Jalview-JS/JAL-3253-applet additional static final preferences

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 2d33478..4dac4df 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -510,7 +510,7 @@ public class Cache implements ApplicationSingletonI
             getDefault("sifts_cache_threshold_in_days",
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
-    IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
+    IdOrgSettings.setUrl(getDefault(Preferences.ID_ORG_HOSTURL,
             "http://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
@@ -518,7 +518,7 @@ public class Cache implements ApplicationSingletonI
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
-            .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+            .getDefault(Preferences.PDB_DOWNLOAD_FORMAT, PDB_DOWNLOAD_FORMAT));
     StructureImportSettings
             .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
     // StructureImportSettings

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 07fd4d6..b39f0e2 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -439,7 +439,7 @@ public class Jalview implements ApplicationSingletonI
      * configure 'full' SO model if preferences say to, 
      * else use the default (SO Lite)
      */
-    if (Cache.getDefault("USE_FULL_SO", false))
+    if (Cache.getDefault(Preferences.USE_FULL_SO, false))
     {
       SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
     }

diff --git a/src/jalview/fts/core/FTSRestRequest.java b/src/jalview/fts/core/FTSRestRequest.java
index 2d9eeb6..b09fcc0 100644 (file)
--- a/src/jalview/fts/core/FTSRestRequest.java
+++ b/src/jalview/fts/core/FTSRestRequest.java
@@ -46,7 +46,7 @@ public class FTSRestRequest
   private boolean allowEmptySequence;
 
   private boolean allowUnpublishedEntries = Cache
-          .getDefault("ALLOW_UNPUBLISHED_PDB_QUERYING", false);
+          .getDefault(Preferences.ALLOW_UNPUBLISHED_PDB_QUERYING, false);
 
   private boolean facet;
 

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 9570dd3..d56bcbf 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -59,7 +59,7 @@ public class UniProtFTSRestClient extends FTSRestClient
   {
     // singleton -- use getInstance()
 
-    uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
+    uniprotSearchEndpoint = Cache.getDefault(Preferences.UNIPROT_DOMAIN,
             DEFAULT_UNIPROT_DOMAIN) + "/uniprot/";    
   }
 

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bc08c4f..b56f269 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -407,7 +407,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       wrapMenuItem_actionPerformed(null);
     }
 
-    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+    if (jalview.bin.Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
     {
       this.overviewMenuItem_actionPerformed(null);
     }
@@ -4461,7 +4461,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     // BH 2018
     return avc.parseFeaturesFile(file, sourceType,
-            Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+            Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false));
 
   }
 
@@ -4604,7 +4604,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             if (filesmatched.size() > 0)
             {
               boolean autoAssociate = Cache
-                      .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+                      .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false);
               if (!autoAssociate)
               {
                 String msg = MessageManager.formatMessage(

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 4edb580..7c3dca0 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -206,25 +206,26 @@ public class AlignViewport extends AlignmentViewport
    */
   private void applyViewProperties()
   {
-    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+    antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, false);
 
-    viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
+    viewStyle.setShowJVSuffix(
+            Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
     setShowAnnotation(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
 
-    setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
-    setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
-    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+    setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false));
+    setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false));
+    autoCalculateConsensus = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
 
-    setPadGaps(Cache.getDefault("PAD_GAPS", true));
-    setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
-    setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
-    viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
+    setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true));
+    setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true));
+    setShowDBRefs(Cache.getDefault(Preferences.SHOW_DBREFS_TOOLTIP, true));
+    viewStyle.setSeqNameItalics(Cache.getDefault(Preferences.ID_ITALICS, true));
     viewStyle.setWrapAlignment(
             Cache.getDefault(Preferences.WRAP_ALIGNMENT, false));
     viewStyle.setShowUnconserved(
             Cache.getDefault(Preferences.SHOW_UNCONSERVED, false));
     sortByTree = Cache.getDefault(Preferences.SORT_BY_TREE, false);
-    followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+    followSelection = Cache.getDefault(Preferences.FOLLOW_SELECTIONS, true);
     sortAnnotationsBy = SequenceAnnotationOrder
             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
                     SequenceAnnotationOrder.NONE.name()));
@@ -238,9 +239,10 @@ public class AlignViewport extends AlignmentViewport
   {
     applyViewProperties();
 
