JAL-3518 more pull up / test coverage of structure command generation

[jalview.git] / src / jalview / ext / rbvi / chimera / ChimeraCommands.java

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 14699ef..1b1dd35 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -62,14 +62,6 @@ public class ChimeraCommands extends StructureCommandsBase
   private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
 
   @Override
-  public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
-  {
-    List<String> colourCommands = buildColourCommands(colourMap);
-
-    return colourCommands.toArray(new String[colourCommands.size()]);
-  }
-
-  @Override
   public String getColourCommand(String atomSpec, Color colour)
   {
     // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
@@ -83,7 +75,6 @@ public class ChimeraCommands extends StructureCommandsBase
    * @param colour
    * @return
    */
-  @Override
   protected String getColourString(Color colour)
   {
     return ColorUtils.toTkCode(colour);
@@ -108,9 +99,7 @@ public class ChimeraCommands extends StructureCommandsBase
     Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
             ssm, files, seqs, viewPanel);
 
-    List<String> commands = buildSetAttributeCommands(featureMap);
-
-    return commands.toArray(new String[commands.size()]);
+    return setAttributes(featureMap);
   }
 
   /**
@@ -354,7 +343,7 @@ public class ChimeraCommands extends StructureCommandsBase
    * @param featureMap
    * @return
    */
-  protected List<String> buildSetAttributeCommands(
+  protected String[] setAttributes(
           Map<String, Map<Object, AtomSpecModel>> featureMap)
   {
     List<String> commands = new ArrayList<>();
@@ -379,13 +368,13 @@ public class ChimeraCommands extends StructureCommandsBase
         AtomSpecModel atomSpecModel = values.get(value);
         String featureValue = value.toString();
         featureValue = featureValue.replaceAll("\\'", "&#39;");
-        String cmd = getSetAttributeCommand(attributeName, featureValue,
+        String cmd = setAttribute(attributeName, featureValue,
                 atomSpecModel);
         commands.add(cmd);
       }
     }
 
-    return commands;
+    return commands.toArray(new String[commands.size()]);
   }
 
   /**
@@ -401,7 +390,7 @@ public class ChimeraCommands extends StructureCommandsBase
    * @param atomSpecModel
    * @return
    */
-  protected String getSetAttributeCommand(String attributeName,
+  protected String setAttribute(String attributeName,
           String attributeValue,
           AtomSpecModel atomSpecModel)
   {