From: Jim Procter <j.procter@dundee.ac.uk>
Date: Wed, 3 Nov 2021 11:33:14 +0000 (+0000)
Subject: JAL-3915 remove RNAview opts from preferences. Still present in config file ready... 
X-Git-Tag: Release_2_11_2_0~24^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=77591230ecd28c2425e94e6298cc2961eed332d2;p=jalview.git

JAL-3915 remove RNAview opts from preferences. Still present in config file ready for when we have a new RNA structure processing service
---

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 666fb4e..0f80dd5 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -551,7 +551,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     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));
-      ssm.setSecStructServices(Cache.getDefault(Preferences.USE_RNAVIEW, 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);
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index baed0df..d8eee6d 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -396,13 +396,11 @@ public class Preferences extends GPreferences
     /*
      * Set Structure tab defaults
      */
-    final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+    final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
     structFromPdb.setSelected(structSelected);
-    useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
-    useRnaView.setEnabled(structSelected);
-    addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+    addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
     addSecondaryStructure.setEnabled(structSelected);
-    addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+    addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
     addTempFactor.setEnabled(structSelected);
 
     /*
@@ -845,8 +843,6 @@ public class Preferences extends GPreferences
             Boolean.toString(addTempFactor.isSelected()));
     Cache.applicationProperties.setProperty(ADD_SS_ANN,
             Boolean.toString(addSecondaryStructure.isSelected()));
-    Cache.applicationProperties.setProperty(USE_RNAVIEW,
-            Boolean.toString(useRnaView.isSelected()));
     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
             Boolean.toString(structFromPdb.isSelected()));
     String viewer = structViewer.getSelectedItem().toString();
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index e6efed6..debb2ab 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -175,8 +175,6 @@ public class GPreferences extends JPanel
 
   protected JCheckBox structFromPdb = new JCheckBox();
 
-  protected JCheckBox useRnaView = new JCheckBox();
-
   protected JCheckBox addSecondaryStructure = new JCheckBox();
 
   protected JCheckBox addTempFactor = new JCheckBox();
@@ -1652,7 +1650,6 @@ public class GPreferences extends JPanel
       {
         boolean selected = structFromPdb.isSelected();
         // enable other options only when the first is checked
-        useRnaView.setEnabled(selected);
         addSecondaryStructure.setEnabled(selected);
         addTempFactor.setEnabled(selected);
       }
@@ -1661,12 +1658,6 @@ public class GPreferences extends JPanel
 
     // indent checkboxes that are conditional on the first one
     ypos += lineSpacing;
-    useRnaView.setFont(LABEL_FONT);
-    useRnaView.setText(MessageManager.getString("label.use_rnaview"));
-    useRnaView.setBounds(new Rectangle(25, ypos, width, height));
-    structureTab.add(useRnaView);
-
-    ypos += lineSpacing;
     addSecondaryStructure.setFont(LABEL_FONT);
     addSecondaryStructure
             .setText(MessageManager.getString("label.autoadd_secstr"));