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 jalview.jbgui.GPreferences;
import jalview.jbgui.GSequenceLink;
-import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
import jalview.urls.UrlLinkTableModel;
import jalview.urls.api.UrlProviderFactoryI;
import jalview.urls.api.UrlProviderI;
import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.UrlConstants;
import java.util.List;
import javax.help.HelpSetException;
-import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.ListSelectionModel;
import javax.swing.RowFilter;
* @author $author$
* @version $Revision$
*/
+@SuppressWarnings("serial")
public class Preferences extends GPreferences
{
+ 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 SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
public static final String CHIMERA_PATH = "CHIMERA_PATH";
+ public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
+
+ public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
+
public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+ public static final String SORT_BY_TREE = "SORT_BY_TREE";
+
+ public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
+
public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+ public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
+
+ public static final String SHOW_QUALITY = "SHOW_QUALITY";
+
+ public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
+
+ public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
+
+ public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
+
+ 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 NORMALISE_LOGO = "NORMALISE_LOGO";
+
+ public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+
+ public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
+
+ 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 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;
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
*/
- public static UrlProviderI sequenceUrlLinks;
+ public static UrlProviderI sequenceUrlLinks; // must be nonfinal for test
- public static UrlLinkTableModel dataModel;
+ public final static UrlLinkTableModel dataModel;
/**
* Holds name and link separated with | character. Sequence IDS and Sequences
* (TODO: proper escape for using | to separate ids or sequences
*/
- public static List<String> groupURLLinks;
+ public static final List<String> groupURLLinks; // not implemented
+
static
{
// get links selected to be in the menu (SEQUENCE_LINKS)
* .properties file as '|' separated strings
*/
- groupURLLinks = new ArrayList<String>();
+ groupURLLinks = new ArrayList<>(); // not implemented
}
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);
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ wsPrefs = new WsPreferences();
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
+ }
int width = 500, height = 450;
- new jalview.util.Platform();
- if (Platform.isAMac())
+ if (Platform.isAMacAndNotJS())
{
width = 570;
height = 480;
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));
+ conservation.setSelected(Cache.getDefault(SHOW_CONSERVATION, true));
+ quality.setSelected(Cache.getDefault(SHOW_QUALITY, true));
identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
- openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
+ openoverv.setSelected(Cache.getDefault(SHOW_OVERVIEW, false));
showUnconserved
- .setSelected(Cache.getDefault("SHOW_UNCONSERVED", 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));
+ .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));
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));
sortby.addItem("No sort");
sortby.addItem("Id");
sortby.addItem("Pairwise Identity");
- sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
+ sortby.setSelectedItem(Cache.getDefault(SORT_ALIGNMENT, "No sort"));
sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
sortAnnBy
/*
* Set Colours tab defaults
*/
- for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+ protColour.addItem(ResidueColourScheme.NONE);
+ nucColour.addItem(ResidueColourScheme.NONE);
+ for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
{
- protColour.addItem(ColourSchemeProperty.getColourName(i));
- nucColour.addItem(ColourSchemeProperty.getColourName(i));
+ String name = cs.getSchemeName();
+ protColour.addItem(name);
+ nucColour.addItem(name);
}
- String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
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, 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()));
+ structViewer.setSelectedItem(
+ Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