-    String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
-    String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
-    String fontSize = Cache.getDefault("FONT_SIZE", "10");
+    String fontName = Cache.getDefault(Preferences.FONT_NAME, "SansSerif");
+    String fontStyle = Cache.getDefault(Preferences.FONT_STYLE,
+            Font.PLAIN + "");
+    String fontSize = Cache.getDefault(Preferences.FONT_SIZE, "10");
 
     int style = 0;
 
@@ -256,7 +258,8 @@ public class AlignViewport extends AlignmentViewport
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
     alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+            .setGapCharacter(Cache.getDefault(Preferences.GAP_SYMBOL, "-")
+                    .charAt(0));
 
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
@@ -264,21 +267,22 @@ public class AlignViewport extends AlignmentViewport
     {
       if (!alignment.isNucleotide())
       {
-        showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION, true);
+        showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION,
+                true);
         showQuality = Cache.getDefault(Preferences.SHOW_QUALITY, true);
-        showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
-                false);
+        showGroupConservation = Cache
+                .getDefault(Preferences.SHOW_GROUP_CONSERVATION, false);
       }
-      showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
-              true);
-      showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO, false);
-
-      normaliseSequenceLogo = Cache.getDefault(
-              Preferences.NORMALISE_CONSENSUS_LOGO,
+      showConsensusHistogram = Cache
+              .getDefault(Preferences.SHOW_CONSENSUS_HISTOGRAM, true);
+      showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO,
               false);
+
+      normaliseSequenceLogo = Cache
+              .getDefault(Preferences.NORMALISE_CONSENSUS_LOGO, false);
       showGroupConsensus = Cache
               .getDefault(Preferences.SHOW_GROUP_CONSENSUS, false);
-      showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+      showConsensus = Cache.getDefault(Preferences.SHOW_IDENTITY, true);
 
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
@@ -293,8 +297,8 @@ public class AlignViewport extends AlignmentViewport
       schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
               ResidueColourScheme.NONE);
     }
-    ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(this, alignment, schemeName);
+    ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
+            alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -769,20 +773,20 @@ public class AlignViewport extends AlignmentViewport
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
-    
 
     /*
      * options No, Split Window, New Window correspond to
      * dialog responses 0, 1, 2 (even though JOptionPane shows them
      * in reverse order)
      */
-    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane())
+    JvOptionPane dialog = JvOptionPane
+            .newOptionDialog(Desktop.getDesktopPane())
             .setResponseHandler(NO_SPLIT, new Runnable()
             {
               @Override
               public void run()
               {
-                  addDataToAlignment(al);
+                addDataToAlignment(al);
               }
             }).setResponseHandler(SPLIT_FRAME, new Runnable()
             {
@@ -790,8 +794,8 @@ public class AlignViewport extends AlignmentViewport
               public void run()
               {
                 openLinkedAlignmentAs(getAlignPanel().alignFrame,
-                        new Alignment(getAlignment()), al,
-                        title, SPLIT_FRAME);
+                        new Alignment(getAlignment()), al, title,
+                        SPLIT_FRAME);
               }
             }).setResponseHandler(NEW_WINDOW, new Runnable()
             {
@@ -816,9 +820,8 @@ public class AlignViewport extends AlignmentViewport
    * @param mode
    *          SPLIT_FRAME or NEW_WINDOW
    */
-  public static void openLinkedAlignmentAs(AlignFrame thisFrame, AlignmentI thisAlignment,
-          AlignmentI al, String title,
-          int mode)
+  public static void openLinkedAlignmentAs(AlignFrame thisFrame,
+          AlignmentI thisAlignment, AlignmentI al, String title, int mode)
   {
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
@@ -862,8 +865,8 @@ public class AlignViewport extends AlignmentViewport
 
