From faf491e024f9835435f5dd6c20a033250dd9297d Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 15 Dec 2023 15:18:23 +0000
Subject: [PATCH] JAL-4290 Set structureSelectionManager settings more
 generically and when no desktop exists

---
 src/jalview/bin/Commands.java                      |    8 +------
 src/jalview/gui/Desktop.java                       |   17 +--------------
 src/jalview/gui/StructureChooser.java              |    1 +
 .../structure/StructureSelectionManager.java       |   23 ++++++++++++++++++++
 4 files changed, 26 insertions(+), 23 deletions(-)

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index dbc5e23..ece573d 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -908,13 +908,7 @@ public class Commands
           boolean showSSAnnotations, boolean showAnnotations,
           boolean hideTFrows)
   {
-    Console.debug(
-            "##### Setting showSSAnnotations to " + showSSAnnotations);
-    Console.debug("##### Setting showAnnotations to " + showAnnotations);
-    Console.debug("##### Setting hideTFrows to " + hideTFrows);
-    af.setAnnotationsVisibility(showSSAnnotations, true, false);
-
-    af.setAnnotationsVisibility(showAnnotations, false, true);
+    af.setAnnotationsVisibility(true, showSSAnnotations, showAnnotations);
 
     // show temperature factor annotations?
     if (hideTFrows)
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 35c7818..bbd4dae 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -680,22 +680,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     // configure services
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(this);
-    if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
-    {
-      ssm.setAddTempFacAnnot(
-              Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
-      ssm.setProcessSecondaryStructure(
-              Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
-      // JAL-3915 - RNAView is no longer an option so this has no effect
-      ssm.setSecStructServices(
-              Cache.getDefault(Preferences.USE_RNAVIEW, false));
-    }
-    else
-    {
-      ssm.setAddTempFacAnnot(false);
-      ssm.setProcessSecondaryStructure(false);
-      ssm.setSecStructServices(false);
-    }
+    StructureSelectionManager.doConfigureStructurePrefs(ssm);
   }
 
   public void checkForNews()
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 666ff74..6132908 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1826,6 +1826,7 @@ public class StructureChooser extends GStructureChooser
     if (ssm == null)
     {
       ssm = ap.getStructureSelectionManager();
+      StructureSelectionManager.doConfigureStructurePrefs(ssm);
     }
 
     PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ec3e0a0..5865b7f 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -34,6 +34,7 @@ import java.util.Vector;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
@@ -50,6 +51,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.gui.IProgressIndicator;
+import jalview.gui.Preferences;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
@@ -1665,4 +1667,25 @@ public class StructureSelectionManager
     return pdbIdFileName;
   }
 
+  public static void doConfigureStructurePrefs(
+          StructureSelectionManager ssm)
+  {
+    if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
+    {
+      ssm.setAddTempFacAnnot(
+              Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+      ssm.setProcessSecondaryStructure(
+              Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+      // JAL-3915 - RNAView is no longer an option so this has no effect
+      ssm.setSecStructServices(
+              Cache.getDefault(Preferences.USE_RNAVIEW, false));
+    }
+    else
+    {
+      ssm.setAddTempFacAnnot(false);
+      ssm.setProcessSecondaryStructure(false);
+      ssm.setSecStructServices(false);
+    }
+  }
+
 }
-- 
1.7.10.2