X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=38bc74cf410ff6e099f29e82ee6f2929f7f58a12;hb=ead01b555e8b1d6322cecdf7780222c73143a03a;hp=aa8369a0678f8c0029832663e4a7e1acbf0c5b52;hpb=14b1b2a878190d5fffda298c4b9a901c72c74ad3;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index aa8369a..38bc74c 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -24,6 +24,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; 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; @@ -36,6 +37,7 @@ 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; @@ -54,7 +56,7 @@ import java.util.ArrayList; 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.JPanel; @@ -79,43 +81,141 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager; * @author $author$ * @version $Revision$ */ +@SuppressWarnings("serial") public class Preferences extends GPreferences { - public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; + public static final String ADD_SS_ANN = "ADD_SS_ANN"; - public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; + 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 BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE"; + + public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS"; + + public static final String CHIMERA_PATH = "CHIMERA_PATH"; + + public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR"; 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 DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC"; + public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; - public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN"; + public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH"; - public static final String ADD_SS_ANN = "ADD_SS_ANN"; + public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH"; - public static final String USE_RNAVIEW = "USE_RNAVIEW"; + public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS"; - public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB"; + public static final String FONT_NAME = "FONT_NAME"; - public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY"; + public static final String FONT_SIZE = "FONT_SIZE"; - public static final String CHIMERA_PATH = "CHIMERA_PATH"; + public static final String FONT_STYLE = "FONT_STYLE"; - public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; + 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 PAD_GAPS = "PAD_GAPS"; + + public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT"; + + public static final String QUESTIONNAIRE = "QUESTIONNAIRE"; + + public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING"; + + public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS"; + + public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; + + public static final String SHOW_ANNOTATIONS = "SHOW_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 GAP_COLOUR = "GAP_COLOUR"; + 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 HIDDEN_COLOUR = "HIDDEN_COLOUR"; private static final int MIN_FONT_SIZE = 1; @@ -125,9 +225,9 @@ 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; + 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 @@ -137,7 +237,15 @@ public class Preferences extends GPreferences * (TODO: proper escape for using | to separate ids or sequences */ - public static List groupURLLinks; + public static final List groupURLLinks; // not implemented + + 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); + static { // get links selected to be in the menu (SEQUENCE_LINKS) @@ -163,13 +271,11 @@ public class Preferences extends GPreferences * .properties file as '|' separated strings */ - groupURLLinks = new ArrayList<>(); + groupURLLinks = new ArrayList<>(); // not implemented } JInternalFrame frame; - DasSourceBrowser dasSource; - private WsPreferences wsPrefs; private OptionsParam promptEachTimeOpt = new OptionsParam( @@ -190,16 +296,26 @@ public class Preferences extends GPreferences super(); frame = new JInternalFrame(); frame.setContentPane(this); - dasSource = new DasSourceBrowser(); - dasTab.add(dasSource, BorderLayout.CENTER); - wsPrefs = new WsPreferences(); - wsTab.add(wsPrefs, BorderLayout.CENTER); - int width = 500, height = 450; - new jalview.util.Platform(); - if (Platform.isAMac()) + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { + wsPrefs = new WsPreferences(); + wsTab.add(wsPrefs, BorderLayout.CENTER); + } + int width = 700, height = 510; // BH 2019.07.12 added 60 to height and 40 to + // width (for Visual check boxes and Links + // "Double Click" header) + // BH 2019.09.24 added 20 to width + // (structure panel was too small anyway, and I added a default dimension + // for Jmol + if (Platform.isAMacAndNotJS()) { width = 570; - height = 480; + height = 540; // BH 2019.07.12 added 30 } Desktop.addInternalFrame(frame, @@ -209,30 +325,30 @@ 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(); @@ -250,28 +366,28 @@ 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 @@ -312,9 +428,9 @@ 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 @@ -329,7 +445,7 @@ public class Preferences extends GPreferences 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. @@ -342,8 +458,15 @@ public class Preferences extends GPreferences addSecondaryStructure.setEnabled(structSelected); addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false)); addTempFactor.setEnabled(structSelected); + if (!Platform.isJS()) + { 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() { @@ -354,7 +477,7 @@ public class Preferences extends GPreferences } }); - if (Cache.getDefault("MAP_WITH_SIFTS", false)) + if (Cache.getDefault(MAP_WITH_SIFTS, false)) { siftsMapping.setSelected(true); } @@ -364,7 +487,7 @@ public class Preferences extends GPreferences } SiftsSettings - .