From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 15 Dec 2023 21:30:13 +0000 (+0000)
Subject: Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesn... 
X-Git-Tag: Release_2_11_3_3~7^2~2^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cb3f31e3aacf81fa2b33f9eab9657ed40a66161e;hp=25513f2ce9d341344e29677335022a94e7822202;p=jalview.git

Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor' of https://source.jalview.org/git/jalview into bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor
---

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index dbc5e23..5f723c1 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -908,12 +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);
 
     // show temperature factor annotations?
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..9a9e2a2 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 +1667,34 @@ public class StructureSelectionManager
     return pdbIdFileName;
   }
 
+  public static void doConfigureStructurePrefs(
+          StructureSelectionManager ssm)
+  {
+    doConfigureStructurePrefs(ssm,
+            Cache.getDefault(Preferences.ADD_SS_ANN, true),
+            Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true),
+            Cache.getDefault(Preferences.STRUCT_FROM_PDB, true),
+            Cache.getDefault(Preferences.USE_RNAVIEW, false));
+  }
+
+  public static void doConfigureStructurePrefs(
+          StructureSelectionManager ssm, boolean add_ss_ann,
+          boolean add_tempfact_ann, boolean struct_from_pdb,
+          boolean use_rnaview)
+  {
+    if (add_ss_ann)
+    {
+      ssm.setAddTempFacAnnot(add_tempfact_ann);
+      ssm.setProcessSecondaryStructure(struct_from_pdb);
+      // JAL-3915 - RNAView is no longer an option so this has no effect
+      ssm.setSecStructServices(use_rnaview);
+    }
+    else
+    {
+      ssm.setAddTempFacAnnot(false);
+      ssm.setProcessSecondaryStructure(false);
+      ssm.setSecStructServices(false);
+    }
+  }
+
 }