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;
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 ADD_SS_ANN = "ADD_SS_ANN";
-
- public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
-
- public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING";
-
- public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX";
-
- public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN";
-
- public static final String ANTI_ALIAS = "ANTI_ALIAS";
-
- public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS";
-
- public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
-
- public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
-
- public static final String CHIMERA_PATH = "CHIMERA_PATH";
+ public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
- public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
+ public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
- public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
-
public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
- public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
-
- public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
-
- public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
-
- public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS";
-
- public static final String FONT_NAME = "FONT_NAME";
-
- public static final String FONT_SIZE = "FONT_SIZE";
-
- public static final String FONT_STYLE = "FONT_STYLE";
-
- public static final String GAP_COLOUR = "GAP_COLOUR";
-
- public static final String GAP_SYMBOL = "GAP_SYMBOL";
-
- public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
-
- public static final String HIDE_INTRONS = "HIDE_INTRONS";
-
- public static final String ID_ITALICS = "ID_ITALICS";
-
- public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
-
- public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
-
- public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
-
- public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
-
- public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
+ public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
- public static final String PAD_GAPS = "PAD_GAPS";
+ public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
- public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT";
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
- public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
- public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING";
+ public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
- public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
+ public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
- public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+ public static final String CHIMERA_PATH = "CHIMERA_PATH";
- public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
- public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
-
- public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
-
- public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
-
- public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
-
- public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP";
-
- public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS";
-
- public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
-
- public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
-
- public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
-
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 SHOW_OVERVIEW = "SHOW_OVERVIEW";
-
- public static final String SHOW_QUALITY = "SHOW_QUALITY";
-
- public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED";
-
- public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
-
- public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
-
- public static final String SORT_BY_TREE = "SORT_BY_TREE";
-
- public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
-
- public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
-
- public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
-
- public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
-
- public static final String USE_FULL_SO = "USE_FULL_SO";
-
public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
- public static final String USE_RNAVIEW = "USE_RNAVIEW";
-
- public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
-
- public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
+ public static final String GAP_COLOUR = "GAP_COLOUR";
+ public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
private static final int MIN_FONT_SIZE = 1;
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
*/
- public static UrlProviderI sequenceUrlLinks; // must be nonfinal for test
+ public static UrlProviderI sequenceUrlLinks;
- public final static UrlLinkTableModel dataModel;
+ public 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 final List<String> groupURLLinks; // not implemented
-
- public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
-
- public static final String SHOW_IDENTITY = "SHOW_IDENTITY";
-
- public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
-
- public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
- 600, 600);
-
+ public static List<String> groupURLLinks;
static
{
// get links selected to be in the menu (SEQUENCE_LINKS)
* .properties file as '|' separated strings
*/
- groupURLLinks = new ArrayList<>(); // not implemented
