X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=06d3a602ee7a61439e590501d81fc16d01bccc55;hb=5837c2892545c25ef5a8bc75248a997b96cc8e4e;hp=00b2a38122f1313111427088f9e1ae0386077878;hpb=0fcc08f1f633aa9eae854ebe0c78b5fb75471898;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 00b2a38..06d3a60 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,25 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.bin.Cache; -import jalview.gui.Help.HelpId; -import jalview.gui.StructureViewer.ViewerType; -import jalview.io.FileFormatI; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GPreferences; -import jalview.jbgui.GSequenceLink; -import jalview.schemes.ColourSchemeProperty; -import jalview.urls.UrlLinkTableModel; -import jalview.urls.api.UrlProviderFactoryI; -import jalview.urls.api.UrlProviderI; -import jalview.urls.desktop.DesktopUrlProviderFactory; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.util.UrlConstants; -import jalview.ws.sifts.SiftsSettings; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -46,14 +27,13 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.awt.event.MouseEvent; import java.io.File; import java.util.ArrayList; import java.util.List; +import java.util.concurrent.CompletableFuture; import javax.help.HelpSetException; -import javax.swing.JColorChooser; -import javax.swing.JFileChooser; +import javax.swing.JComboBox; import javax.swing.JInternalFrame; import javax.swing.JPanel; import javax.swing.ListSelectionModel; @@ -69,7 +49,33 @@ import javax.swing.table.TableColumn; import javax.swing.table.TableModel; import javax.swing.table.TableRowSorter; +//import edu.stanford.ejalbert.launching.IBrowserLaunching; import ext.edu.ucsf.rbvi.strucviz2.StructureManager; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.bin.Cache; +import jalview.bin.Console; +import jalview.bin.MemorySetting; +import jalview.ext.pymol.PymolManager; +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.jbgui.GPreferences; +import jalview.jbgui.GSequenceLink; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemes; +import jalview.schemes.ResidueColourScheme; +import jalview.urls.UrlLinkTableModel; +import jalview.urls.api.UrlProviderFactoryI; +import jalview.urls.api.UrlProviderI; +import jalview.urls.desktop.DesktopUrlProviderFactory; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.UrlConstants; +import jalview.ws.sifts.SiftsSettings; /** * DOCUMENT ME! @@ -77,6 +83,10 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager; * @author $author$ * @version $Revision$ */ +/* + * for merge with Jalview-JS + public class Preferences extends GPreferences implements ApplicationSingletonI + */ public class Preferences extends GPreferences { public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; @@ -101,14 +111,32 @@ public class Preferences extends GPreferences public static final String CHIMERA_PATH = "CHIMERA_PATH"; + public static final String CHIMERAX_PATH = "CHIMERAX_PATH"; + + public static final String PYMOL_PATH = "PYMOL_PATH"; + public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE"; + 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 USE_LEGACY_GAP = "USE_LEGACY_GAP"; + + public static final String GAP_COLOUR = "GAP_COLOUR"; + + public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR"; + private static final int MIN_FONT_SIZE = 1; private static final int MAX_FONT_SIZE = 30; + private String previousProxyType; + + private static Preferences INSTANCE = null; // add "final" + /** * Holds name and link separated with | character. Sequence ID must be * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$ @@ -151,13 +179,11 @@ public class Preferences extends GPreferences * .properties file as '|' separated strings */ - groupURLLinks = new ArrayList(); + groupURLLinks = new ArrayList<>(); } JInternalFrame frame; - DasSourceBrowser dasSource; - private WsPreferences wsPrefs; private OptionsParam promptEachTimeOpt = new OptionsParam( @@ -170,21 +196,72 @@ public class Preferences extends GPreferences private OptionsParam textOpt = new OptionsParam( MessageManager.getString("action.text"), "Text"); + // get singleton Preferences instance + public static Preferences getInstance() + { + if (INSTANCE == null || INSTANCE.frame == null + || INSTANCE.frame.isClosed()) + { + INSTANCE = new Preferences(); + } + return INSTANCE; + + /* + * Replace code with the following for Jalvew-JS + Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class); + if (INSTANCE == null || INSTANCE.frame == null + || INSTANCE.frame.isClosed()) + { + ApplicationSingletonProvider.remove(Preferences.class); + INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class); + } + return INSTANCE; + */ + } + + public static void openPreferences() + { + openPreferences(null, null); + } + + public static void openPreferences(TabRef selectTab, String message) + { + Preferences p = getInstance(); + if (selectTab != null) + p.selectTab(selectTab, message); + p.frame.show(); + p.frame.moveToFront(); + p.frame.grabFocus(); + } + + public void selectTab(TabRef selectTab, String message) + { + this.selectTab(selectTab); + if (message != null) + this.setMessage(message); + this.frame.show(); + } + /** * Creates a new Preferences object. */ - public Preferences() + private Preferences() { super(); frame = new JInternalFrame(); frame.setContentPane(this); - dasSource = new DasSourceBrowser(); - dasTab.add(dasSource, BorderLayout.CENTER); - wsPrefs = new WsPreferences(); - wsTab.add(wsPrefs, BorderLayout.CENTER); + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { + wsPrefs = new WsPreferences(); + wsTab.add(wsPrefs, BorderLayout.CENTER); + } int width = 500, height = 450; - new jalview.util.Platform(); - if (Platform.isAMac()) + if (Platform.isAMacAndNotJS()) { width = 570; height = 480; @@ -208,18 +285,19 @@ public class Preferences extends GPreferences openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false)); showUnconserved .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false)); - showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", - false)); - showGroupConservation.setSelected(Cache.getDefault( - "SHOW_GROUP_CONSERVATION", false)); - showConsensHistogram.setSelected(Cache.getDefault( - "SHOW_CONSENSUS_HISTOGRAM", true)); - showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", - false)); - showNpTooltip.setSelected(Cache - .getDefault("SHOW_NPFEATS_TOOLTIP", true)); - showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", - true)); + showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false)); + showGroupConsensus + .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false)); + showGroupConservation.setSelected( + Cache.getDefault("SHOW_GROUP_CONSERVATION", false)); + showConsensHistogram.setSelected( + Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true)); + showConsensLogo + .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false)); + showNpTooltip + .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); + showDbRefTooltip + .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); String[] fonts = java.awt.GraphicsEnvironment .getLocalGraphicsEnvironment().getAvailableFontFamilyNames(); @@ -239,12 +317,12 @@ public class Preferences extends GPreferences fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif")); fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10")); - fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN - + "")); + fontStyleCB.setSelectedItem( + Cache.getDefault("FONT_STYLE", Font.PLAIN + "")); - smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false)); - scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, - false)); + smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true)); + scaleProteinToCdna + .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false)); idItalics.setSelected(Cache.getDefault("ID_ITALICS", true)); @@ -278,47 +356,118 @@ public class Preferences extends GPreferences startupCheckbox .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true)); startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE", - Cache.getDefault("www.jalview.org", "http://www.jalview.org") - + "/examples/exampleFile_2_3.jar")); + Cache.getDefault("www.jalview.org", "https://www.jalview.org") + + "/examples/exampleFile_2_7.jvp")); /* * Set Colours tab defaults */ - for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++) + protColour.addItem(ResidueColourScheme.NONE); + nucColour.addItem(ResidueColourScheme.NONE); + for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes()) { - protColour.addItem(ColourSchemeProperty.getColourName(i)); - nucColour.addItem(ColourSchemeProperty.getColourName(i)); + String name = cs.getSchemeName(); + protColour.addItem(name); + nucColour.addItem(name); } - String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None"); + String oldProp = Cache.getDefault(DEFAULT_COLOUR, + ResidueColourScheme.NONE); String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null); protColour.setSelectedItem(newProp != null ? newProp : oldProp); newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null); nucColour.setSelectedItem(newProp != null ? newProp : oldProp); - minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", - Color.orange)); - maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", - Color.red)); + minColour.setBackground( + Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); + maxColour.setBackground( + Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); /* - * Set Structure tab defaults. + * Set overview panel defaults */ - final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false); + gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP)); + hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN)); + useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false)); + gapLabel.setEnabled(!useLegacyGap.isSelected()); + gapColour.setEnabled(!useLegacyGap.isSelected()); + showHiddenAtStart + .