JAL-3518 separation of ChimeraXManager, pull up of closeViewer etc

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

diff --git a/test/jalview/structure/AtomSpecTest.java b/test/jalview/structure/AtomSpecTest.java
index ff6e6cb..9881baf 100644 (file)
--- a/test/jalview/structure/AtomSpecTest.java
+++ b/test/jalview/structure/AtomSpecTest.java
@@ -9,23 +9,23 @@ 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 +34,7 @@ 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 +44,7 @@ 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 +54,7 @@ public class AtomSpecTest
     spec = "";
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, false);
+      as = AtomSpec.fromChimeraAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (IllegalArgumentException e)
     {
@@ -64,7 +64,7 @@ public class AtomSpecTest
     spec = null;
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, false);
+      as = AtomSpec.fromChimeraAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (NullPointerException e)
     {
@@ -73,23 +73,23 @@ 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(), "");
@@ -98,7 +98,7 @@ public class AtomSpecTest
     String spec = "3:12.B";
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, true);
+      as = AtomSpec.fromChimeraXAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (IllegalArgumentException e)
     {
@@ -108,7 +108,7 @@ public class AtomSpecTest
     spec = "#3:12-14.B";
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, true);
+      as = AtomSpec.fromChimeraXAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (IllegalArgumentException e)
     {
@@ -118,7 +118,7 @@ public class AtomSpecTest
     spec = "";
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, true);
+      as = AtomSpec.fromChimeraXAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (IllegalArgumentException e)
     {
@@ -128,7 +128,7 @@ public class AtomSpecTest
     spec = null;
     try
     {
-      as = AtomSpec.fromChimeraAtomspec(spec, true);
+      as = AtomSpec.fromChimeraXAtomspec(spec);
       fail("Expected exception for " + spec);
     } catch (NullPointerException e)
     {