+ groupURLLinks = new ArrayList<>();
}
JInternalFrame frame;
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
}
- int width = 500, height = 510; // BH 2019.07.12 added 60 to height
- // (structure panel was too small anyway, and I added a default dimension
- // for Jmol
+ int width = 500, height = 450;
if (Platform.isAMacAndNotJS())
{
width = 570;
- height = 540; // BH 2019.07.12 added 30
+ height = 480;
}
Desktop.addInternalFrame(frame,
/*
* Set Visual tab defaults
*/
- seqLimit.setSelected(Cache.getDefault(SHOW_JVSUFFIX, true));
- rightAlign.setSelected(Cache.getDefault(RIGHT_ALIGN_IDS, false));
- 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));
- identity.setSelected(Cache.getDefault(SHOW_IDENTITY, true));
- openoverv.setSelected(Cache.getDefault(SHOW_OVERVIEW, false));
+ seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
+ rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+ 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));
+ identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
+ 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));
+ .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
showDbRefTooltip
- .setSelected(Cache.getDefault(SHOW_DBREFS_TOOLTIP, true));
+ .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
fontStyleCB.addItem("bold");
fontStyleCB.addItem("italic");
- fontNameCB.setSelectedItem(Cache.getDefault(FONT_NAME, "SansSerif"));
- fontSizeCB.setSelectedItem(Cache.getDefault(FONT_SIZE, "10"));
+ fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
+ fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
fontStyleCB.setSelectedItem(
- Cache.getDefault(FONT_STYLE, Font.PLAIN + ""));
+ Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
- smoothFont.setSelected(Cache.getDefault(ANTI_ALIAS, false));
+ smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
scaleProteinToCdna
.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
- idItalics.setSelected(Cache.getDefault(ID_ITALICS, true));
+ idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
- wrap.setSelected(Cache.getDefault(WRAP_ALIGNMENT, false));
+ wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
gapSymbolCB.addItem("-");
gapSymbolCB.addItem(".");
- gapSymbolCB.setSelectedItem(Cache.getDefault(GAP_SYMBOL, "-"));
+ gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
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
addTempFactor.setEnabled(structSelected);
structViewer.setSelectedItem(
Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
- Dimension d = Cache.getDefaultDim(STRUCTURE_DIMENSIONS,
- DEFAULT_STRUCTURE_DIMENSIONS);
- String s = d.width + "," + d.height;
- structureDimensions.setText(s);
chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
chimeraPath.addActionListener(new ActionListener()
{
}
});
- if (Cache.getDefault(MAP_WITH_SIFTS, false))
+ if (Cache.getDefault("MAP_WITH_SIFTS", false))
{
siftsMapping.setSelected(true);
}
}
SiftsSettings
- .setMapWithSifts(Cache.getDefault(MAP_WITH_SIFTS, false));
+ .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
/*
* Set Connections tab defaults
usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
// note antisense here: default is true
questionnaire
- .setSelected(Cache.getProperty(NOQUESTIONNAIRES) == null);
+ .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
/*
setupOutputCombo(epsRendering, "EPS_RENDERING");
setupOutputCombo(htmlRendering, "HTML_RENDERING");
setupOutputCombo(svgRendering, "SVG_RENDERING");
- autoIdWidth.setSelected(Cache.getDefault(FIGURE_AUTOIDWIDTH, false));
+ autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
userIdWidth.setEnabled(!autoIdWidth.isSelected());
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
- Integer wi = Cache.getIntegerProperty(FIGURE_FIXEDIDWIDTH);
+ 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
* Set Editing 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));
+ .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
*/
- loadLastSavedBackupsOptions();
+ if (!Platform.isJS())
+ {
+ loadLastSavedBackupsOptions();
+ }
}
/**
/*
* Save Visual settings
*/
- Cache.setPropertyNoSave(SHOW_JVSUFFIX,
+ Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
Boolean.toString(seqLimit.isSelected()));
- Cache.setPropertyNoSave(RIGHT_ALIGN_IDS,
+ Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
Boolean.toString(rightAlign.isSelected()));
- Cache.setPropertyNoSave(SHOW_FULLSCREEN,
+ Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
Boolean.toString(fullScreen.isSelected()));
- Cache.setPropertyNoSave(SHOW_OVERVIEW,
+ Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
Boolean.toString(openoverv.isSelected()));
- Cache.setPropertyNoSave(SHOW_ANNOTATIONS,
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
Boolean.toString(annotations.isSelected()));
- Cache.setPropertyNoSave(SHOW_CONSERVATION,
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
Boolean.toString(conservation.isSelected()));
- Cache.setPropertyNoSave(SHOW_QUALITY,
+ Cache.applicationProperties.setProperty("SHOW_QUALITY",
Boolean.toString(quality.isSelected()));
- Cache.setPropertyNoSave(SHOW_IDENTITY,
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.toString(identity.isSelected()));
- Cache.setPropertyNoSave(GAP_SYMBOL,
+ Cache.applicationProperties.setProperty("GAP_SYMBOL",
gapSymbolCB.getSelectedItem().toString());
- Cache.setPropertyNoSave(FONT_NAME,
+ Cache.applicationProperties.setProperty("FONT_NAME",