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false)); + + /* + * Set Structure tab defaults + */ + final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true); structFromPdb.setSelected(structSelected); - useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false)); - useRnaView.setEnabled(structSelected); - addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false)); + addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true)); addSecondaryStructure.setEnabled(structSelected); - addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false)); + addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true)); addTempFactor.setEnabled(structSelected); - structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY, - ViewerType.JMOL.name())); - chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, "")); - chimeraPath.addActionListener(new ActionListener() + + /* + * set choice of structure viewer, and path if saved as a preference; + * default to Jmol (first choice) if an unexpected value is found + */ + String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, + ViewerType.JMOL.name()); + structViewer.setSelectedItem(viewerType); + String viewerPath = ""; + ViewerType type = null; + try + { + type = ViewerType.valueOf(viewerType); + switch (type) + { + case JMOL: + break; + case CHIMERA: + viewerPath = Cache.getDefault(CHIMERA_PATH, ""); + break; + case CHIMERAX: + viewerPath = Cache.getDefault(CHIMERAX_PATH, ""); + break; + case PYMOL: + viewerPath = Cache.getDefault(PYMOL_PATH, ""); + break; + } + } catch (IllegalArgumentException e) + { + Console.error("Unknown structure viewer type: " + viewerType + + ", defaulting to Jmol"); + type = ViewerType.JMOL; + } + structureViewerPath.setText(viewerPath); + + structureViewerPath.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - validateChimeraPath(); + if (validateViewerPath()) + { + String path = structureViewerPath.getText(); + try + { + ViewerType type = ViewerType.valueOf(viewerType); + switch (type) + { + case JMOL: + break; + case CHIMERA: + Cache.setProperty(CHIMERA_PATH, path); + break; + case CHIMERAX: + Cache.setProperty(CHIMERAX_PATH, path); + break; + case PYMOL: + Cache.setProperty(PYMOL_PATH, path); + break; + } + } catch (IllegalArgumentException x) + { + Console.error("Failed to set path - unknown viewer type", x); + } + } } }); @@ -346,16 +495,17 @@ public class Preferences extends GPreferences List sortKeys = new ArrayList<>(); UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel(); - sortKeys.add(new RowSorter.SortKey(m.getDefaultColumn(), + sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(), SortOrder.DESCENDING)); sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(), SortOrder.DESCENDING)); - sortKeys.add(new RowSorter.SortKey(m.getNameColumn(), - SortOrder.ASCENDING)); + sortKeys.add( + new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING)); sorter.setSortKeys(sortKeys); - sorter.sort(); - + // BH 2018 setSortKeys will do the sort + // sorter.sort(); + // set up filtering ActionListener onReset; onReset = new ActionListener() @@ -404,35 +554,35 @@ public class Preferences extends GPreferences @Override public void changedUpdate(DocumentEvent e) { - sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag - + filterTB.getText())); + sorter.setRowFilter(RowFilter + .regexFilter(caseInsensitiveFlag + filterTB.getText())); } @Override public void removeUpdate(DocumentEvent e) { - sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag - + filterTB.getText())); + sorter.setRowFilter(RowFilter + .regexFilter(caseInsensitiveFlag + filterTB.getText())); } @Override public void insertUpdate(DocumentEvent e) { - sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag - + filterTB.getText())); + sorter.setRowFilter(RowFilter + .regexFilter(caseInsensitiveFlag + filterTB.getText())); } }); // set up list selection functionality - linkUrlTable.getSelectionModel().addListSelectionListener( - new UrlListSelectionHandler()); + linkUrlTable.getSelectionModel() + .addListSelectionListener(new UrlListSelectionHandler()); // set up radio buttons