chimeraPath.addActionListener(new ActionListener()
{
List<RowSorter.SortKey> sortKeys = new ArrayList<>();
UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
- sortKeys.add(new RowSorter.SortKey(m.getDefaultColumn(),
+ sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
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();
-
+ // BH 2018 setSortKeys will do the sort
+ // 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())
- .getDefaultColumn();
+ .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,
useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
useProxy_actionPerformed(); // make sure useProxy is correctly initialised
- proxyServerTB.setEnabled(useProxy.isSelected());
- proxyPortTB.setEnabled(useProxy.isSelected());
proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
/*
* Set Output tab defaults
*/
- epsRendering.addItem(promptEachTimeOpt);
- epsRendering.addItem(lineArtOpt);
- epsRendering.addItem(textOpt);
- String defaultEPS = Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
- if (defaultEPS.equalsIgnoreCase("Text"))
- {
- epsRendering.setSelectedItem(textOpt);
- }
- else if (defaultEPS.equalsIgnoreCase("Lineart"))
- {
- epsRendering.setSelectedItem(lineArtOpt);
- }
- else
- {
- epsRendering.setSelectedItem(promptEachTimeOpt);
- }
+ setupOutputCombo(epsRendering, "EPS_RENDERING");
+ setupOutputCombo(htmlRendering, "HTML_RENDERING");
+ setupOutputCombo(svgRendering, "SVG_RENDERING");
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));
+ sortByTree.setSelected(Cache.getDefault(SORT_BY_TREE, false));
annotations_actionPerformed(null); // update the display of the annotation
// settings
+
+
+ /*
+ * Set Backups tab defaults
+ */
+ loadLastSavedBackupsOptions();
+ }
+
+ /**
+ * A helper method that sets the items and initial selection in a character
+ * rendering option list (Prompt each time/Lineart/Text)
+ *
+ * @param comboBox
+ * @param propertyKey
+ */
+ protected void setupOutputCombo(JComboBox<Object> comboBox,
+ String propertyKey)
+ {
+ comboBox.addItem(promptEachTimeOpt);
+ comboBox.addItem(lineArtOpt);
+ comboBox.addItem(textOpt);
+
+ /*
+ * JalviewJS doesn't support Lineart so force it to Text
+ */
+ String defaultOption = Platform.isJS() ? "Text"
+ : Cache.getDefault(propertyKey, "Prompt each time");
+ if (defaultOption.equalsIgnoreCase("Text"))
+ {
+ comboBox.setSelectedItem(textOpt);
+ }
+ else if (defaultOption.equalsIgnoreCase("Lineart"))
+ {
+ comboBox.setSelectedItem(lineArtOpt);
+ }
+ else
+ {
+ comboBox.setSelectedItem(promptEachTimeOpt);
+ }
}
/**
/*
* Save Visual settings
*/
- Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
+ Cache.setPropertyNoSave("SHOW_JVSUFFIX",
Boolean.toString(seqLimit.isSelected()));
- Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
+ Cache.setPropertyNoSave("RIGHT_ALIGN_IDS",
Boolean.toString(rightAlign.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
+ Cache.setPropertyNoSave("SHOW_FULLSCREEN",
Boolean.toString(fullScreen.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
+ Cache.setPropertyNoSave("SHOW_OVERVIEW",
Boolean.toString(openoverv.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
Boolean.toString(annotations.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave(SHOW_CONSERVATION,
Boolean.toString(conservation.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Cache.setPropertyNoSave(SHOW_QUALITY,
Boolean.toString(quality.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Cache.setPropertyNoSave("SHOW_IDENTITY",
Boolean.toString(identity.isSelected()));
- Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
- .getSelectedItem().toString());
+ Cache.setPropertyNoSave("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.setPropertyNoSave("FONT_NAME",
+ fontNameCB.getSelectedItem().toString());
+ Cache.setPropertyNoSave("FONT_STYLE",
+ fontStyleCB.getSelectedItem().toString());
+ Cache.setPropertyNoSave("FONT_SIZE",
+ fontSizeCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("ID_ITALICS",
+ Cache.setPropertyNoSave("ID_ITALICS",
Boolean.toString(idItalics.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
+ Cache.setPropertyNoSave("SHOW_UNCONSERVED",
Boolean.toString(showUnconserved.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+ Cache.setPropertyNoSave(SHOW_OCCUPANCY,
+ Boolean.toString(showOccupancy.isSelected()));
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS,
Boolean.toString(showGroupConsensus.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
+ Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION,
