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;
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";
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));
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.
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());
+ }
}
});
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(
/*
* Set Backups tab defaults
*/
- enableBackupFiles
- .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
- suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX,
- ".v" + BackupFiles.NUM_PLACEHOLDER));
- 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();
}
/**
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());
/*
* 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();
{
useLegacyGap.setSelected(false);
useLegacyGaps_actionPerformed(null);
- showHiddenAtStart.setSelected(true);
+ showHiddenAtStart.setSelected(false);
hiddenColour.setBackground(
jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
}
}
/**
- * 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)
{