     try
     {
-      newAlignFrame.setMaximum(
-              jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+      newAlignFrame.setMaximum(jalview.bin.Cache
+              .getDefault(Preferences.SHOW_FULLSCREEN, false));
     } catch (java.beans.PropertyVetoException ex)
     {
     }
@@ -886,8 +889,7 @@ public class AlignViewport extends AlignmentViewport
    * @return the protein alignment in the split frame
    */
   static protected AlignmentI openSplitFrame(AlignFrame thisFrame,
-          AlignFrame newAlignFrame,
-          AlignmentI complement)
+          AlignFrame newAlignFrame, AlignmentI complement)
   {
     /*
      * Make a new frame with a copy of the alignment we are adding to. If this

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 20d06e9..0040dd7 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1148,13 +1148,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public int getVisibleIdWidth(boolean onscreen)
   {
     // see if rendering offscreen - check preferences and calc width accordingly
-    if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
+    if (!onscreen && Cache.getDefault(Preferences.FIGURE_AUTOIDWIDTH, false))
     {
       return calculateIdWidth(-1).width + 4;
     }
     Integer idwidth = null;
     if (onscreen || (idwidth = Cache
-            .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+            .getIntegerProperty(Preferences.FIGURE_FIXEDIDWIDTH)) == null)
     {
       int w = getIdPanel().getWidth();
       return (w > 0 ? w : calculateIdWidth().width + 4);

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 093eb48..45bf2d7 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -500,7 +500,8 @@ public class CalculationChooser extends JPanel
      * for backwards compatibility with Jalview < 2.8 (JAL-2962)
      */
     if (nucleotide && forPca
-            && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false))
+            && Cache.getDefault(Preferences.BLOSUM62_PCA_FOR_NUCLEOTIDE,
+                    false))
     {
       filtered.add(scoreModels.getBlosum62());
     }

diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java
index 2d20ad9..2ee741b 100644 (file)
--- a/src/jalview/gui/CrossRefAction.java
+++ b/src/jalview/gui/CrossRefAction.java
@@ -141,7 +141,7 @@ public class CrossRefAction implements Runnable
        */
       AlignFrame newFrame = new AlignFrame(xrefsAlignment,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-      if (Cache.getDefault("HIDE_INTRONS", true))
+      if (Cache.getDefault(Preferences.HIDE_INTRONS, true))
       {
         newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
       }

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 4badcba..3514b75 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -330,7 +330,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         try
         {
           af.setMaximum(
-                  jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+                  jalview.bin.Cache.getDefault(Preferences.SHOW_FULLSCREEN,
+                          false));
         } catch (Exception ex)
         {
         }

diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index 92cc4c6..ad41293 100755 (executable)
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -408,10 +408,10 @@ public class FontChooser extends GFontChooser
   @Override
   public void defaultButton_actionPerformed()
   {
-    Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());
-    Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex() + "");
-    Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());
-    Cache.setProperty("ANTI_ALIAS",
+    Cache.setProperty(Preferences.FONT_NAME, fontName.getSelectedItem().toString());
+    Cache.setProperty(Preferences.FONT_STYLE, fontStyle.getSelectedIndex() + "");
+    Cache.setProperty(Preferences.FONT_SIZE, fontSize.getSelectedItem().toString());
+    Cache.setProperty(Preferences.ANTI_ALIAS,
             Boolean.toString(smoothFont.isSelected()));
     Cache.setProperty(Preferences.SCALE_PROTEIN_TO_CDNA,
             Boolean.toString(scaleAsCdna.isSelected()));

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index e80b28b..dbb5aec 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -85,81 +85,194 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
 public class Preferences extends GPreferences
 {
 
-  public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
 
-  public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
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+  public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+  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 ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+  public static final String ANTI_ALIAS = "ANTI_ALIAS";
 
