Merge branch 'features/JAL-2376_add-horizontal-bar' into develop

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 82e188f..00fd679 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,11 +20,11 @@
  */
 package jalview.ext.jmol;
 
-import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
@@ -222,11 +222,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    *          TODO
    */
   public void superposeStructures(AlignmentI alignment, int refStructure,
-          ColumnSelection hiddenCols)
+          HiddenColumns hiddenCols)
   {
     superposeStructures(new AlignmentI[] { alignment },
             new int[] { refStructure },
-            new ColumnSelection[] { hiddenCols });
+ new HiddenColumns[] { hiddenCols });
   }
 
   /**
@@ -234,7 +234,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   @Override
   public String superposeStructures(AlignmentI[] _alignment,
-          int[] _refStructure, ColumnSelection[] _hiddenCols)
+          int[] _refStructure, HiddenColumns[] _hiddenCols)
   {
     while (viewer.isScriptExecuting())
     {
@@ -278,7 +278,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       int refStructure = _refStructure[a];
       AlignmentI alignment = _alignment[a];
-      ColumnSelection hiddenCols = _hiddenCols[a];
+      HiddenColumns hiddenCols = _hiddenCols[a];
       if (a > 0
               && selectioncom.length() > 0
               && !selectioncom.substring(selectioncom.length() - 1).equals(
@@ -499,17 +499,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   /**
    * @param files
    * @param sr
-   * @param fr
-   * @param viewport
+   * @param viewPanel
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignViewportI viewport)
+          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
   {
     return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, fr, viewport);
+            getSequence(), sr, viewPanel);
   }
 
   /**