand = commands[0];
     // M colour is #82827d == (130, 130, 125) (see strand.html help page)
-    assertTrue(chainACommand
-            .contains("select 21:A/1.1;color[130,130,125]")); // first one
+    assertTrue(
+            chainACommand.contains("select 21:A/1.1;color[130,130,125]")); // first
+                                                                           // one
     // H colour is #60609f == (96, 96, 159)
     assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
     // hidden columns are Gray (128, 128, 128)
     assertTrue(chainACommand
             .contains(";select 23-25:A/1.1;color[128,128,128]"));
     // S and G are both coloured #4949b6 == (73, 73, 182)
-    assertTrue(chainACommand
-            .contains(";select 26-30:A/1.1;color[73,73,182]"));
+    assertTrue(
+            chainACommand.contains(";select 26-30:A/1.1;color[73,73,182]"));
 
-    String chainBCommand = commands[1].commands[0];
+    String chainBCommand = commands[1];
     // M colour is #82827d == (130, 130, 125)
-    assertTrue(chainBCommand
-            .contains("select 21:B/2.1;color[130,130,125]"));
+    assertTrue(
+            chainBCommand.contains("select 21:B/2.1;color[130,130,125]"));
     // V colour is #ffff00 == (255, 255, 0)
-    assertTrue(chainBCommand
-.contains(";select 22:B/2.1;color[255,255,0]"));
+    assertTrue(chainBCommand.contains(";select 22:B/2.1;color[255,255,0]"));
     // hidden columns are Gray (128, 128, 128)
     assertTrue(chainBCommand
             .contains(";select 23-25:B/2.1;color[128,128,128]"));
     // S and G are both coloured #4949b6 == (73, 73, 182)
-    assertTrue(chainBCommand
-            .contains(";select 26-30:B/2.1;color[73,73,182]"));
+    assertTrue(
+            chainBCommand.contains(";select 26-30:B/2.1;color[73,73,182]"));
   }
 }