JAL-4036 use the legacy endpoint (and report the FTS query when debug/trace enabled)

[jalview.git] / test / jalview / structure / AtomSpecTest.java

diff --git a/test/jalview/structure/AtomSpecTest.java b/test/jalview/structure/AtomSpecTest.java
index ff6e6cb..39d10ae 100644 (file)
--- a/test/jalview/structure/AtomSpecTest.java
+++ b/test/jalview/structure/AtomSpecTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.structure;
 
 import static org.testng.Assert.assertEquals;
@@ -9,23 +29,23 @@ import org.testng.annotations.Test;
 public class AtomSpecTest
 {
   @Test
-  public void testFromChimeraAtomSpec_chimera()
+  public void testFromChimeraAtomSpec()
   {
-    AtomSpec as = AtomSpec.fromChimeraAtomspec("#1:12.B", false);
+    AtomSpec as = AtomSpec.fromChimeraAtomspec("#1:12.B");
     assertEquals(as.getModelNumber(), 1);
     assertEquals(as.getPdbResNum(), 12);
     assertEquals(as.getChain(), "B");
     assertNull(as.getPdbFile());
 
     // no model - default to zero
-    as = AtomSpec.fromChimeraAtomspec(":13.C", false);
+    as = AtomSpec.fromChimeraAtomspec(":13.C");
     assertEquals(as.getModelNumber(), 0);
     assertEquals(as.getPdbResNum(), 13);
     assertEquals(as.getChain(), "C");
     assertNull(as.getPdbFile());
 
     // model.submodel
-    as = AtomSpec.fromChimeraAtomspec("#3.2:15", false);
+    as = AtomSpec.fromChimeraAtomspec("#3.2:15");
     assertEquals(as.getModelNumber(), 3);
     assertEquals(as.getPdbResNum(), 15);
     assertEquals(as.getChain(), "");
@@ -34,7 +54,7 @@ public class AtomSpecTest
     String spec = "3:12.B";
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, false);
+      as = AtomSpec.fromChimeraAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (IllegalArgumentException e)
     {
@@ -44,7 +64,7 @@ public class AtomSpecTest
     spec = "#3:12-14.B";
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, false);
+      as = AtomSpec.fromChimeraAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (IllegalArgumentException e)
     {
@@ -54,7 +74,7 @@ public class AtomSpecTest
     spec = "";
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, false);
+      as = AtomSpec.fromChimeraAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (IllegalArgumentException e)
     {
@@ -64,7 +84,7 @@ public class AtomSpecTest
     spec = null;
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, false);
+      as = AtomSpec.fromChimeraAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (NullPointerException e)
     {
@@ -73,62 +93,62 @@ public class AtomSpecTest
   }
 
   @Test
-  public void testFromChimeraAtomSpec_chimeraX()
+  public void testFromChimeraXAtomSpec()
   {
-    AtomSpec as = AtomSpec.fromChimeraAtomspec("#1/B:12", true);
+    AtomSpec as = AtomSpec.fromChimeraXAtomspec("#1/B:12");
     assertEquals(as.getModelNumber(), 1);
     assertEquals(as.getPdbResNum(), 12);
     assertEquals(as.getChain(), "B");
     assertNull(as.getPdbFile());
-  
+
     // no model - default to zero
-    as = AtomSpec.fromChimeraAtomspec("/C:13", true);
+    as = AtomSpec.fromChimeraXAtomspec("/C:13");
     assertEquals(as.getModelNumber(), 0);
     assertEquals(as.getPdbResNum(), 13);
     assertEquals(as.getChain(), "C");
     assertNull(as.getPdbFile());
-  
+
     // model.submodel
-    as = AtomSpec.fromChimeraAtomspec("#3.2/:15", true);
+    as = AtomSpec.fromChimeraXAtomspec("#3.2/:15");
     assertEquals(as.getModelNumber(), 3);
     assertEquals(as.getPdbResNum(), 15);
     assertEquals(as.getChain(), "");
     assertNull(as.getPdbFile());
-  
+
     String spec = "3:12.B";
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, true);
+      as = AtomSpec.fromChimeraXAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (IllegalArgumentException e)
     {
       // ok
     }
-  
+
     spec = "#3:12-14.B";
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, true);
+      as = AtomSpec.fromChimeraXAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (IllegalArgumentException e)
     {
       // ok
     }
-  
+
     spec = "";
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, true);
+      as = AtomSpec.fromChimeraXAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (IllegalArgumentException e)
     {
       // ok
     }
-  
+
     spec = null;
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, true);
+      as = AtomSpec.fromChimeraXAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (NullPointerException e)
     {