int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel()) - .getDefaultColumn(); + .getPrimaryColumn(); String onClickName = linkUrlTable.getColumnName(onClickCol); - linkUrlTable.getColumn(onClickName).setCellRenderer( - new RadioButtonRenderer()); + linkUrlTable.getColumn(onClickName) + .setCellRenderer(new RadioButtonRenderer()); linkUrlTable.getColumn(onClickName) .setCellEditor(new RadioButtonEditor()); @@ -442,8 +592,8 @@ public class Preferences extends GPreferences if (linkUrlTable.getModel().getColumnClass(column) .equals(Boolean.class)) { - TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn( - column); + TableColumn tableColumn = linkUrlTable.getColumnModel() + .getColumn(column); int preferredWidth = tableColumn.getMinWidth(); TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0, @@ -457,14 +607,36 @@ public class Preferences extends GPreferences } } - useProxy.setSelected(Cache.getDefault("USE_PROXY", false)); - useProxy_actionPerformed(); // make sure useProxy is correctly initialised - proxyServerTB.setEnabled(useProxy.isSelected()); - proxyPortTB.setEnabled(useProxy.isSelected()); - proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", "")); - proxyPortTB.setText(Cache.getDefault("PROXY_PORT", "")); - - defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", "")); + String proxyTypeString = Cache.getDefault("USE_PROXY", "false"); + previousProxyType = proxyTypeString; + switch (proxyTypeString) + { + case Cache.PROXYTYPE_NONE: + proxyType.setSelected(noProxy.getModel(), true); + break; + case Cache.PROXYTYPE_SYSTEM: + proxyType.setSelected(systemProxy.getModel(), true); + break; + case Cache.PROXYTYPE_CUSTOM: + proxyType.setSelected(customProxy.getModel(), true); + break; + default: + Console.warn( + "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): " + + proxyTypeString); + } + proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", "")); + proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", "")); + proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", "")); + proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", "")); + proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false)); + proxyAuthUsernameTB + .setText(Cache.getDefault("PROXY_AUTH_USERNAME", "")); + // we are not storing or retrieving proxy password from .jalview_properties + proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? "" + : new String(Cache.proxyAuthPassword)); + setCustomProxyEnabled(); + applyProxyButtonEnabled(false); usagestats.setSelected(Cache.getDefault("USAGESTATS", false)); // note antisense here: default is true @@ -475,28 +647,16 @@ public class Preferences extends GPreferences /* * Set Output tab defaults */ - epsRendering.addItem(promptEachTimeOpt); - epsRendering.addItem(lineArtOpt); - epsRendering.addItem(textOpt); - String defaultEPS = Cache.getDefault("EPS_RENDERING", - "Prompt each time"); - if (defaultEPS.equalsIgnoreCase("Text")) - { - epsRendering.setSelectedItem(textOpt); - } - else if (defaultEPS.equalsIgnoreCase("Lineart")) - { - epsRendering.setSelectedItem(lineArtOpt); - } - else - { - epsRendering.setSelectedItem(promptEachTimeOpt); - } + setupOutputCombo(epsRendering, "EPS_RENDERING"); + setupOutputCombo(htmlRendering, "HTML_RENDERING"); + setupOutputCombo(svgRendering, "SVG_RENDERING"); autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); userIdWidth.setEnabled(!autoIdWidth.isSelected()); userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); - Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH"); + Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"); userIdWidth.setText(wi == null ? "" : wi.toString()); + // TODO: refactor to use common enum via FormatAdapter and allow extension + // for new flat file formats blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true)); clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true)); fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true)); @@ -505,19 +665,62 @@ public class Preferences extends GPreferences pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true)); pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true)); modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false)); - embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", - true)); + embbedBioJSON + .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true)); /* * Set Editing tab defaults */ - autoCalculateConsCheck.setSelected(Cache.getDefault( - "AUTO_CALC_CONSENSUS", true)); + autoCalculateConsCheck + .