fontNameCB.getSelectedItem().toString());
- Cache.setPropertyNoSave(FONT_STYLE,
+ Cache.applicationProperties.setProperty("FONT_STYLE",
fontStyleCB.getSelectedItem().toString());
- Cache.setPropertyNoSave(FONT_SIZE,
+ Cache.applicationProperties.setProperty("FONT_SIZE",
fontSizeCB.getSelectedItem().toString());
- Cache.setPropertyNoSave(ID_ITALICS,
+ Cache.applicationProperties.setProperty("ID_ITALICS",
Boolean.toString(idItalics.isSelected()));
- Cache.setPropertyNoSave(SHOW_UNCONSERVED,
+ Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
Boolean.toString(showUnconserved.isSelected()));
- Cache.setPropertyNoSave(SHOW_OCCUPANCY,
+ Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
Boolean.toString(showOccupancy.isSelected()));
- Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS,
+ Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
Boolean.toString(showGroupConsensus.isSelected()));
- Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION,
+ Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
Boolean.toString(showGroupConservation.isSelected()));
- Cache.setPropertyNoSave(SHOW_CONSENSUS_HISTOGRAM,
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
Boolean.toString(showConsensHistogram.isSelected()));
- Cache.setPropertyNoSave(SHOW_CONSENSUS_LOGO,
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
Boolean.toString(showConsensLogo.isSelected()));
- Cache.setPropertyNoSave(ANTI_ALIAS,
+ Cache.applicationProperties.setProperty("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
- Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
+ Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
Boolean.toString(scaleProteinToCdna.isSelected()));
- Cache.setPropertyNoSave(SHOW_NPFEATS_TOOLTIP,
+ Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
Boolean.toString(showNpTooltip.isSelected()));
- Cache.setPropertyNoSave(SHOW_DBREFS_TOOLTIP,
+ Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
Boolean.toString(showDbRefTooltip.isSelected()));
- Cache.setPropertyNoSave(WRAP_ALIGNMENT,
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
Boolean.toString(wrap.isSelected()));
- Cache.setPropertyNoSave("STARTUP_FILE",
+ Cache.applicationProperties.setProperty("STARTUP_FILE",
startupFileTextfield.getText());
- Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
+ Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
Boolean.toString(startupCheckbox.isSelected()));
- Cache.setPropertyNoSave(SORT_ALIGNMENT,
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
sortby.getSelectedItem().toString());
// convert description of sort order to enum name for save
.forDescription(sortAnnBy.getSelectedItem().toString());
if (annSortOrder != null)
{
- Cache.setPropertyNoSave(SORT_ANNOTATIONS,
+ Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
annSortOrder.name());
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
Boolean.valueOf(showAutocalcFirst).toString());
/*
* Save Colours settings
*/
- Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
protColour.getSelectedItem().toString());
- Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
+ Cache.applicationProperties.setProperty(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.setPropertyNoSave(USE_LEGACY_GAP,
+ Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
Boolean.toString(useLegacyGap.isSelected()));
- Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
+ Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
Boolean.toString(showHiddenAtStart.isSelected()));
/*
* Save Structure settings
*/
- Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
+ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
Boolean.toString(addTempFactor.isSelected()));
- Cache.setPropertyNoSave(ADD_SS_ANN,
+ Cache.applicationProperties.setProperty(ADD_SS_ANN,
Boolean.toString(addSecondaryStructure.isSelected()));
- Cache.setPropertyNoSave(USE_RNAVIEW,
+ Cache.applicationProperties.setProperty(USE_RNAVIEW,
Boolean.toString(useRnaView.isSelected()));
- Cache.setPropertyNoSave(STRUCT_FROM_PDB,
+ Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
Boolean.toString(structFromPdb.isSelected()));
- Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
structViewer.getSelectedItem().toString());
- Cache.setPropertyNoSave(STRUCTURE_DIMENSIONS,
- structureDimensions.getText()); // BH 2019.07.12
Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
- Cache.setPropertyNoSave(MAP_WITH_SIFTS,
+ Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
Boolean.toString(siftsMapping.isSelected()));
SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
/*
* Save Output settings
*/
- Cache.setPropertyNoSave("EPS_RENDERING",
+ Cache.applicationProperties.setProperty("EPS_RENDERING",
((OptionsParam) epsRendering.getSelectedItem()).getCode());
- Cache.setPropertyNoSave("HTML_RENDERING",
+ Cache.applicationProperties.setProperty("HTML_RENDERING",
((OptionsParam) htmlRendering.getSelectedItem()).getCode());
- Cache.setPropertyNoSave("SVG_RENDERING",
+ Cache.applicationProperties.setProperty("SVG_RENDERING",
((OptionsParam) svgRendering.getSelectedItem()).getCode());
- if (!Platform.isJS())
- /**
- * @j2sNative
+ /*
+ * Save Connections settings
*/
- {
- // Java only
- // Save Connections settings
- Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
- BrowserLauncher.resetBrowser();
- }
+ Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+
+ jalview.util.BrowserLauncher.resetBrowser();