-  public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+  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_ALIGNMENT = "SORT_ALIGNMENT";
+  public static final String GAP_COLOUR = "GAP_COLOUR";
 
-  public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
+  public static final String GAP_SYMBOL = "GAP_SYMBOL";
 
-  public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+  public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 
-  public static final String SORT_BY_TREE = "SORT_BY_TREE";
+  public static final String HIDE_INTRONS = "HIDE_INTRONS";
 
-  public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
+  public static final String ID_ITALICS = "ID_ITALICS";
 
-  public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+  public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
 
-  public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
+  public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
 
-  public static final String SHOW_QUALITY = "SHOW_QUALITY";
+  public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
 
-  public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
+  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 NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
+  public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
 
-  public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
+  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 SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+  public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
 
-  public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+  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 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;
 
@@ -183,6 +296,12 @@ public class Preferences extends GPreferences
 
   public static final List<String> groupURLLinks; // not implemented
 
+  public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
+
+  public static final String SHOW_IDENTITY = "SHOW_IDENTITY";
+
+  public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
+
 
   static
   {
@@ -258,14 +377,14 @@ public class Preferences extends GPreferences
     /*
      * Set Visual tab defaults
      */
-    seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
-    rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
-    fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
-    annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
+    seqLimit.setSelected(Cache.getDefault(SHOW_JVSUFFIX, true));
+    rightAlign.setSelected(Cache.getDefault(RIGHT_ALIGN_IDS, false));
+    fullScreen.setSelected(Cache.getDefault(SHOW_FULLSCREEN, false));
+    annotations.setSelected(Cache.getDefault(SHOW_ANNOTATIONS, true));
 
     conservation.setSelected(Cache.getDefault(SHOW_CONSERVATION, true));
     quality.setSelected(Cache.getDefault(SHOW_QUALITY, true));
-    identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
+    identity.setSelected(Cache.getDefault(SHOW_IDENTITY, true));
     openoverv.setSelected(Cache.getDefault(SHOW_OVERVIEW, false));
     showUnconserved
             .setSelected(Cache.getDefault(SHOW_UNCONSERVED, false));
@@ -279,9 +398,9 @@ public class Preferences extends GPreferences
     showConsensLogo
             .setSelected(Cache.getDefault(SHOW_CONSENSUS_LOGO, false));
     showNpTooltip
-            .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+            .setSelected(Cache.getDefault(SHOW_NPFEATS_TOOLTIP, true));
     showDbRefTooltip
-            .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+            .setSelected(Cache.getDefault(SHOW_DBREFS_TOOLTIP, true));
 
     String[] fonts = java.awt.GraphicsEnvironment
             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
@@ -299,23 +418,23 @@ public class Preferences extends GPreferences
     fontStyleCB.addItem("bold");
     fontStyleCB.addItem("italic");
 
-    fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
-    fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
+    fontNameCB.setSelectedItem(Cache.getDefault(FONT_NAME, "SansSerif"));
+    fontSizeCB.setSelectedItem(Cache.getDefault(FONT_SIZE, "10"));
     fontStyleCB.setSelectedItem(
-            Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
+            Cache.getDefault(FONT_STYLE, Font.PLAIN + ""));
 
-    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+    smoothFont.setSelected(Cache.getDefault(ANTI_ALIAS, false));
     scaleProteinToCdna
             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 
-    idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
+    idItalics.setSelected(Cache.getDefault(ID_ITALICS, true));
 
-    wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+    wrap.setSelected(Cache.getDefault(WRAP_ALIGNMENT, false));
 
     gapSymbolCB.addItem("-");
     gapSymbolCB.addItem(".");
 
-    gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
+    gapSymbolCB.setSelectedItem(Cache.getDefault(GAP_SYMBOL, "-"));
 
     sortby.addItem("No sort");
     sortby.addItem("Id");
@@ -403,7 +522,7 @@ public class Preferences extends GPreferences
       }
     });
 