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true)); padGaps.setSelected(Cache.getDefault("PAD_GAPS", false)); sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false)); annotations_actionPerformed(null); // update the display of the annotation // settings + + /* + * Set Backups tab defaults + */ + loadLastSavedBackupsOptions(); + + /* + * Set Startup tab defaults + */ + + } + + /** + * 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); + } } /** @@ -534,6 +737,11 @@ public class Preferences extends GPreferences return; } + /* + * Set proxy settings first (to be before web services refresh) + */ + saveProxySettings(); + /* * Save Visual settings */ @@ -554,20 +762,22 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected())); - Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB - .getSelectedItem().toString()); + Cache.applicationProperties.setProperty("GAP_SYMBOL", + gapSymbolCB.getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB - .getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB - .getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB - .getSelectedItem().toString()); + Cache.applicationProperties.setProperty("FONT_NAME", + fontNameCB.getSelectedItem().toString()); + Cache.applicationProperties.setProperty("FONT_STYLE", + fontStyleCB.getSelectedItem().toString()); + Cache.applicationProperties.setProperty("FONT_SIZE", + fontSizeCB.getSelectedItem().toString()); Cache.applicationProperties.setProperty("ID_ITALICS", Boolean.toString(idItalics.isSelected())); Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", Boolean.toString(showUnconserved.isSelected())); + Cache.applicationProperties.setProperty(SHOW_OCCUPANCY, + Boolean.toString(showOccupancy.isSelected())); Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", Boolean.toString(showGroupConsensus.isSelected())); Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION", @@ -593,8 +803,8 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected())); - Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby - .getSelectedItem().toString()); + Cache.applicationProperties.setProperty("SORT_ALIGNMENT", + sortby.getSelectedItem().toString()); // convert description of sort order to enum name for save SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder @@ -606,35 +816,55 @@ public class Preferences extends GPreferences } final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0; - Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean - .valueOf(showAutocalcFirst).toString()); + Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, + Boolean.valueOf(showAutocalcFirst).toString()); /* * Save Colours settings */ - Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour - .getSelectedItem().toString()); - Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour - .getSelectedItem().toString()); + Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, + protColour.getSelectedItem().toString()); + Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, + nucColour.getSelectedItem().toString()); Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground()); Cache.setColourProperty("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, + Boolean.toString(useLegacyGap.isSelected())); + Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START, + Boolean.toString(showHiddenAtStart.isSelected())); + + /* * Save Structure settings */ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN, Boolean.toString(addTempFactor.isSelected())); Cache.applicationProperties.setProperty(ADD_SS_ANN, Boolean.toString(addSecondaryStructure.isSelected())); - Cache.applicationProperties.setProperty(USE_RNAVIEW, - Boolean.toString(useRnaView.isSelected())); Cache.applicationProperties.setProperty(STRUCT_FROM_PDB, Boolean.toString(structFromPdb.isSelected())); - Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer - .getSelectedItem().toString()); - Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText()); + String viewer = structViewer.getSelectedItem().toString(); + String viewerPath = structureViewerPath.getText(); + Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer); + if (viewer.equals(ViewerType.CHIMERA.name())) + { + Cache.setOrRemove(CHIMERA_PATH, viewerPath); + } + else if (viewer.equals(ViewerType.CHIMERAX.name())) + { + Cache.setOrRemove(CHIMERAX_PATH, viewerPath); + } + else if (viewer.equals(ViewerType.PYMOL.name())) + { + Cache.setOrRemove(PYMOL_PATH, viewerPath); + } Cache.applicationProperties.setProperty("MAP_WITH_SIFTS", Boolean.toString(siftsMapping.isSelected())); SiftsSettings.setMapWithSifts(siftsMapping.isSelected()); @@ -644,13 +874,15 @@ public class Preferences extends GPreferences */ Cache.applicationProperties.setProperty("EPS_RENDERING", ((OptionsParam) epsRendering.getSelectedItem()).getCode()); + Cache.applicationProperties.setProperty("HTML_RENDERING", + ((OptionsParam) htmlRendering.getSelectedItem()).getCode()); + Cache.applicationProperties.setProperty("SVG_RENDERING", + ((OptionsParam) svgRendering.getSelectedItem()).getCode()); /* * Save