Merge branch 'bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesn...

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ec3e0a0..9a9e2a2 100644 (file)
--- 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);
+    }
+  }
+
 }