-    if (Cache.getDefault("MAP_WITH_SIFTS", false))
+    if (Cache.getDefault(MAP_WITH_SIFTS, false))
     {
       siftsMapping.setSelected(true);
     }
@@ -413,7 +532,7 @@ public class Preferences extends GPreferences
     }
 
     SiftsSettings
-            .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+            .setMapWithSifts(Cache.getDefault(MAP_WITH_SIFTS, false));
 
     /*
      * Set Connections tab defaults
@@ -558,10 +677,10 @@ public class Preferences extends GPreferences
     setupOutputCombo(epsRendering, "EPS_RENDERING");
     setupOutputCombo(htmlRendering, "HTML_RENDERING");
     setupOutputCombo(svgRendering, "SVG_RENDERING");
-    autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+    autoIdWidth.setSelected(Cache.getDefault(FIGURE_AUTOIDWIDTH, false));
     userIdWidth.setEnabled(!autoIdWidth.isSelected());
     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
-    Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
+    Integer wi = Cache.getIntegerProperty(FIGURE_FIXEDIDWIDTH);
     userIdWidth.setText(wi == null ? "" : wi.toString());
     // TODO: refactor to use common enum via FormatAdapter and allow extension
     // for new flat file formats
@@ -580,8 +699,8 @@ public class Preferences extends GPreferences
      * Set Editing tab defaults
      */
     autoCalculateConsCheck
-            .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
-    padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+            .setSelected(Cache.getDefault(AUTO_CALC_CONSENSUS, true));
+    padGaps.setSelected(Cache.getDefault(PAD_GAPS, false));
     sortByTree.setSelected(Cache.getDefault(SORT_BY_TREE, false));
 
     annotations_actionPerformed(null); // update the display of the annotation
@@ -644,36 +763,36 @@ public class Preferences extends GPreferences
     /*
      * Save Visual settings
      */
-    Cache.setPropertyNoSave("SHOW_JVSUFFIX",
+    Cache.setPropertyNoSave(SHOW_JVSUFFIX,
             Boolean.toString(seqLimit.isSelected()));
-    Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
+    Cache.setPropertyNoSave(RIGHT_ALIGN_IDS,
             Boolean.toString(rightAlign.isSelected()));
-    Cache.setPropertyNoSave("SHOW_FULLSCREEN",
+    Cache.setPropertyNoSave(SHOW_FULLSCREEN,
             Boolean.toString(fullScreen.isSelected()));
-    Cache.setPropertyNoSave("SHOW_OVERVIEW",
+    Cache.setPropertyNoSave(SHOW_OVERVIEW,
             Boolean.toString(openoverv.isSelected()));
-    Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
+    Cache.setPropertyNoSave(SHOW_ANNOTATIONS,
             Boolean.toString(annotations.isSelected()));
     Cache.setPropertyNoSave(SHOW_CONSERVATION,
             Boolean.toString(conservation.isSelected()));
     Cache.setPropertyNoSave(SHOW_QUALITY,
             Boolean.toString(quality.isSelected()));
-    Cache.setPropertyNoSave("SHOW_IDENTITY",
+    Cache.setPropertyNoSave(SHOW_IDENTITY,
             Boolean.toString(identity.isSelected()));
 
-    Cache.setPropertyNoSave("GAP_SYMBOL",
+    Cache.setPropertyNoSave(GAP_SYMBOL,
             gapSymbolCB.getSelectedItem().toString());
 
-    Cache.setPropertyNoSave("FONT_NAME",
+    Cache.setPropertyNoSave(FONT_NAME,
             fontNameCB.getSelectedItem().toString());
-    Cache.setPropertyNoSave("FONT_STYLE",
+    Cache.setPropertyNoSave(FONT_STYLE,
             fontStyleCB.getSelectedItem().toString());
-    Cache.setPropertyNoSave("FONT_SIZE",
+    Cache.setPropertyNoSave(FONT_SIZE,
             fontSizeCB.getSelectedItem().toString());
 