Connections settings */ - Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText()); - - jalview.util.BrowserLauncher.resetBrowser(); + // Proxy settings set first (to catch web services) // save user-defined and selected links String menuLinks = sequenceUrlLinks.writeUrlsAsString(true); @@ -676,25 +908,8 @@ public class Preferences extends GPreferences } Cache.applicationProperties.setProperty("DEFAULT_URL", - sequenceUrlLinks.getDefaultUrlId()); - - Cache.applicationProperties.setProperty("USE_PROXY", - Boolean.toString(useProxy.isSelected())); - - Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText()); - - Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText()); + sequenceUrlLinks.getPrimaryUrlId()); - if (useProxy.isSelected()) - { - System.setProperty("http.proxyHost", proxyServerTB.getText()); - System.setProperty("http.proxyPort", proxyPortTB.getText()); - } - else - { - System.setProperty("http.proxyHost", ""); - System.setProperty("http.proxyPort", ""); - } Cache.setProperty("VERSION_CHECK", Boolean.toString(versioncheck.isSelected())); if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected()) @@ -740,7 +955,7 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", Boolean.toString(autoIdWidth.isSelected())); userIdWidth_actionPerformed(); - Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH", + Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH", userIdWidth.getText()); /* @@ -753,8 +968,49 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("PAD_GAPS", Boolean.toString(padGaps.isSelected())); - dasSource.saveProperties(Cache.applicationProperties); - wsPrefs.updateAndRefreshWsMenuConfig(false); + if (!Platform.isJS()) + { + wsPrefs.updateAndRefreshWsMenuConfig(false); + } + + /* + * Save Backups settings + */ + Cache.applicationProperties.setProperty(BackupFiles.ENABLED, + Boolean.toString(enableBackupFiles.isSelected())); + 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()); + + /* + * Save Memory Settings + */ + Cache.applicationProperties.setProperty( + MemorySetting.CUSTOMISED_SETTINGS, + Boolean.toString(customiseMemorySetting.isSelected())); + Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC, + Integer.toString(jvmMemoryPercentSlider.getValue())); + Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX, + jvmMemoryMaxTextField.getText()); + + /* + * save and close Preferences + */ + Cache.saveProperties(); Desktop.instance.doConfigureStructurePrefs(); try @@ -765,6 +1021,30 @@ public class Preferences extends GPreferences } } + public void saveProxySettings() + { + String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM + : noProxy.isSelected() ? Cache.PROXYTYPE_NONE + : Cache.PROXYTYPE_SYSTEM; + Cache.applicationProperties.setProperty("USE_PROXY", newProxyType); + Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText()); + Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText()); + Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText()); + Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText()); + Cache.setOrRemove("PROXY_AUTH", + Boolean.toString(proxyAuth.isSelected())); + Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText()); + Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword(); + Cache.setProxyPropertiesFromPreferences(previousProxyType); + if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM) + || !newProxyType.equals(previousProxyType)) + { + // force a re-lookup of ws if proxytype is custom or has changed + wsPrefs.update++; + } + previousProxyType = newProxyType; + } + /** * Do any necessary validation before saving settings. Return focus to the * first tab which fails validation. @@ -784,7 +1064,7 @@ public class Preferences extends GPreferences @Override protected boolean validateStructure() { - return validateChimeraPath(); + return validateViewerPath(); } @@ -794,12 +1074,13 @@ public class Preferences extends GPreferences @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); + JalviewFileChooser chooser = JalviewFileChooser + .