X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fpymol%2FPymolCommandsTest.java;h=d5dbc8604270d24afaca49236601300b73ab7b3b;hb=f1fa440f885429399436bb09ef6d0639c8acd991;hp=bc125426f194c384920c732bae3d97fc2c152f15;hpb=a77aa990660f31c3e92f7f6bcb964c69fc4091c1;p=jalview.git

diff --git a/test/jalview/ext/pymol/PymolCommandsTest.java b/test/jalview/ext/pymol/PymolCommandsTest.java
index bc12542..d5dbc86 100644
--- a/test/jalview/ext/pymol/PymolCommandsTest.java
+++ b/test/jalview/ext/pymol/PymolCommandsTest.java
@@ -36,6 +36,7 @@ import jalview.ext.rbvi.chimera.ChimeraCommands;
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
 
 public class PymolCommandsTest
 {
@@ -80,32 +81,32 @@ public class PymolCommandsTest
   public void testGetAtomSpec()
   {
     AtomSpecModel model = new AtomSpecModel();
-    assertEquals(testee.getAtomSpec(model, false), "");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
     model.addRange("1", 2, 4, "A");
-    assertEquals(testee.getAtomSpec(model, false), "1//A/2-4/");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4/");
     model.addRange("1", 8, 8, "A");
-    assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/");
     model.addRange("1", 5, 7, "B");
-    assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/ 1//B/5-7/");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/ 1//B/5-7/");
     model.addRange("1", 3, 5, "A");
-    assertEquals(testee.getAtomSpec(model, false), "1//A/2-5+8/ 1//B/5-7/");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-5+8/ 1//B/5-7/");
     model.addRange("0", 1, 4, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
     model.addRange("0", 5, 9, "C");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
     model.addRange("1", 8, 10, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
     model.addRange("1", 8, 9, "B");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
     model.addRange("0", 3, 10, "C"); // subsumes 5-9
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
     model.addRange("5", 25, 35, " ");
-    assertEquals(testee.getAtomSpec(model, false),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
             "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
 
   }
@@ -122,18 +123,18 @@ public class PymolCommandsTest
     toAlign.addRange("2", 20, 21, "B");
     toAlign.addRange("2", 22, 22, "C");
     List<StructureCommandI> commands = testee.superposeStructures(ref,
-            toAlign, false);
-    assertEquals(commands.size(), 2);
+            toAlign, AtomSpecType.ALPHA);
+    assertEquals(commands.size(), 4);
     String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA";
     String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
     String refSpec = "1//A/12-14/ 1//B/18+22-23/";
     String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
     String altLoc =  " and (altloc '' or altloc 'a'))";
     // super command: separate arguments for regions to align
-    assertEquals(commands.get(0),
+    assertEquals(commands.get(1),
             new StructureCommand("pair_fit", toAlignSpecCA+altLoc, refSpecCA+altLoc));
     // show aligned regions: one argument for combined atom specs
-    assertEquals(commands.get(1), new StructureCommand("show", "cartoon",
+    assertEquals(commands.get(3), new StructureCommand("show", "cartoon",
             refSpec + " " + toAlignSpec));
   }
 
@@ -141,34 +142,34 @@ public class PymolCommandsTest
   public void testGetAtomSpec_alphaOnly()
   {
     AtomSpecModel model = new AtomSpecModel();
-    assertEquals(testee.getAtomSpec(model, true), "");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
     model.addRange("1", 2, 4, "A");
-    assertEquals(testee.getAtomSpec(model, true), "1//A/2-4/CA");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4/CA");
     model.addRange("1", 8, 8, "A");
-    assertEquals(testee.getAtomSpec(model, true), "1//A/2-4+8/CA");
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4+8/CA");
     model.addRange("1", 5, 7, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "1//A/2-4+8/CA 1//B/5-7/CA");
     model.addRange("1", 3, 5, "A");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "1//A/2-5+8/CA 1//B/5-7/CA");
     model.addRange("0", 1, 4, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
     model.addRange("0", 5, 9, "C");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
     model.addRange("1", 8, 10, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
     model.addRange("1", 8, 9, "B");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
     model.addRange("0", 3, 10, "C"); // subsumes 5-9
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
     model.addRange("5", 25, 35, " ");
-    assertEquals(testee.getAtomSpec(model, true),
+    assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
             "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA 5///25-35/CA");
   }