Boolean.toString(showGroupConservation.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
+ Cache.setPropertyNoSave(SHOW_CONSENSUS_HISTOGRAM,
Boolean.toString(showConsensHistogram.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+ Cache.setPropertyNoSave(SHOW_CONSENSUS_LOGO,
Boolean.toString(showConsensLogo.isSelected()));
- Cache.applicationProperties.setProperty("ANTI_ALIAS",
+ Cache.setPropertyNoSave("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
- Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+ Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
Boolean.toString(scaleProteinToCdna.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+ Cache.setPropertyNoSave("SHOW_NPFEATS_TOOLTIP",
Boolean.toString(showNpTooltip.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+ Cache.setPropertyNoSave("SHOW_DBREFS_TOOLTIP",
Boolean.toString(showDbRefTooltip.isSelected()));
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
+ Cache.setPropertyNoSave("WRAP_ALIGNMENT",
Boolean.toString(wrap.isSelected()));
- Cache.applicationProperties.setProperty("STARTUP_FILE",
+ Cache.setPropertyNoSave("STARTUP_FILE",
startupFileTextfield.getText());
- Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
+ Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
Boolean.toString(startupCheckbox.isSelected()));
- Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
- .getSelectedItem().toString());
+ Cache.setPropertyNoSave(SORT_ALIGNMENT,
+ sortby.getSelectedItem().toString());
// convert description of sort order to enum name for save
SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
.forDescription(sortAnnBy.getSelectedItem().toString());
if (annSortOrder != null)
{
- Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
+ Cache.setPropertyNoSave(SORT_ANNOTATIONS,
annSortOrder.name());
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
- .valueOf(showAutocalcFirst).toString());
+ Cache.setPropertyNoSave(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.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
+ protColour.getSelectedItem().toString());
+ Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
+ nucColour.getSelectedItem().toString());
+ Cache.setColourProperty(ANNOTATIONCOLOUR_MIN,
minColour.getBackground());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ Cache.setColourProperty(ANNOTATIONCOLOUR_MAX,
maxColour.getBackground());
/*
+ * Save Overview settings
+ */
+ Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
+ Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
+ Cache.setPropertyNoSave(USE_LEGACY_GAP,
+ Boolean.toString(useLegacyGap.isSelected()));
+ Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
+ Boolean.toString(showHiddenAtStart.isSelected()));
+
+ /*
* Save Structure settings
*/
- Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+ Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
Boolean.toString(addTempFactor.isSelected()));
- Cache.applicationProperties.setProperty(ADD_SS_ANN,
+ Cache.setPropertyNoSave(ADD_SS_ANN,
Boolean.toString(addSecondaryStructure.isSelected()));
- Cache.applicationProperties.setProperty(USE_RNAVIEW,
+ Cache.setPropertyNoSave(USE_RNAVIEW,
Boolean.toString(useRnaView.isSelected()));
- Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+ Cache.setPropertyNoSave(STRUCT_FROM_PDB,
Boolean.toString(structFromPdb.isSelected()));
- Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
- .getSelectedItem().toString());
+ Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
+ structViewer.getSelectedItem().toString());
Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
- Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
+ Cache.setPropertyNoSave("MAP_WITH_SIFTS",
Boolean.toString(siftsMapping.isSelected()));
SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
/*
* Save Output settings
*/
- Cache.applicationProperties.setProperty("EPS_RENDERING",
+ Cache.setPropertyNoSave("EPS_RENDERING",
((OptionsParam) epsRendering.getSelectedItem()).getCode());
+ Cache.setPropertyNoSave("HTML_RENDERING",
+ ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
+ Cache.setPropertyNoSave("SVG_RENDERING",
+ ((OptionsParam) svgRendering.getSelectedItem()).getCode());
- /*
- * Save Connections settings
+ if (!Platform.isJS())
+ /**
+ * @j2sNative
*/
- Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
-
- jalview.util.BrowserLauncher.resetBrowser();
+ {
+ // Java only
+ // Save Connections settings
+ Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+ BrowserLauncher.resetBrowser();
+ }
