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;
* @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";
* 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<>();
+ groupURLLinks = new ArrayList<>(); // not implemented
}
JInternalFrame frame;
frame = new JInternalFrame();
frame.setContentPane(this);
if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
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));
+ .setSelected(Cache.getDefault(SHOW_UNCONSERVED, false));
showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
showGroupConsensus
- .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
+ .setSelected(Cache.getDefault(SHOW_GROUP_CONSENSUS, false));
showGroupConservation.setSelected(
- Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+ Cache.getDefault(SHOW_GROUP_CONSERVATION, false));
showConsensHistogram.setSelected(
- Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
+ Cache.getDefault(SHOW_CONSENSUS_HISTOGRAM, true));
showConsensLogo
- .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ .setSelected(Cache.getDefault(SHOW_CONSENSUS_LOGO, false));
showNpTooltip
.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
showDbRefTooltip
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
newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
minColour.setBackground(
- Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ Cache.getDefaultColour(ANNOTATIONCOLOUR_MIN, Color.orange));
maxColour.setBackground(
- Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+ Cache.getDefaultColour(ANNOTATIONCOLOUR_MAX, Color.red));
/*
* Set overview panel defaults
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.
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
/*
* 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",
+ Cache.setPropertyNoSave("GAP_SYMBOL",
gapSymbolCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_NAME",
+ Cache.setPropertyNoSave("FONT_NAME",
fontNameCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_STYLE",
+ Cache.setPropertyNoSave("FONT_STYLE",
fontStyleCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_SIZE",
+ 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_OCCUPANCY,
+ Cache.setPropertyNoSave(SHOW_OCCUPANCY,
Boolean.toString(showOccupancy.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+ 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",
+ Cache.setPropertyNoSave(SORT_ALIGNMENT,
sortby.getSelectedItem().toString());
// convert description of sort order to enum name for save
.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,
+ Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
Boolean.valueOf(showAutocalcFirst).toString());
/*
* Save Colours settings
*/
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
+ Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
protColour.getSelectedItem().toString());
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
+ Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
nucColour.getSelectedItem().toString());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ Cache.setColourProperty(ANNOTATIONCOLOUR_MIN,
minColour.getBackground());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ Cache.setColourProperty(ANNOTATIONCOLOUR_MAX,
maxColour.getBackground());
/*
*/
Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
- Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+ Cache.setPropertyNoSave(USE_LEGACY_GAP,
Boolean.toString(useLegacyGap.isSelected()));
- Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+ 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,
+ 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.applicationProperties.setProperty("HTML_RENDERING",
+ Cache.setPropertyNoSave("HTML_RENDERING",
((OptionsParam) htmlRendering.getSelectedItem()).getCode());
- Cache.applicationProperties.setProperty("SVG_RENDERING",
+ 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",
+ 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_FIXEDIDWIDTH",
+ 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()));
if (!Platform.isJS())
/*
* Save Backups settings
*/
- Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
+ Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
Boolean.toString(backupfilesConfirmDelete.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+ Cache.setPropertyNoSave(BackupFiles.ENABLED,
Boolean.toString(enableBackupFiles.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
+ Cache.setPropertyNoSave(BackupFiles.NO_MAX,
Boolean.toString(backupfilesKeepAll.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
+ Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
Boolean.toString(suffixReverse.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
+ Cache.setPropertyNoSave(BackupFiles.SUFFIX,
suffixTemplate.getText());
- Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
+ Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
- Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
+ Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
- Cache.applicationProperties.setProperty(BackupFiles.NS+"_PRESET",
+ 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.
FileFormatI format = chooser.getSelectedFormat();
if (format != null)
{
- Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+ Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
format.getName());
}
startupFileTextfield
boolean valid = false;
while (!valid)
{
- if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
MessageManager.getString("label.new_sequence_url_link"),
JvOptionPane.OK_CANCEL_OPTION, -1,
null) == JvOptionPane.OK_OPTION)
boolean valid = false;
while (!valid)
{
- if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
MessageManager.getString("label.edit_sequence_url_link"),
JvOptionPane.OK_CANCEL_OPTION, -1,
null) == JvOptionPane.OK_OPTION)
public void defaultBrowser_mouseClicked(MouseEvent e)
{
// TODO: JAL-3048 not needed for j2s
- /*
- * @j2sNative
+ if (!Platform.isJS()) // BH 2019
+ /**
+ * Java only
+ *
+ * @j2sIgnore
*/
{
JFileChooser chooser = new JFileChooser(".");
super.showunconserved_actionPerformed(e);
}
+ /**
+ * not implemented -- returns empty list
+ *
+ * @return
+ */
public static List<String> getGroupURLLinks()
{
return groupURLLinks;
{
useLegacyGap.setSelected(false);
useLegacyGaps_actionPerformed(null);
- showHiddenAtStart.setSelected(true);
+ showHiddenAtStart.setSelected(false);
hiddenColour.setBackground(
jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
}
} catch (NumberFormatException x)
{
userIdWidth.setText("");
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
* 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())
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.invalid_chimera_path"),
MessageManager.getString("label.invalid_name"),
JvOptionPane.ERROR_MESSAGE);
if (!found)
{
String[] options = { "OK", "Help" };
- int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+ int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
"", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
}
}
- private class UrlListSelectionHandler implements ListSelectionListener
+ protected class UrlListSelectionHandler implements ListSelectionListener
{
@Override
git://source.jalview.org / jalview.git / blobdiff