JAL-3390 move StructureCommands to utils package

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 972f093..f0ae6dc 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -28,7 +28,6 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.AtomSpecModel;
-import jalview.ext.rbvi.chimera.StructureCommands;
 import jalview.gui.IProgressIndicator;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
@@ -38,6 +37,7 @@ import jalview.structure.AtomSpec;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
+import jalview.util.StructureCommands;
 
 import java.awt.Color;
 import java.awt.Container;

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index f0949b8..a900701 100644 (file)
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -28,11 +28,11 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.AtomSpecModel;
-import jalview.ext.rbvi.chimera.StructureCommands;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.StructureCommands;
 
 import java.awt.Color;
 import java.util.ArrayList;

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 8c00e74..bfec5b2 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -33,6 +33,7 @@ import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.ColorUtils;
+import jalview.util.StructureCommands;
 
 import java.awt.Color;
 import java.util.ArrayList;

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 2bb24d9..dd0a75e 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -40,6 +40,7 @@ import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
+import jalview.util.StructureCommands;
 
 import java.awt.Color;
 import java.io.File;

diff --git a/src/jalview/ext/rbvi/chimera/StructureCommands.java b/src/jalview/util/StructureCommands.java
similarity index 97%
rename from src/jalview/ext/rbvi/chimera/StructureCommands.java
rename to src/jalview/util/StructureCommands.java
index 5f707ae..8e66da8 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/StructureCommands.java
+++ b/src/jalview/util/StructureCommands.java
@@ -1,4 +1,4 @@
-package jalview.ext.rbvi.chimera;
+package jalview.util;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -7,11 +7,10 @@ import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.AtomSpecModel;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.Comparison;
-import jalview.util.IntRangeComparator;
 
 import java.awt.Color;
 import java.util.Collections;
@@ -44,7 +43,7 @@ public abstract class StructureCommands
    * @param endPos
    * @param chain
    */
-  protected static void addAtomSpecRange(Map<Object, AtomSpecModel> map,
+  public static void addAtomSpecRange(Map<Object, AtomSpecModel> map,
           Object value,
           int model, int startPos, int endPos, String chain)
   {

diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index e140fe1..45e66ce 100644 (file)
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -32,7 +32,6 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.AtomSpecModel;
-import jalview.ext.rbvi.chimera.StructureCommands;
 import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
 import jalview.gui.SequenceRenderer;
@@ -43,6 +42,7 @@ import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.StructureCommands;
 
 import java.awt.Color;
 import java.util.HashMap;
@@ -274,7 +274,7 @@ public class JmolCommandsTest
   }
 
   @Test(groups = "Functional")
-  public void testGetColourBySequenceCommand_mapVersion()
+  public void testGetColourBySequenceCommand()
   {
     /*
      * load these sequences, coloured by Strand propensity,

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index 9adbd8e..fb8626c 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -40,6 +40,7 @@ import jalview.structure.AtomSpec;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.StructureCommands;
 
 import java.awt.Color;
 import java.util.HashMap;