From a663c1c844de90b4c125dbbcf5c8b953b00a809d Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 7 Aug 2019 16:56:17 +0100
Subject: [PATCH] JAL-3390 showSelectedChains pulled up to base class for
 Jmol/Chimera

---
 src/jalview/ext/jmol/JalviewJmolBinding.java        |   15 +++++++++------
 src/jalview/gui/AppJmol.java                        |    7 -------
 src/jalview/gui/ChimeraViewFrame.java               |   14 --------------
 src/jalview/gui/StructureViewerBase.java            |   19 +++++++++++++++++--
 .../structures/models/AAStructureBindingModel.java  |    2 +-
 5 files changed, 27 insertions(+), 30 deletions(-)

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 2a9a698..d820273 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -133,9 +133,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * prepare the view for a given set of models/chains. chainList contains
-   * strings of the form 'pdbfilename:Chaincode'
+   * prepare the view for a given set of models/chains. chainList contains strings
+   * of the form 'pdbfilename:Chaincode'
+   * 
+   * @deprecated now only used by applet code
    */
+  @Deprecated
   public void centerViewer()
   {
     StringBuilder cmd = new StringBuilder(128);
@@ -1440,10 +1443,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       cmd.append("hide *;");
 
-    AtomSpecModel model = getShownResidues(av);
-    String atomSpec = JmolCommands.getAtomSpec(model);
+      AtomSpecModel model = getShownResidues(av);
+      String atomSpec = JmolCommands.getAtomSpec(model);
 
-    cmd.append("display ").append(atomSpec);
+      cmd.append("display ").append(atomSpec);
     }
     else
     {
@@ -1452,7 +1455,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     cmd.append("; cartoon");
     if (refocus)
     {
-      cmd.append("; zoom 100");
+      cmd.append("; zoom 0");
     }
     evalStateCommand(cmd.toString());
   }
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 9179be6..205c33b 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -259,13 +259,6 @@ public class AppJmol extends StructureViewerBase
   }
 
   @Override
-  void showSelectedChains()
-  {
-    setSelectedChains();
-    jmb.centerViewer();
-  }
-
-  @Override
   public void closeViewer(boolean closeExternalViewer)
   {
     // Jmol does not use an external viewer
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 1a5ed5e..71e90d9 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -357,20 +357,6 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * Show only the selected chain(s) in the viewer
-   */
-  @Override
-  void showSelectedChains()
-  {
-    setSelectedChains();
-
-    /*
-     * refresh display without resizing - easier to see what changed
-     */
-    jmb.showStructures(getAlignmentPanel().getAlignViewport(), false);
-  }
-
-  /**
    * Close down this instance of Jalview's Chimera viewer, giving the user the
    * option to close the associated Chimera window (process). They may wish to
    * keep it open until they have had an opportunity to save any work.
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 2ffcee1..d04d1d6 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -556,8 +556,6 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
-  abstract void showSelectedChains();
-
   /**
    * Action on selecting one of Jalview's registered colour schemes
    */
@@ -1069,4 +1067,21 @@ public abstract class StructureViewerBase extends GStructureViewer
     toFront();
   }
 
+  @Override
+  public abstract AAStructureBindingModel getBinding();
+
+  /**
+   * Show only the selected chain(s) in the viewer
+   */
+  protected void showSelectedChains()
+  {
+    setSelectedChains();
+  
+    /*
+     * refresh display without resizing - easier to see what changed
+     */
+    getBinding().showStructures(getAlignmentPanel().getAlignViewport(),
+            false);
+  }
+
 }
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 47e7f30..8a7c355 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -108,7 +108,7 @@ public abstract class AAStructureBindingModel
    * a list of chains "pdbid:chainid" to show in the viewer;
    * empty means show all
    */
-  // TODO make private once showStructures() deals with this
+  // TODO make private once deprecated JalviewJmolBinding.centerViewer removed
   protected List<String> chainsToShow;
 
   private boolean hideHiddenRegions;
-- 
1.7.10.2