// save user-defined and selected links
String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
if (menuLinks.isEmpty())
{
- Cache.applicationProperties.remove("SEQUENCE_LINKS");
+ Cache.removePropertyNoSave("SEQUENCE_LINKS");
}
else
{
- Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+ Cache.setPropertyNoSave("SEQUENCE_LINKS",
menuLinks.toString());
}
String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
if (nonMenuLinks.isEmpty())
{
- Cache.applicationProperties.remove("STORED_LINKS");
+ Cache.removePropertyNoSave("STORED_LINKS");
}
else
{
- Cache.applicationProperties.setProperty("STORED_LINKS",
+ Cache.setPropertyNoSave("STORED_LINKS",
nonMenuLinks.toString());
}
- Cache.applicationProperties.setProperty("DEFAULT_URL",
- sequenceUrlLinks.getDefaultUrlId());
+ Cache.setPropertyNoSave("DEFAULT_URL",
+ sequenceUrlLinks.getPrimaryUrlId());
- Cache.applicationProperties.setProperty("USE_PROXY",
+ Cache.setPropertyNoSave("USE_PROXY",
Boolean.toString(useProxy.isSelected()));
Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
/*
* Save Output settings
*/
- Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
+ Cache.setPropertyNoSave("BLC_JVSUFFIX",
Boolean.toString(blcjv.isSelected()));
- Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
+ Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
Boolean.toString(clustaljv.isSelected()));
- Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
+ Cache.setPropertyNoSave("FASTA_JVSUFFIX",
Boolean.toString(fastajv.isSelected()));
- Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
+ Cache.setPropertyNoSave("MSF_JVSUFFIX",
Boolean.toString(msfjv.isSelected()));
- Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
+ Cache.setPropertyNoSave("PFAM_JVSUFFIX",
Boolean.toString(pfamjv.isSelected()));
- Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
+ Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
Boolean.toString(pileupjv.isSelected()));
- Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
+ Cache.setPropertyNoSave("PIR_JVSUFFIX",
Boolean.toString(pirjv.isSelected()));
- Cache.applicationProperties.setProperty("PIR_MODELLER",
+ Cache.setPropertyNoSave("PIR_MODELLER",
Boolean.toString(modellerOutput.isSelected()));
- Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+ Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
Boolean.toString(embbedBioJSON.isSelected()));
- jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
-
- Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+ Cache.setPropertyNoSave("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
- Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+ Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
userIdWidth.getText());
/*
* Save Editing settings
*/
- Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+ Cache.setPropertyNoSave("AUTO_CALC_CONSENSUS",
Boolean.toString(autoCalculateConsCheck.isSelected()));
- Cache.applicationProperties.setProperty("SORT_BY_TREE",
+ Cache.setPropertyNoSave("SORT_BY_TREE",
Boolean.toString(sortByTree.isSelected()));
- Cache.applicationProperties.setProperty("PAD_GAPS",
+ Cache.setPropertyNoSave("PAD_GAPS",
Boolean.toString(padGaps.isSelected()));
- dasSource.saveProperties(Cache.applicationProperties);
- wsPrefs.updateAndRefreshWsMenuConfig(false);
+ if (!Platform.isJS())
+ {
+ wsPrefs.updateAndRefreshWsMenuConfig(false);
+ }
+
+ /*
+ * Save Backups settings
+ */
+ Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
+ Boolean.toString(backupfilesConfirmDelete.isSelected()));
+ Cache.setPropertyNoSave(BackupFiles.ENABLED,
+ Boolean.toString(enableBackupFiles.isSelected()));
+ Cache.setPropertyNoSave(BackupFiles.NO_MAX,
+ Boolean.toString(backupfilesKeepAll.isSelected()));
+ Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
+ Boolean.toString(suffixReverse.isSelected()));
+ Cache.setPropertyNoSave(BackupFiles.SUFFIX,
+ suffixTemplate.getText());
+ Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
+ Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
+ Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
+ Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
+ Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET",
+ Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
+
Cache.saveProperties();
- Desktop.instance.doConfigureStructurePrefs();
+ Desktop.getInstance().doConfigureStructurePrefs();
try
{
frame.setClosed(true);
}
}
+ public static void setAppletDefaults()
+ {
+
+ // http://www.jalview.org/old/v2_8/examples/appletParameters.html
+
+ // showConservation true or false Default is true.