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.select_startup_file")); + chooser.setDialogTitle( + MessageManager.getString("label.select_startup_file")); int value = chooser.showOpenDialog(this); @@ -809,10 +1090,10 @@ public class Preferences extends GPreferences if (format != null) { Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT", - format.toString()); + format.getName()); } - startupFileTextfield.setText(chooser.getSelectedFile() - .getAbsolutePath()); + startupFileTextfield + .setText(chooser.getSelectedFile().getAbsolutePath()); } } @@ -827,8 +1108,11 @@ 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) { @@ -847,6 +1131,7 @@ public class Preferences extends GPreferences conservation.setEnabled(annotations.isSelected()); quality.setEnabled(annotations.isSelected()); identity.setEnabled(annotations.isSelected()); + showOccupancy.setEnabled(annotations.isSelected()); showGroupConsensus.setEnabled(annotations.isSelected()); showGroupConservation.setEnabled(annotations.isSelected()); showConsensHistogram.setEnabled(annotations.isSelected() @@ -864,15 +1149,16 @@ public class Preferences extends GPreferences { if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, MessageManager.getString("label.new_sequence_url_link"), - JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION, -1, + null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { if (((UrlLinkTableModel) linkUrlTable.getModel()) .isUniqueName(link.getName())) { - ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow( - link.getName(), link.getURL()); + ((UrlLinkTableModel) linkUrlTable.getModel()) + .insertRow(link.getName(), link.getURL()); valid = true; } else @@ -898,27 +1184,34 @@ public class Preferences extends GPreferences if (index == -1) { // button no longer enabled if row is not selected - Cache.log.debug("Edit with no row selected in linkUrlTable"); + Console.debug("Edit with no row selected in linkUrlTable"); return; } - link.setName(linkUrlTable.getValueAt(index, 0).toString()); - link.setURL(linkUrlTable.getValueAt(index, 1).toString()); + int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getNameColumn(); + int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getUrlColumn(); + String oldName = linkUrlTable.getValueAt(index, nameCol).toString(); + link.setName(oldName); + link.setURL(linkUrlTable.getValueAt(index, urlCol).toString()); boolean valid = false; while (!valid) { if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, MessageManager.getString("label.edit_sequence_url_link"), - JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION, -1, + null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { - if (((UrlLinkTableModel) linkUrlTable.getModel()) - .isUniqueName(link.getName())) + if ((oldName.equals(link.getName())) + || (((UrlLinkTableModel) linkUrlTable.getModel()) + .isUniqueName(link.getName()))) { - linkUrlTable.setValueAt(link.getName(), index, 0); - linkUrlTable.setValueAt(link.getURL(), index, 1); + linkUrlTable.setValueAt(link.getName(), index, nameCol); + linkUrlTable.setValueAt(link.getURL(), index, urlCol); valid = true; } else @@ -943,7 +1236,7 @@ public class Preferences extends GPreferences if (index == -1) { // button no longer enabled if row is not selected - Cache.log.debug("Delete with no row selected in linkUrlTable"); + Console.debug("Delete with no row selected in linkUrlTable"); return; } else @@ -955,23 +1248,6 @@ public class Preferences extends GPreferences ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex); } - - @Override - public void defaultBrowser_mouseClicked(MouseEvent e) - { - JFileChooser chooser = new JFileChooser("."); - chooser.setDialogTitle(MessageManager - .getString("label.select_default_browser")); - - int value = chooser.showOpenDialog(this); - - if (value == JFileChooser.APPROVE_OPTION) - { - defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath()); - } - - } - /* * (non-Javadoc) * @@ -994,27 +1270,62 @@ 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); + } + + @Override + public void gapColour_actionPerformed(JPanel gap) + { + if (!useLegacyGap.isSelected()) { - panel.setBackground(col); + JalviewColourChooser.showColourChooser(this, + MessageManager.getString("label.select_gap_colour"), gap); } - panel.repaint(); + } + + @Override + public void hiddenColour_actionPerformed(JPanel hidden) + { + JalviewColourChooser.showColourChooser(this, + MessageManager.getString("label.select_hidden_colour"), hidden); + } + + @Override + protected void useLegacyGaps_actionPerformed(ActionEvent e) + { + boolean enabled = useLegacyGap.isSelected(); + if (enabled) + { + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP); + } + else + { + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + } + gapColour.setEnabled(!enabled); + gapLabel.setEnabled(!enabled); + } + + @Override + protected void resetOvDefaults_actionPerformed(ActionEvent e) + { + useLegacyGap.setSelected(false); + useLegacyGaps_actionPerformed(null); + showHiddenAtStart.setSelected(false); + hiddenColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); } @Override @@ -1034,11 +1345,12 @@ public class Preferences extends GPreferences } } catch (NumberFormatException x) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager - .getString("warn.user_defined_width_requirements"), + userIdWidth.setText(""); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager + .getString("warn.user_defined_width_requirements"), MessageManager.getString("label.invalid_id_column_width"), JvOptionPane.WARNING_MESSAGE); - userIdWidth.setText(""); } } @@ -1050,19 +1362,20 @@ public class Preferences extends GPreferences } /** - * Returns true if chimera path is to a valid executable, else show an error - * dialog. + * Returns true if structure viewer path is to a valid executable, else shows + * an error dialog. Does nothing if the path is empty, as is the case for Jmol + * (built in to Jalview) or when Jalview is left to try default paths. */ - private boolean validateChimeraPath() + private boolean validateViewerPath() { - if (chimeraPath.getText().trim().length() > 0) + if (structureViewerPath.getText().trim().length() > 0) { - File f = new File(chimeraPath.getText()); + File f = new File(structureViewerPath.getText()); if (!f.canExecute()) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.invalid_chimera_path"), - MessageManager.getString("label.invalid_name"), + MessageManager.getString("label.invalid_viewer_path"), + MessageManager.getString("label.invalid_viewer_path"), JvOptionPane.ERROR_MESSAGE); return false; } @@ -1071,23 +1384,57 @@ public class Preferences extends GPreferences } /** - * If Chimera is selected, check it can be found on default or user-specified - * path, if not show a warning/help dialog. + * If Chimera or ChimeraX or Pymol is selected, check it can be found on + * default or user-specified path, if not show a warning/help dialog */ @Override protected void structureViewer_actionPerformed(String selectedItem) { - if (!selectedItem.equals(ViewerType.CHIMERA.name())) + if (selectedItem.equals(ViewerType.JMOL.name())) { + structureViewerPath.setEnabled(false); + structureViewerPathLabel.setEnabled(false); return; } boolean found = false; + structureViewerPath.setEnabled(true); + structureViewerPathLabel.setEnabled(true); + structureViewerPathLabel.setText(MessageManager + .formatMessage("label.viewer_path", selectedItem)); /* - * Try user-specified and standard paths for Chimera executable. + * Try user-specified and standard paths for structure viewer executable */ - List paths = StructureManager.getChimeraPaths(); - paths.add(0, chimeraPath.getText()); + String viewerPath = ""; + List paths = null; + try + { + ViewerType viewerType = ViewerType.valueOf(selectedItem); + switch (viewerType) + { + case JMOL: + // dealt with above + break; + case CHIMERA: + viewerPath = Cache.getDefault(CHIMERA_PATH, ""); + paths = StructureManager.getChimeraPaths(false); + break; + case CHIMERAX: + viewerPath = Cache.getDefault(CHIMERAX_PATH, ""); + paths = StructureManager.getChimeraPaths(true); + break; + case PYMOL: + viewerPath = Cache.getDefault(PYMOL_PATH, ""); + paths = PymolManager.getPymolPaths(); + break; + } + } catch (IllegalArgumentException e) + { + // only valid entries should be in the drop-down + } + structureViewerPath.setText(viewerPath); + + paths.add(0, structureViewerPath.getText()); for (String path : paths) { if (new File(path.trim()).canExecute()) @@ -1096,17 +1443,19 @@ public class Preferences extends GPreferences break; } } + if (!found) { String[] options = { "OK", "Help" }; - int showHelp = JvOptionPane.showInternalOptionDialog( - Desktop.desktop, + int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop, JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.chimera_missing")), + MessageManager.getString("label.viewer_missing")), "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, null, options, options[0]); + if (showHelp == JvOptionPane.NO_OPTION) { + this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null); try { Help.showHelpWindow(HelpId.StructureViewer); @@ -1115,6 +1464,24 @@ public class Preferences extends GPreferences e.printStackTrace(); } } + else if (showHelp == JvOptionPane.OK_OPTION) + { + this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null); + CompletableFuture cf = CompletableFuture.runAsync(() -> { + try + { + for (int i = 0; i < 3; i++) + { + structureViewerPath.setBackground(Color.PINK); + Thread.sleep(500); + structureViewerPath.setBackground(Color.WHITE); + Thread.sleep(500); + } + } catch (InterruptedException e) + { + } + }); + } } } @@ -1172,7 +1539,7 @@ public class Preferences extends GPreferences return name.hashCode() + code.hashCode(); } } - + private class UrlListSelectionHandler implements ListSelectionListener { @@ -1212,5 +1579,5 @@ public class Preferences extends GPreferences editLink.setEnabled(false); } } -} + } }