-    Cache.setPropertyNoSave("ID_ITALICS",
+    Cache.setPropertyNoSave(ID_ITALICS,
             Boolean.toString(idItalics.isSelected()));
-    Cache.setPropertyNoSave("SHOW_UNCONSERVED",
+    Cache.setPropertyNoSave(SHOW_UNCONSERVED,
             Boolean.toString(showUnconserved.isSelected()));
     Cache.setPropertyNoSave(SHOW_OCCUPANCY,
             Boolean.toString(showOccupancy.isSelected()));
@@ -685,16 +804,16 @@ public class Preferences extends GPreferences
             Boolean.toString(showConsensHistogram.isSelected()));
     Cache.setPropertyNoSave(SHOW_CONSENSUS_LOGO,
             Boolean.toString(showConsensLogo.isSelected()));
-    Cache.setPropertyNoSave("ANTI_ALIAS",
+    Cache.setPropertyNoSave(ANTI_ALIAS,
             Boolean.toString(smoothFont.isSelected()));
     Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
             Boolean.toString(scaleProteinToCdna.isSelected()));
-    Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
+    Cache.setPropertyNoSave(SHOW_NPFEATS_TOOLTIP,
             Boolean.toString(showNpTooltip.isSelected()));
-    Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
+    Cache.setPropertyNoSave(SHOW_DBREFS_TOOLTIP,
             Boolean.toString(showDbRefTooltip.isSelected()));
 
-    Cache.setPropertyNoSave("WRAP_ALIGNMENT",
+    Cache.setPropertyNoSave(WRAP_ALIGNMENT,
             Boolean.toString(wrap.isSelected()));
 
     Cache.setPropertyNoSave("STARTUP_FILE",
@@ -754,7 +873,7 @@ public class Preferences extends GPreferences
     Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
             structViewer.getSelectedItem().toString());
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
-    Cache.setPropertyNoSave("MAP_WITH_SIFTS",
+    Cache.setPropertyNoSave(MAP_WITH_SIFTS,
             Boolean.toString(siftsMapping.isSelected()));
     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 
@@ -862,7 +981,7 @@ public class Preferences extends GPreferences
             Boolean.toString(modellerOutput.isSelected()));
     Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
             Boolean.toString(embbedBioJSON.isSelected()));
-    Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
+    Cache.setPropertyNoSave(FIGURE_AUTOIDWIDTH,
             Boolean.toString(autoIdWidth.isSelected()));
     userIdWidth_actionPerformed();
     Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
@@ -871,11 +990,11 @@ public class Preferences extends GPreferences
     /*
      * Save Editing settings
      */
-    Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
+    Cache.setPropertyNoSave(AUTO_CALC_CONSENSUS,
             Boolean.toString(autoCalculateConsCheck.isSelected()));
-    Cache.setPropertyNoSave("SORT_BY_TREE",
+    Cache.setPropertyNoSave(SORT_BY_TREE,
             Boolean.toString(sortByTree.isSelected()));
-    Cache.setPropertyNoSave("PAD_GAPS",
+    Cache.setPropertyNoSave(PAD_GAPS,
             Boolean.toString(padGaps.isSelected()));
 
     if (!Platform.isJS())
@@ -943,9 +1062,9 @@ public class Preferences extends GPreferences
     Cache.setPropertyNoSave(SHOW_CONSERVATION, "true");
     Cache.setPropertyNoSave(SHOW_QUALITY, "false");
     Cache.setPropertyNoSave(SHOW_CONSENSUS, "true");
-    Cache.setPropertyNoSave("SHOW_UNCONSERVED", "false");
-    Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION", "false");
-    Cache.setPropertyNoSave("SHOW_GROUP_CONCENSUS", "false");
+    Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false");
+    Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false");
+    Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false");
 