+ // showQuality true or false Default is true.
+ // showConsensus true or false Default is true.
+ // showFeatureSettings true or false Shows the feature settings window when
+ // startin
+ // showTreeBootstraps true or false (default is true) show or hide branch
+ // bootstraps
+ // showTreeDistances true or false (default is true) show or hide branch
+ // lengths
+ // showUnlinkedTreeNodes true or false (default is false) indicate if
+ // unassociated nodes should be highlighted in the tree view
+ // showUnconserved true of false (default is false) When true, only gaps and
+ // symbols different to the consensus sequence ions of the alignment
+ // showGroupConsensus true of false (default is false) When true, shows
+ // consensus annotation row for any groups on the alignment. (since 2.7)
+ // showGroupConservation true of false (default is false) When true, shows
+ // amino-acid property conservation annotation row for any groups on the
+ // showConsensusHistogram true of false (default is true) When true, shows
+ // the percentage occurence of the consensus symbol for each column as a
+ // showSequenceLogo true of false (default is false) When true, shows a
+ // sequence logo above the consensus sequence (overlaid above the Consensus
+
+ 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");
+
+ // TODO -- just a start here
+ }
+
/**
* Do any necessary validation before saving settings. Return focus to the
* first tab which fails validation.
@Override
public void startupFileTextfield_mouseClicked()
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
- "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
- "PIR", "BLC", "Jalview" },
- jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+ // TODO: JAL-3048 not needed for Jalview-JS
+ String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ 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);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- jalview.bin.Cache.applicationProperties.setProperty(
- "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
- startupFileTextfield.setText(chooser.getSelectedFile()
- .getAbsolutePath());
+ FileFormatI format = chooser.getSelectedFormat();
+ if (format != null)
+ {
+ Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
+ format.getName());
+ }
+ startupFileTextfield
+ .setText(chooser.getSelectedFile().getAbsolutePath());
}
}
{
try
{
- wsPrefs.updateWsMenuConfig(true);
- wsPrefs.refreshWs_actionPerformed(e);
+ if (!Platform.isJS())
+ {
+ wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
+ }
frame.setClosed(true);
} catch (Exception ex)
{
conservation.setEnabled(annotations.isSelected());
quality.setEnabled(annotations.isSelected());
identity.setEnabled(annotations.isSelected());
+ showOccupancy.setEnabled(annotations.isSelected());
showGroupConsensus.setEnabled(annotations.isSelected());
showGroupConservation.setEnabled(annotations.isSelected());
showConsensHistogram.setEnabled(annotations.isSelected()
boolean valid = false;
while (!valid)
{
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
MessageManager.getString("label.new_sequence_url_link"),
- JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1,
+ null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
- ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
- link.getName(), link.getURL());
- valid = true;
+ if (((UrlLinkTableModel) linkUrlTable.getModel())
+ .isUniqueName(link.getName()))
+ {
+ ((UrlLinkTableModel) linkUrlTable.getModel())
+ .insertRow(link.getName(), link.getURL());
+ valid = true;
+ }
+ else
+ {
+ link.notifyDuplicate();
+ continue;
+ }
}
}
else
return;
}
- link.setName(linkUrlTable.getValueAt(index, 0).toString());
- link.setURL(linkUrlTable.getValueAt(index, 1).toString());
+ int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+ .getNameColumn();
+ int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+ .getUrlColumn();
+ String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
+ link.setName(oldName);
+ link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
boolean valid = false;
while (!valid)
{
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
MessageManager.getString("label.edit_sequence_url_link"),
- JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1,
+ null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
- linkUrlTable.setValueAt(link.getName(), index, 0);
