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;
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;
* .properties file as '|' separated strings
*/
- groupURLLinks = new ArrayList<String>();
+ groupURLLinks = new ArrayList<>();
}
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;
showUnconserved
.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
- showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
- false));
- showGroupConservation.setSelected(Cache.getDefault(
- "SHOW_GROUP_CONSERVATION", false));
- showConsensHistogram.setSelected(Cache.getDefault(
- "SHOW_CONSENSUS_HISTOGRAM", true));
- showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
- false));
- showNpTooltip.setSelected(Cache
- .getDefault("SHOW_NPFEATS_TOOLTIP", true));
- showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
- true));
+ showGroupConsensus
+ .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
+ showGroupConservation.setSelected(
+ Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+ showConsensHistogram.setSelected(
+ Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
+ showConsensLogo
+ .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ showNpTooltip
+ .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ showDbRefTooltip
+ .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
- fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
- + ""));
+ fontStyleCB.setSelectedItem(
+ Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
- scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
- false));
+ scaleProteinToCdna
+ .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
protColour.setSelectedItem(newProp != null ? newProp : oldProp);
newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
+ minColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+
+ /*
+ * Set overview panel defaults
+ */
+ gapColour.setBackground(
+ Cache.getDefaultColour(GAP_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+ hiddenColour.setBackground(
+ 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.
addSecondaryStructure.setEnabled(structSelected);
addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
addTempFactor.setEnabled(structSelected);
- structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
- ViewerType.JMOL.name()));
+ structViewer.setSelectedItem(
+ Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
chimeraPath.addActionListener(new ActionListener()
{
SortOrder.DESCENDING));
sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
SortOrder.DESCENDING));
- sortKeys.add(new RowSorter.SortKey(m.getNameColumn(),
- SortOrder.ASCENDING));
+ sortKeys.add(
+ new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
sorter.setSortKeys(sortKeys);
sorter.sort();
-
+
// set up filtering
ActionListener onReset;
onReset = new ActionListener()
@Override
public void changedUpdate(DocumentEvent e)
{
- sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
- + filterTB.getText()));
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
}
@Override
public void removeUpdate(DocumentEvent e)
{
- sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
- + filterTB.getText()));
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
}
@Override
public void insertUpdate(DocumentEvent e)
{
- sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
- + filterTB.getText()));
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
}
});
// set up list selection functionality
- linkUrlTable.getSelectionModel().addListSelectionListener(
- new UrlListSelectionHandler());
+ linkUrlTable.getSelectionModel()
+ .addListSelectionListener(new UrlListSelectionHandler());
// set up radio buttons
int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
.getPrimaryColumn();
String onClickName = linkUrlTable.getColumnName(onClickCol);
- linkUrlTable.getColumn(onClickName).setCellRenderer(
- new RadioButtonRenderer());
+ linkUrlTable.getColumn(onClickName)
+ .setCellRenderer(new RadioButtonRenderer());
linkUrlTable.getColumn(onClickName)
.setCellEditor(new RadioButtonEditor());
if (linkUrlTable.getModel().getColumnClass(column)
.equals(Boolean.class))
{
- TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
- column);
+ TableColumn tableColumn = linkUrlTable.getColumnModel()
+ .getColumn(column);
int preferredWidth = tableColumn.getMinWidth();
TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
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));
pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
- embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
- true));
+ embbedBioJSON
+ .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
/*
* Set Editing tab defaults
*/
- autoCalculateConsCheck.setSelected(Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
+ autoCalculateConsCheck
+ .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
// settings
+
+
+ /*
+ * 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()));
+ */
+
}
/**
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.toString(identity.isSelected()));
- Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("GAP_SYMBOL",
+ gapSymbolCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
- .getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
- .getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_NAME",
+ fontNameCB.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_STYLE",
+ fontStyleCB.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_SIZE",
+ fontSizeCB.getSelectedItem().toString());
Cache.applicationProperties.setProperty("ID_ITALICS",
Boolean.toString(idItalics.isSelected()));
Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
Boolean.toString(startupCheckbox.isSelected()));
- Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
+ sortby.getSelectedItem().toString());
// convert description of sort order to enum name for save
SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
- .valueOf(showAutocalcFirst).toString());
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
+ Boolean.valueOf(showAutocalcFirst).toString());
/*
* Save Colours settings
*/
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
- .getSelectedItem().toString());
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
+ protColour.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
+ nucColour.getSelectedItem().toString());
Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
minColour.getBackground());
Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
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,
Boolean.toString(useRnaView.isSelected()));
Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
Boolean.toString(structFromPdb.isSelected()));
- Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
+ structViewer.getSelectedItem().toString());
Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
Boolean.toString(siftsMapping.isSelected()));
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.saveProperties();
Desktop.instance.doConfigureStructurePrefs();
try
public void startupFileTextfield_mouseClicked()
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser chooser = JalviewFileChooser.forRead(
- Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ JalviewFileChooser chooser = JalviewFileChooser
+ .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.select_startup_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.select_startup_file"));
int value = chooser.showOpenDialog(this);
Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
format.getName());
}
- startupFileTextfield.setText(chooser.getSelectedFile()
- .getAbsolutePath());
+ startupFileTextfield
+ .setText(chooser.getSelectedFile().getAbsolutePath());
}
}
{
if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.new_sequence_url_link"),
- JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1,
+ null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
if (((UrlLinkTableModel) linkUrlTable.getModel())
.isUniqueName(link.getName()))
{
- ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
- link.getName(), link.getURL());
+ ((UrlLinkTableModel) linkUrlTable.getModel())
+ .insertRow(link.getName(), link.getURL());
valid = true;
}
else
{
if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.edit_sequence_url_link"),
- JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1,
+ null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
}
-
@Override
public void defaultBrowser_mouseClicked(MouseEvent e)
{
JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle(MessageManager
- .getString("label.select_default_browser"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.select_default_browser"));
int value = chooser.showOpenDialog(this);
}
@Override
+ public void gapColour_actionPerformed(JPanel gap)
+ {
+ if (!useLegacyGap.isSelected())
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_gap_colour"),
+ gapColour.getBackground());
+ if (col != null)
+ {
+ gap.setBackground(col);
+ }
+ gap.repaint();
+ }
+ }
+
+ @Override
+ public void hiddenColour_actionPerformed(JPanel hidden)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_hidden_colour"),
+ hiddenColour.getBackground());
+ if (col != null)
+ {
+ 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);
+ }
+ 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
protected void userIdWidth_actionPerformed()
{
try
}
} catch (NumberFormatException x)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .getString("warn.user_defined_width_requirements"),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
JvOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
if (!found)
{
String[] options = { "OK", "Help" };
- int showHelp = JvOptionPane.showInternalOptionDialog(
- Desktop.desktop,
+ int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
"", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
return name.hashCode() + code.hashCode();
}
}
-
+
private class UrlListSelectionHandler implements ListSelectionListener
{
editLink.setEnabled(false);
}
}
-}
+ }
}
git://source.jalview.org / jalview.git / blobdiff