JAL-3262 from JAL-3253-applet Preferences final static String upgrade

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 04b83a3..66962d6 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -83,41 +83,137 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  */
 public class Preferences extends GPreferences
 {
-  public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+  
+  public static final String ADD_SS_ANN = "ADD_SS_ANN";
 
-  public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+  public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+
+  public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING";
+
+  public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX";
+
+  public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN";
+
+  public static final String ANTI_ALIAS = "ANTI_ALIAS";
+
+  public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS";
+
+  public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
+
+  public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
+
+  public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+  public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
 
   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
 
+  public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+
   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
 
-  public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+  public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
 
-  public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+  public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
 
-  public static final String ADD_SS_ANN = "ADD_SS_ANN";
+  public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
 
-  public static final String USE_RNAVIEW = "USE_RNAVIEW";
+  public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS";
 
-  public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+  public static final String FONT_NAME = "FONT_NAME";
 
-  public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+  public static final String FONT_SIZE = "FONT_SIZE";
 
-  public static final String CHIMERA_PATH = "CHIMERA_PATH";
+  public static final String FONT_STYLE = "FONT_STYLE";
 
-  public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+  public static final String GAP_COLOUR = "GAP_COLOUR";
+
+  public static final String GAP_SYMBOL = "GAP_SYMBOL";
+
+  public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
+  public static final String HIDE_INTRONS = "HIDE_INTRONS";
+
+  public static final String ID_ITALICS = "ID_ITALICS";
+
+  public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
+
+  public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
+
+  public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
+
+  public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
+
+  public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
+
+  public static final String PAD_GAPS = "PAD_GAPS";
+
+  public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT";
+
+  public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
+
+  public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING";
+
+  public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
+
+  public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
+  public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
 
   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 
+  public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
+
+  public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
+
+  public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
+
+  public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
+
+  public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP";
+
+  public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS";
+
+  public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
+
+  public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
+
+  public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
+
   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 
   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 
+  public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
+
+  public static final String SHOW_QUALITY = "SHOW_QUALITY";
+
+  public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED";
+
+  public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
+
+  public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+  public static final String SORT_BY_TREE = "SORT_BY_TREE";
+
+  public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+  public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+  public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
+
+  public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
+
+  public static final String USE_FULL_SO = "USE_FULL_SO";
+
   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 
-  public static final String GAP_COLOUR = "GAP_COLOUR";
+  public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+  public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+
+  public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
 
-  public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 
   private static final int MIN_FONT_SIZE = 1;