import jalview.bin.Cache;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFiles;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.util.List;
import javax.help.HelpSetException;
-import javax.swing.JButton;
import javax.swing.JColorChooser;
import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
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 USE_LEGACY_GAP = "USE_LEGACY_GAP";
+
+ public static final String GAP_COLOUR = "GAP_COLOUR";
+
+ public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
private static final int MIN_FONT_SIZE = 1;
private static final int MAX_FONT_SIZE = 30;
JInternalFrame frame;
- DasSourceBrowser dasSource;
-
private WsPreferences wsPrefs;
private OptionsParam promptEachTimeOpt = new OptionsParam(
super();
frame = new JInternalFrame();
frame.setContentPane(this);
- dasSource = new DasSourceBrowser();
- dasTab.add(dasSource, BorderLayout.CENTER);
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
int width = 500, height = 450;
Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
maxColour.setBackground(
Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+
+ /*
+ * Set overview panel defaults
+ */
gapColour.setBackground(
- Cache.getDefaultColour("GAP_COLOUR", Color.lightGray));
+ Cache.getDefaultColour(GAP_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
hiddenColour.setBackground(
- Cache.getDefaultColour("HIDDEN_COLOUR", Color.darkGray));
+ Cache.getDefaultColour(HIDDEN_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+ useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
+ gapLabel.setEnabled(!useLegacyGap.isSelected());
+ gapColour.setEnabled(!useLegacyGap.isSelected());
+ showHiddenAtStart
+ .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
/*
* Set Structure tab defaults.
autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
userIdWidth.setEnabled(!autoIdWidth.isSelected());
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
- Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+ 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
blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
annotations_actionPerformed(null); // update the display of the annotation
// settings
+
+
+ /*
+ * Set Backups tab defaults
+ */
+ loadLastSavedBackupsOptions();
}
/**
maxColour.getBackground());
/*
+ * Save Overview settings
+ */
+ Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
+ Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
+ Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+ Boolean.toString(useLegacyGap.isSelected()));
+ Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+ Boolean.toString(showHiddenAtStart.isSelected()));
+
+ /*
* Save Structure settings
*/
Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
- Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+ Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
userIdWidth.getText());
/*
Cache.applicationProperties.setProperty("PAD_GAPS",
Boolean.toString(padGaps.isSelected()));
- dasSource.saveProperties(Cache.applicationProperties);
wsPrefs.updateAndRefreshWsMenuConfig(false);
+
+ /*
+ * 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)));
+ Cache.applicationProperties.setProperty(BackupFiles.NS+"_PRESET",
+ Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
+
Cache.saveProperties();
Desktop.instance.doConfigureStructurePrefs();
try
}
@Override
- public void gapColour_actionPerformed(JButton btn)
+ public void gapColour_actionPerformed(JPanel gap)
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_gap_colour"),
- gapColour.getForeground());
- if (col != null)
+ if (!useLegacyGap.isSelected())
{
- btn.setForeground(col);
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_gap_colour"),
+ gapColour.getBackground());
+ if (col != null)
+ {
+ gap.setBackground(col);
+ }
+ gap.repaint();
}
- btn.repaint();
}
@Override
- public void hiddenColour_actionPerformed(JButton btn)
+ public void hiddenColour_actionPerformed(JPanel hidden)
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_hidden_colour"),
- hiddenColour.getForeground());
+ hiddenColour.getBackground());
if (col != null)
{
- btn.setForeground(col);
+ hidden.setBackground(col);
+ }
+ hidden.repaint();
+ }
+
+ @Override
+ protected void useLegacyGaps_actionPerformed(ActionEvent e)
+ {
+ boolean enabled = useLegacyGap.isSelected();
+ if (enabled)
+ {
+ gapColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
}
- btn.repaint();
+ else
+ {
+ gapColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+ }
+ gapColour.setEnabled(!enabled);
+ gapLabel.setEnabled(!enabled);
+ }
+
+ @Override
+ protected void resetOvDefaults_actionPerformed(ActionEvent e)
+ {
+ useLegacyGap.setSelected(false);
+ useLegacyGaps_actionPerformed(null);
+ showHiddenAtStart.setSelected(true);
+ hiddenColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
}
@Override