// save user-defined and selected links
String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
if (menuLinks.isEmpty())
{
- Cache.removePropertyNoSave("SEQUENCE_LINKS");
+ Cache.applicationProperties.remove("SEQUENCE_LINKS");
}
else
{
- Cache.setPropertyNoSave("SEQUENCE_LINKS",
+ Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
menuLinks.toString());
}
String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
if (nonMenuLinks.isEmpty())
{
- Cache.removePropertyNoSave("STORED_LINKS");
+ Cache.applicationProperties.remove("STORED_LINKS");
}
else
{
- Cache.setPropertyNoSave("STORED_LINKS",
+ Cache.applicationProperties.setProperty("STORED_LINKS",
nonMenuLinks.toString());
}
- Cache.setPropertyNoSave("DEFAULT_URL",
+ Cache.applicationProperties.setProperty("DEFAULT_URL",
sequenceUrlLinks.getPrimaryUrlId());
- Cache.setPropertyNoSave("USE_PROXY",
+ Cache.applicationProperties.setProperty("USE_PROXY",
Boolean.toString(useProxy.isSelected()));
Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
}
if (!questionnaire.isSelected())
{
- Cache.setProperty(NOQUESTIONNAIRES, "true");
+ Cache.setProperty("NOQUESTIONNAIRES", "true");
}
else
{
// special - made easy to edit a property file to disable questionnaires
// by just adding the given line
- Cache.removeProperty(NOQUESTIONNAIRES);
+ Cache.removeProperty("NOQUESTIONNAIRES");
}
/*
* Save Output settings
*/
- Cache.setPropertyNoSave("BLC_JVSUFFIX",
+ Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
Boolean.toString(blcjv.isSelected()));
- Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
+ Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
Boolean.toString(clustaljv.isSelected()));
- Cache.setPropertyNoSave("FASTA_JVSUFFIX",
+ Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
Boolean.toString(fastajv.isSelected()));
- Cache.setPropertyNoSave("MSF_JVSUFFIX",
+ Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
Boolean.toString(msfjv.isSelected()));
- Cache.setPropertyNoSave("PFAM_JVSUFFIX",
+ Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
Boolean.toString(pfamjv.isSelected()));
- Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
+ Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
Boolean.toString(pileupjv.isSelected()));
- Cache.setPropertyNoSave("PIR_JVSUFFIX",
+ Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
Boolean.toString(pirjv.isSelected()));
- Cache.setPropertyNoSave("PIR_MODELLER",
+ Cache.applicationProperties.setProperty("PIR_MODELLER",
Boolean.toString(modellerOutput.isSelected()));
- Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
+ Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
Boolean.toString(embbedBioJSON.isSelected()));
- Cache.setPropertyNoSave(FIGURE_AUTOIDWIDTH,
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+
+ Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
- Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
+ Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
userIdWidth.getText());
/*
* Save Editing settings
*/
- Cache.setPropertyNoSave(AUTO_CALC_CONSENSUS,
+ Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
Boolean.toString(autoCalculateConsCheck.isSelected()));
- Cache.setPropertyNoSave(SORT_BY_TREE,
+ Cache.applicationProperties.setProperty("SORT_BY_TREE",
Boolean.toString(sortByTree.isSelected()));
- Cache.setPropertyNoSave(PAD_GAPS,
+ Cache.applicationProperties.setProperty("PAD_GAPS",
Boolean.toString(padGaps.isSelected()));
if (!Platform.isJS())
/*
* 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.applicationProperties.setProperty(BackupFiles.ENABLED,
+ Platform.isJS() ? Boolean.FALSE.toString()
+ : Boolean.toString(enableBackupFiles.isSelected()));
+ if (!Platform.isJS())
+ {
+ 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.getInstance().doConfigureStructurePrefs();
+ Desktop.instance.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_CONSENSUS, "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.setPropertyNoSave("DEFAULT_FILE_FORMAT",
+ Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
format.getName());
}
startupFileTextfield
boolean valid = false;
while (!valid)
{
- if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, 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.getDesktopPane(), link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.edit_sequence_url_link"),
JvOptionPane.OK_CANCEL_OPTION, -1,
null) == JvOptionPane.OK_OPTION)
super.showunconserved_actionPerformed(e);
}
- /**
- * not implemented -- returns empty list
- *
- * @return
- */
public static List<String> getGroupURLLinks()
{
return groupURLLinks;
} catch (NumberFormatException x)
{
userIdWidth.setText("");
- JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
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.
*/
- protected boolean validateChimeraPath()
+ private boolean validateChimeraPath()
{
if (chimeraPath.getText().trim().length() > 0)
{
File f = new File(chimeraPath.getText());
if (!f.canExecute())
{
- JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
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.getDesktopPane(),
+ int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
"", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
}
}
- protected class UrlListSelectionHandler implements ListSelectionListener
+ private class UrlListSelectionHandler implements ListSelectionListener
{
@Override
git://source.jalview.org / jalview.git / blobdiff