- linkUrlTable.setValueAt(link.getURL(), index, 1);
- valid = true;
+ if ((oldName.equals(link.getName()))
+ || (((UrlLinkTableModel) linkUrlTable.getModel())
+ .isUniqueName(link.getName())))
+ {
+ linkUrlTable.setValueAt(link.getName(), index, nameCol);
+ linkUrlTable.setValueAt(link.getURL(), index, urlCol);
+ valid = true;
+ }
+ else
+ {
+ link.notifyDuplicate();
+ continue;
+ }
}
}
else
((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
}
-
@Override
public void defaultBrowser_mouseClicked(MouseEvent e)
{
- JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle(MessageManager
- .getString("label.select_default_browser"));
+ // TODO: JAL-3048 not needed for j2s
+ if (!Platform.isJS()) // BH 2019
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ JFileChooser chooser = new JFileChooser(".");
+ chooser.setDialogTitle(
+ MessageManager.getString("label.select_default_browser"));
- int value = chooser.showOpenDialog(this);
+ int value = chooser.showOpenDialog(this);
- if (value == JFileChooser.APPROVE_OPTION)
- {
- defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+ }
}
-
}
/*
super.showunconserved_actionPerformed(e);
}
+ /**
+ * not implemented -- returns empty list
+ *
+ * @return
+ */
public static List<String> getGroupURLLinks()
{
return groupURLLinks;
@Override
public void minColour_actionPerformed(JPanel panel)
{
- Color col = JColorChooser.showDialog(this,
+ JalviewColourChooser.showColourChooser(this,
MessageManager.getString("label.select_colour_minimum_value"),
- minColour.getBackground());
- if (col != null)
- {
- panel.setBackground(col);
- }
- panel.repaint();
+ panel);
}
@Override
public void maxColour_actionPerformed(JPanel panel)
{
- Color col = JColorChooser.showDialog(this,
+ JalviewColourChooser.showColourChooser(this,
MessageManager.getString("label.select_colour_maximum_value"),
- maxColour.getBackground());
- if (col != null)
+ panel);
+ }
+
+ @Override
+ public void gapColour_actionPerformed(JPanel gap)
+ {
+ if (!useLegacyGap.isSelected())
+ {
+ JalviewColourChooser.showColourChooser(this,
+ MessageManager.getString("label.select_gap_colour"),
+ gap);
+ }
+ }
+
+ @Override
+ public void hiddenColour_actionPerformed(JPanel hidden)
+ {
+ JalviewColourChooser.showColourChooser(this,
+ MessageManager.getString("label.select_hidden_colour"),
+ hidden);
+ }
+
+ @Override
+ protected void useLegacyGaps_actionPerformed(ActionEvent e)
+ {
+ boolean enabled = useLegacyGap.isSelected();
+ if (enabled)
{
- panel.setBackground(col);
+ gapColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
}
- panel.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(false);
+ hiddenColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
}
@Override
}
} catch (NumberFormatException x)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .getString("warn.user_defined_width_requirements"),
- MessageManager.getString("label.invalid_id_column_width"),
- JOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ MessageManager
+ .getString("warn.user_defined_width_requirements"),
+ MessageManager.getString("label.invalid_id_column_width"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
* Returns true if chimera path is to a valid executable, else show an error
* dialog.
*/
- private boolean validateChimeraPath()
+ protected boolean validateChimeraPath()
{
if (chimeraPath.getText().trim().length() > 0)
{
File f = new File(chimeraPath.getText());
if (!f.canExecute())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.invalid_chimera_path"),
MessageManager.getString("label.invalid_name"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
return false;
}
}
if (!found)
{
String[] options = { "OK", "Help" };
- int showHelp = JOptionPane.showInternalOptionDialog(
- Desktop.desktop,
+ int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
- "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+ "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
null, options, options[0]);
- if (showHelp == JOptionPane.NO_OPTION)
+ if (showHelp == JvOptionPane.NO_OPTION)
{
try
{
return name.hashCode() + code.hashCode();
}
}
-
- private class UrlListSelectionHandler implements ListSelectionListener
+
+ protected class UrlListSelectionHandler implements ListSelectionListener
{
@Override
editLink.setEnabled(false);
}
}
-}
+ }
}
git://source.jalview.org / jalview.git / blobdiff