Merge branch 'develop' into feature/JAL-2422ChimeraX

[jalview.git] / src / jalview / gui / StructureViewerBase.java

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index d3e6d75..6dd7d50 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -22,9 +22,7 @@ package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
@@ -604,7 +602,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        viewerColour_actionPerformed(actionEvent);
+        viewerColour_actionPerformed();
       }
     });
     colourMenu.add(viewerColour);
@@ -620,7 +618,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        background_actionPerformed(actionEvent);
+        background_actionPerformed();
       }
     });
     colourMenu.add(backGround);
@@ -651,7 +649,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        seqColour_actionPerformed(actionEvent);
+        seqColour_actionPerformed();
       }
     });
 
@@ -663,7 +661,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        chainColour_actionPerformed(actionEvent);
+        chainColour_actionPerformed();
       }
     });
 
@@ -675,7 +673,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        chargeColour_actionPerformed(actionEvent);
+        chargeColour_actionPerformed();
       }
     });
 
@@ -707,7 +705,7 @@ public abstract class StructureViewerBase extends GStructureViewer
                 else
                 {
                   // update the Chimera display now.
-                  seqColour_actionPerformed(null);
+                  seqColour_actionPerformed();
                 }
               }
             });
@@ -757,12 +755,7 @@ public abstract class StructureViewerBase extends GStructureViewer
    * the operation.
    */
   @Override
-  protected String alignStructs_actionPerformed(ActionEvent actionEvent)
-  {
-    return alignStructs_withAllAlignPanels();
-  }
-
-  protected String alignStructs_withAllAlignPanels()
+  protected String alignStructsWithAllAlignPanels()
   {
     if (getAlignmentPanel() == null)
     {
@@ -777,19 +770,8 @@ public abstract class StructureViewerBase extends GStructureViewer
     String reply = null;
     try
     {
-      AlignmentI[] als = new Alignment[_alignwith.size()];
-      HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
-      int[] alm = new int[_alignwith.size()];
-      int a = 0;
-
-      for (AlignmentViewPanel alignPanel : _alignwith)
-      {
-        als[a] = alignPanel.getAlignment();
-        alm[a] = -1;
-        alc[a++] = alignPanel.getAlignment().getHiddenColumns();
-      }
-      reply = getBinding().superposeStructures(als, alm, alc);
-      if (reply != null)
+      reply = getBinding().superposeStructures(_alignwith);
+      if (reply != null && !reply.isEmpty())
       {
         String text = MessageManager
                 .formatMessage("error.superposition_failed", reply);
@@ -809,7 +791,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void background_actionPerformed(ActionEvent actionEvent)
+  public void background_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
             MessageManager.getString("label.select_background_colour"),
@@ -821,7 +803,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void viewerColour_actionPerformed(ActionEvent actionEvent)
+  public void viewerColour_actionPerformed()
   {
     if (viewerColour.isSelected())
     {
@@ -831,21 +813,21 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void chainColour_actionPerformed(ActionEvent actionEvent)
+  public void chainColour_actionPerformed()
   {
     chainColour.setSelected(true);
     getBinding().colourByChain();
   }
 
   @Override
-  public void chargeColour_actionPerformed(ActionEvent actionEvent)
+  public void chargeColour_actionPerformed()
   {
     chargeColour.setSelected(true);
     getBinding().colourByCharge();
   }
 
   @Override
-  public void seqColour_actionPerformed(ActionEvent actionEvent)
+  public void seqColour_actionPerformed()
   {
     AAStructureBindingModel binding = getBinding();
     binding.setColourBySequence(seqColour.isSelected());
@@ -873,7 +855,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void pdbFile_actionPerformed(ActionEvent actionEvent)
+  public void pdbFile_actionPerformed()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"));
@@ -924,7 +906,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void viewMapping_actionPerformed(ActionEvent actionEvent)
+  public void viewMapping_actionPerformed()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
@@ -986,7 +968,7 @@ public abstract class StructureViewerBase extends GStructureViewer
 
     if (!binding.isLoadingFromArchive())
     {
-      seqColour_actionPerformed(null);
+      seqColour_actionPerformed();
     }
   }