From 77591230ecd28c2425e94e6298cc2961eed332d2 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 3 Nov 2021 11:33:14 +0000 Subject: [PATCH] JAL-3915 remove RNAview opts from preferences. Still present in config file ready for when we have a new RNA structure processing service --- src/jalview/gui/Desktop.java | 3 ++- src/jalview/gui/Preferences.java | 10 +++------- src/jalview/jbgui/GPreferences.java | 9 --------- 3 files changed, 5 insertions(+), 17 deletions(-) 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")); -- 1.7.10.2