     // TODO -- just a start here
   }

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 518654e..b8e3b33 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -815,7 +815,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         {
           af.getViewport().applyFeaturesStyle(preferredFeatureColours);
         }
-        if (Cache.getDefault("HIDE_INTRONS", true))
+        if (Cache.getDefault(Preferences.HIDE_INTRONS, true))
         {
           af.hideFeatureColumns(SequenceOntologyI.EXON, false);
         }
@@ -827,7 +827,8 @@ public class SequenceFetcher extends JPanel implements Runnable
 
         try
         {
-          af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
+          af.setMaximum(
+                  Cache.getDefault(Preferences.SHOW_FULLSCREEN, false));
         } catch (Exception ex)
         {
         }

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 85cf48a..b0414af 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -30,6 +30,7 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Preferences;
 import jalview.util.Comparison;
 
 import java.io.File;
@@ -63,13 +64,16 @@ public class FormatAdapter extends AppletFormatAdapter
 
   private void init()
   {
-    if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+    if (jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true))
     {
-      annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+      annotFromStructure = jalview.bin.Cache.getDefault(
+              Preferences.ADD_TEMPFACT_ANN,
               true);
-      localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+      localSecondaryStruct = jalview.bin.Cache.getDefault(
+              Preferences.ADD_SS_ANN,
               true);
-      serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+      serviceSecondaryStruct = jalview.bin.Cache
+              .getDefault(Preferences.USE_RNAVIEW,
               true);
     }
     else

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index dbe46f6..1263adb 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -556,7 +556,7 @@ public class GAlignFrame extends JInternalFrame
     annotationPanelMenuItem
             .setText(MessageManager.getString("label.show_annotations"));
     annotationPanelMenuItem
-            .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
+            .setState(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
     annotationPanelMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1065,7 +1065,7 @@ public class GAlignFrame extends JInternalFrame
     });
     seqLimits.setText(
             MessageManager.getString("label.show_sequence_limits"));
-    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+    seqLimits.setState(jalview.bin.Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
     seqLimits.addActionListener(new ActionListener()
     {
       @Override
@@ -1216,7 +1216,7 @@ public class GAlignFrame extends JInternalFrame
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
     padGapsMenuitem
-            .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+            .setState(jalview.bin.Cache.getDefault(Preferences.PAD_GAPS, false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       @Override
@@ -1359,7 +1359,7 @@ public class GAlignFrame extends JInternalFrame
     autoCalculate.setText(
             MessageManager.getString("label.autocalculate_consensus"));
     autoCalculate.setState(
-            jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+            jalview.bin.Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true));
     autoCalculate.addActionListener(new ActionListener()
     {
       @Override
@@ -1373,7 +1373,8 @@ public class GAlignFrame extends JInternalFrame
     sortByTree.setToolTipText("<html>" + MessageManager.getString(
             "label.enable_automatically_sort_alignment_when_open_new_tree"));
     sortByTree
-            .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+            .setState(jalview.bin.Cache.getDefault(Preferences.SORT_BY_TREE,
+                    false));
     sortByTree.addActionListener(new ActionListener()
     {
       @Override

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 6c21941..7745b74 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -32,6 +32,7 @@ import jalview.gui.Desktop;
 import jalview.gui.FeatureSettings;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.OOMWarning;
+import jalview.gui.Preferences;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.ws.seqfetcher.DbSourceProxy;
@@ -302,7 +303,7 @@ public class DBRefFetcher implements Runnable
     }
     try
     {
-      if (Cache.getDefault("DBREFFETCH_USEPICR", false))
+      if (Cache.getDefault(Preferences.DBREFFETCH_USEPICR, false))
       {
         picrClient = new AccessionMapperServiceLocator()
                 .getAccessionMapperPort();

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 6f5f033..a3d6dbf 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -81,7 +81,7 @@ public class Uniprot extends DbSourceProxyImpl
 
   private String getDomain()
   {
-    return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
+    return Cache.getDefault(Preferences.UNIPROT_DOMAIN, DEFAULT_UNIPROT_DOMAIN);
   }
 
   /*