X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=94f67f616c458c712118b3fe25074ff7a1682cb5;hb=4f77328104498504339216829abf5ea87e2791ec;hp=b1206a229e7f448066b142c5be315e1622831456;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index b1206a2..94f67f6 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -25,6 +25,7 @@ import jalview.bin.Cache; 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; @@ -37,7 +38,6 @@ 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; @@ -81,139 +81,43 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager; * @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; @@ -223,9 +127,9 @@ public class Preferences extends GPreferences * 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 @@ -235,17 +139,7 @@ public class Preferences extends GPreferences * (TODO: proper escape for using | to separate ids or sequences */ - public static final List 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 groupURLLinks; static { // get links selected to be in the menu (SEQUENCE_LINKS) @@ -271,7 +165,7 @@ public class Preferences extends GPreferences * .properties file as '|' separated strings */ - groupURLLinks = new ArrayList<>(); // not implemented + groupURLLinks = new ArrayList<>(); } JInternalFrame frame; @@ -306,13 +200,11 @@ public class Preferences extends GPreferences 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, @@ -322,30 +214,30 @@ public class Preferences extends GPreferences /* * 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(); @@ -363,28 +255,28 @@ public class Preferences extends GPreferences 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 @@ -425,9 +317,9 @@ public class Preferences extends GPreferences 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 @@ -457,10 +349,6 @@ public class Preferences extends GPreferences 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() { @@ -471,7 +359,7 @@ public class Preferences extends GPreferences } }); - if (Cache.getDefault(MAP_WITH_SIFTS, false)) + if (Cache.getDefault("MAP_WITH_SIFTS", false)) { siftsMapping.setSelected(true); } @@ -481,7 +369,7 @@ public class Preferences extends GPreferences } SiftsSettings - .setMapWithSifts(Cache.getDefault(MAP_WITH_SIFTS, false)); + .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); /* * Set Connections tab defaults @@ -617,7 +505,7 @@ public class Preferences extends GPreferences 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)); /* @@ -626,10 +514,10 @@ public class Preferences extends GPreferences 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 @@ -648,9 +536,9 @@ public class Preferences extends GPreferences * 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 @@ -659,7 +547,10 @@ public class Preferences extends GPreferences /* * Set Backups tab defaults */ - loadLastSavedBackupsOptions(); + if (!Platform.isJS()) + { + loadLastSavedBackupsOptions(); + } } /** @@ -712,65 +603,65 @@ public class Preferences extends GPreferences /* * 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 @@ -778,24 +669,24 @@ public class Preferences extends GPreferences .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()); /* @@ -803,79 +694,73 @@ public class Preferences extends GPreferences */ 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()); @@ -902,50 +787,52 @@ public class Preferences extends GPreferences } 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()) @@ -956,25 +843,32 @@ public class Preferences extends GPreferences /* * 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); @@ -983,43 +877,6 @@ public class Preferences extends GPreferences } } - 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. @@ -1064,7 +921,7 @@ public class Preferences extends GPreferences FileFormatI format = chooser.getSelectedFormat(); if (format != null) { - Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT", + Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT", format.getName()); } startupFileTextfield @@ -1122,7 +979,7 @@ public class Preferences extends GPreferences 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) @@ -1174,7 +1031,7 @@ public class Preferences extends GPreferences 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) @@ -1261,11 +1118,6 @@ public class Preferences extends GPreferences super.showunconserved_actionPerformed(e); } - /** - * not implemented -- returns empty list - * - * @return - */ public static List getGroupURLLinks() { return groupURLLinks; @@ -1352,7 +1204,7 @@ public class Preferences extends GPreferences } 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"), @@ -1371,14 +1223,14 @@ public class Preferences extends GPreferences * 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); @@ -1417,7 +1269,7 @@ public class Preferences extends GPreferences 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, @@ -1490,7 +1342,7 @@ public class Preferences extends GPreferences } } - protected class UrlListSelectionHandler implements ListSelectionListener + private class UrlListSelectionHandler implements ListSelectionListener { @Override