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); + .setMapWithSifts(Cache.getDefault(MAP_WITH_SIFTS, false)); /* * Set Connections tab defaults @@ -386,7 +509,8 @@ public class Preferences extends GPreferences 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; @@ -499,33 +623,19 @@ 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)); /* * 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); - } - autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); + 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 @@ -544,12 +654,55 @@ 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 + + + /* + * Set Backups tab defaults + */ + if (!Platform.isJS()) + { + 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 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); + } } /** @@ -569,65 +722,64 @@ public class Preferences extends GPreferences /* * 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", - startupFileTextfield.getText()); - Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", + Cache.setPropertyNoSave("STARTUP_FILE", startupFileTextfield.getText()); + 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 @@ -635,94 +787,102 @@ public class Preferences extends GPreferences .forDescription(sortAnnBy.getSelectedItem().toString()); if (annSortOrder != null) { - Cache.applicationProperties.setProperty(SORT_ANNOTATIONS, - annSortOrder.name()); + 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.setColourPropertyNoSave(ANNOTATIONCOLOUR_MIN, minColour.getBackground()); - Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", + Cache.setColourPropertyNoSave(ANNOTATIONCOLOUR_MAX, maxColour.getBackground()); /* * Save Overview settings */ - Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground()); - Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground()); - Cache.applicationProperties.setProperty(USE_LEGACY_GAP, + Cache.setColourPropertyNoSave(GAP_COLOUR, gapColour.getBackground()); + Cache.setColourPropertyNoSave(HIDDEN_COLOUR, + hiddenColour.getBackground()); + 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.setPropertyNoSave(STRUCTURE_DIMENSIONS, + structureDimensions.getText()); // BH 2019.07.12 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", - menuLinks.toString()); + 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", - nonMenuLinks.toString()); + 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()); @@ -749,58 +909,77 @@ 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.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", - userIdWidth.getText()); + 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); @@ -809,6 +988,43 @@ 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. @@ -833,11 +1049,13 @@ public class Preferences extends GPreferences } /** - * DOCUMENT ME! + * Opens a file browser, and if a file is chosen, sets its path as the text of + * the 'startup file' text field */ @Override public void startupFileTextfield_mouseClicked() { + // TODO: JAL-3048 not needed for Jalview-JS String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser chooser = JalviewFileChooser .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); @@ -852,8 +1070,10 @@ public class Preferences extends GPreferences FileFormatI format = chooser.getSelectedFormat(); if (format != null) { - Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT", - format.getName()); + /* + * saving properties to file is deferred to the 'OK' action + */ + Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT", format.getName()); } startupFileTextfield .setText(chooser.getSelectedFile().getAbsolutePath()); @@ -871,8 +1091,11 @@ public class Preferences extends GPreferences { try { - wsPrefs.updateWsMenuConfig(true); - wsPrefs.refreshWs_actionPerformed(e); + if (!Platform.isJS()) + { + wsPrefs.updateWsMenuConfig(true); + wsPrefs.refreshWs_actionPerformed(e); + } frame.setClosed(true); } catch (Exception ex) { @@ -907,7 +1130,7 @@ public class Preferences extends GPreferences 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) @@ -959,7 +1182,7 @@ public class Preferences extends GPreferences 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) @@ -1011,17 +1234,25 @@ public class Preferences extends GPreferences @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()); + } } - } /* @@ -1038,6 +1269,11 @@ public class Preferences extends GPreferences super.showunconserved_actionPerformed(e); } + /** + * not implemented -- returns empty list + * + * @return + */ public static List getGroupURLLinks() { return groupURLLinks; @@ -1046,27 +1282,17 @@ public class Preferences extends GPreferences @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.setBackground(col); - } - panel.repaint(); + panel); } @Override @@ -1074,28 +1300,18 @@ public class Preferences extends GPreferences { if (!useLegacyGap.isSelected()) { - Color col = JColorChooser.showDialog(this, + JalviewColourChooser.showColourChooser(this, MessageManager.getString("label.select_gap_colour"), - gapColour.getBackground()); - if (col != null) - { - gap.setBackground(col); - } - gap.repaint(); + gap); } } @Override public void hiddenColour_actionPerformed(JPanel hidden) { - Color col = JColorChooser.showDialog(this, + JalviewColourChooser.showColourChooser(this, MessageManager.getString("label.select_hidden_colour"), - hiddenColour.getBackground()); - if (col != null) - { - hidden.setBackground(col); - } - hidden.repaint(); + hidden); } @Override @@ -1121,7 +1337,7 @@ public class Preferences extends GPreferences { useLegacyGap.setSelected(false); useLegacyGaps_actionPerformed(null); - showHiddenAtStart.setSelected(true); + showHiddenAtStart.setSelected(false); hiddenColour.setBackground( jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); } @@ -1143,12 +1359,12 @@ public class Preferences extends GPreferences } } catch (NumberFormatException x) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + userIdWidth.setText(""); + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager .getString("warn.user_defined_width_requirements"), MessageManager.getString("label.invalid_id_column_width"), JvOptionPane.WARNING_MESSAGE); - userIdWidth.setText(""); } } @@ -1163,14 +1379,14 @@ public class Preferences extends GPreferences * 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); @@ -1209,7 +1425,7 @@ public class Preferences extends GPreferences 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, @@ -1282,7 +1498,7 @@ public class Preferences extends GPreferences } } - private class UrlListSelectionHandler implements ListSelectionListener + protected class UrlListSelectionHandler implements ListSelectionListener { @Override