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Merge branch 'develop' into feature/JAL-2422ChimeraX
[jalview.git] / src / jalview / gui / Preferences.java
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 255c8fc..3070ca1 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -25,6 +25,7 @@ import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
 import jalview.io.FileFormatI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -104,6 +105,8 @@ public class Preferences extends GPreferences
 
   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 
+  public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
+
   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 
   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
@@ -252,7 +255,7 @@ public class Preferences extends GPreferences
     fontStyleCB.setSelectedItem(
             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 
-    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
     scaleProteinToCdna
             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 
@@ -326,7 +329,7 @@ public class Preferences extends GPreferences
     gapLabel.setEnabled(!useLegacyGap.isSelected());
     gapColour.setEnabled(!useLegacyGap.isSelected());
     showHiddenAtStart
-            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
+            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 
     /*
      * Set Structure tab defaults.
@@ -339,15 +342,30 @@ public class Preferences extends GPreferences
     addSecondaryStructure.setEnabled(structSelected);
     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
     addTempFactor.setEnabled(structSelected);
-    structViewer.setSelectedItem(
-            Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
-    chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
+    String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
+    structViewer.setSelectedItem(viewerType);
+    boolean isChimeraX = viewerType.equals(ViewerType.CHIMERAX.name());
+    if (viewerType.equals(ViewerType.JMOL.name()))
+    {
+      chimeraPath.setText("");
+    }
+    else
+    {
+      chimeraPath.setText(Cache
+              .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, ""));
+    }
     chimeraPath.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        validateChimeraPath();
+        if (validateChimeraPath())
+        {
+          Cache.setProperty(structViewer.getSelectedItem()
+                  .equals(ViewerType.CHIMERAX.name())
+                  ? CHIMERAX_PATH
+                  : CHIMERA_PATH, chimeraPath.getText());
+        }
       }
     });
 
@@ -400,7 +418,7 @@ public class Preferences extends GPreferences
     doReset.addActionListener(onReset);
 
     // filter to display only custom urls
-    final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
+    final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
     {
       @Override
       public boolean include(
@@ -552,31 +570,7 @@ public class Preferences extends GPreferences
     /*
      * Set Backups tab defaults
      */
-    enableBackupFiles
-            .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
-    suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX,
-            "-v" + BackupFiles.getNumPlaceHolder()));
-    suffixDigitsSpinner
-            .setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3));
-    suffixReverse.setSelected(
-            Cache.getDefault(BackupFiles.REVERSE_ORDER, false));
-    backupfilesKeepAll
-            .setSelected(Cache.getDefault(BackupFiles.NO_MAX, false));
-    backupfilesRollMaxSpinner
-            .setValue(Cache.getDefault(BackupFiles.ROLL_MAX, 4));
-    backupfilesConfirmDelete.setSelected(
-            Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true));
-    backupsOptionsSetEnabled(enableBackupFiles.isSelected());
-    updateBackupFilesExampleLabel();
-    /*
-    suffixPanel.setPreferredSize(
-            new Dimension(width, suffixPanel.getHeight()));
-    keepfilesPanel.setPreferredSize(
-            new Dimension(width, keepfilesPanel.getHeight()));
-    exampleFilesPanel.setPreferredSize(
-            new Dimension(width, exampleFilesPanel.getHeight()));
-            */
-
+    loadLastSavedBackupsOptions();
   }
 
   /**
@@ -705,7 +699,10 @@ public class Preferences extends GPreferences
             Boolean.toString(structFromPdb.isSelected()));
     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
             structViewer.getSelectedItem().toString());
-    Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+    boolean isChimeraX = structViewer.getSelectedItem().toString()
+            .equals(ViewerType.CHIMERAX.name());
+    Cache.setOrRemove(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH,
+            chimeraPath.getText());
     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
             Boolean.toString(siftsMapping.isSelected()));
     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
@@ -829,20 +826,25 @@ public class Preferences extends GPreferences
     /*
      * Save Backups settings
      */
-    Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
-            Boolean.toString(backupfilesConfirmDelete.isSelected()));
     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
             Boolean.toString(enableBackupFiles.isSelected()));
-    Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
-            Boolean.toString(backupfilesKeepAll.isSelected()));
-    Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
-            Boolean.toString(suffixReverse.isSelected()));
-    Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
-            suffixTemplate.getText());
-    Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
-            Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
-    Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
-            Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
+    int preset = getComboIntStringKey(backupfilesPresetsCombo);
+    Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+
+    if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+    {
+      BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
+      BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+              BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
+      Cache.applicationProperties
+              .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
+                      customBFPE.toString());
+    }
+
+    BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+            .get(preset);
+    Cache.applicationProperties.setProperty(
+            BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
 
     Cache.saveProperties();
     Desktop.instance.doConfigureStructurePrefs();
@@ -1166,7 +1168,7 @@ public class Preferences extends GPreferences
   {
     useLegacyGap.setSelected(false);
     useLegacyGaps_actionPerformed(null);
-    showHiddenAtStart.setSelected(true);
+    showHiddenAtStart.setSelected(false);
     hiddenColour.setBackground(
             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
   }
@@ -1226,22 +1228,32 @@ public class Preferences extends GPreferences
   }
 
   /**
-   * If Chimera is selected, check it can be found on default or user-specified
-   * path, if not show a warning/help dialog.
+   * If Chimera or ChimeraX is selected, check it can be found on default or
+   * user-specified path, if not show a warning/help dialog.
    */
   @Override
   protected void structureViewer_actionPerformed(String selectedItem)
   {
-    if (!selectedItem.equals(ViewerType.CHIMERA.name()))
+    if (selectedItem.equals(ViewerType.JMOL.name()))
     {
+      chimeraPath.setEnabled(false);
+      chimeraPathLabel.setEnabled(false);
       return;
     }
     boolean found = false;
+    chimeraPath.setEnabled(true);
+    chimeraPathLabel.setEnabled(true);
+    chimeraPathLabel.setText(MessageManager
+            .formatMessage("label.chimera_path", selectedItem));
 
     /*
-     * Try user-specified and standard paths for Chimera executable.
+     * Try user-specified and standard paths for Chimera executable
      */
-    List<String> paths = StructureManager.getChimeraPaths();
+    boolean isChimeraX = selectedItem.equals(ViewerType.CHIMERAX.name());
+    chimeraPath.setText(Cache
+            .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, ""));
+
+    List<String> paths = StructureManager.getChimeraPaths(isChimeraX);
     paths.add(0, chimeraPath.getText());
     for (String path : paths)
     {