X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=7a4dbc01d29256833aee1b57c971dba56ca8c34a;hp=3070ca13b0a888e167427278ae51a4cd72ba12f4;hb=892a62261b740199fbc664c012107ae4392b7521;hpb=09ec96d9ac0fd717d6cf32417d9916cca781d92c diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 3070ca1..7a4dbc0 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,29 +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.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; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -54,9 +31,10 @@ 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.JComboBox; import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JPanel; @@ -73,7 +51,34 @@ 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.BrowserLauncher; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.UrlConstants; +import jalview.ws.sifts.SiftsSettings; /** * DOCUMENT ME! @@ -81,6 +86,10 @@ 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"; @@ -107,6 +116,8 @@ public class Preferences extends GPreferences 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"; @@ -125,6 +136,10 @@ public class Preferences extends GPreferences 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 $SEQUENCE_ID=/.possible | chars ./=$ @@ -184,19 +199,72 @@ 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); - 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; @@ -291,8 +359,8 @@ 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 @@ -319,12 +387,10 @@ public class Preferences extends GPreferences /* * Set overview panel defaults */ - gapColour.setBackground( - Cache.getDefaultColour(GAP_COLOUR, - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP)); - hiddenColour.setBackground( - Cache.getDefaultColour(HIDDEN_COLOUR, - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN)); + 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()); @@ -332,39 +398,78 @@ public class Preferences extends GPreferences .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false)); /* - * Set Structure tab defaults. + * Set Structure tab defaults */ - final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false); + 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); - String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()); + + /* + * 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); - boolean isChimeraX = viewerType.equals(ViewerType.CHIMERAX.name()); - if (viewerType.equals(ViewerType.JMOL.name())) + String viewerPath = ""; + ViewerType type = null; + try { - chimeraPath.setText(""); - } - else + 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) { - chimeraPath.setText(Cache - .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, "")); + Console.error("Unknown structure viewer type: " + viewerType + + ", defaulting to Jmol"); + type = ViewerType.JMOL; } - chimeraPath.addActionListener(new ActionListener() + structureViewerPath.setText(viewerPath); + + structureViewerPath.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - if (validateChimeraPath()) + if (validateViewerPath()) { - Cache.setProperty(structViewer.getSelectedItem() - .equals(ViewerType.CHIMERAX.name()) - ? CHIMERAX_PATH - : CHIMERA_PATH, chimeraPath.getText()); + 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); + } } } }); @@ -401,7 +506,8 @@ 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; @@ -418,7 +524,7 @@ public class Preferences extends GPreferences doReset.addActionListener(onReset); // filter to display only custom urls - final RowFilter customUrlFilter = new RowFilter<>() + final RowFilter customUrlFilter = new RowFilter() { @Override public boolean include( @@ -504,10 +610,36 @@ public class Preferences extends GPreferences } } - useProxy.setSelected(Cache.getDefault("USE_PROXY", false)); - useProxy_actionPerformed(); // make sure useProxy is correctly initialised - proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", "")); - proxyPortTB.setText(Cache.getDefault("PROXY_PORT", "")); + 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); defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", "")); @@ -520,23 +652,9 @@ 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()); @@ -565,12 +683,49 @@ public class Preferences extends GPreferences 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); + } } /** @@ -587,6 +742,11 @@ public class Preferences extends GPreferences return; } + /* + * Set proxy settings first (to be before web services refresh) + */ + saveProxySettings(); + /* * Save Visual settings */ @@ -693,16 +853,23 @@ public class Preferences extends GPreferences 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()); - boolean isChimeraX = structViewer.getSelectedItem().toString() - .equals(ViewerType.CHIMERAX.name()); - Cache.setOrRemove(isChimeraX ? CHIMERAX_PATH : 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()); @@ -712,13 +879,27 @@ 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()); + // Proxy settings set first (to catch web services) - jalview.util.BrowserLauncher.resetBrowser(); + Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText()); + if (Cache.getProperty("DEFAULT_BROWSER") != null) + { + System.setProperty(IBrowserLaunching.BROWSER_SYSTEM_PROPERTY, + Cache.getProperty("DEFAULT_BROWSER")); + } + else + { + System.clearProperty(IBrowserLaunching.BROWSER_SYSTEM_PROPERTY); + } + BrowserLauncher.resetBrowser(); // save user-defined and selected links String menuLinks = sequenceUrlLinks.writeUrlsAsString(true); @@ -746,23 +927,6 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("DEFAULT_URL", sequenceUrlLinks.getPrimaryUrlId()); - Cache.applicationProperties.setProperty("USE_PROXY", - Boolean.toString(useProxy.isSelected())); - - Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText()); - - Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText()); - - 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()) @@ -821,7 +985,10 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("PAD_GAPS", Boolean.toString(padGaps.isSelected())); - wsPrefs.updateAndRefreshWsMenuConfig(false); + if (!Platform.isJS()) + { + wsPrefs.updateAndRefreshWsMenuConfig(false); + } /* * Save Backups settings @@ -829,16 +996,16 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty(BackupFiles.ENABLED, Boolean.toString(enableBackupFiles.isSelected())); int preset = getComboIntStringKey(backupfilesPresetsCombo); - Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset)); + 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()); + Cache.applicationProperties.setProperty( + BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString()); } BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues @@ -846,6 +1013,21 @@ public class Preferences extends GPreferences 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 @@ -856,6 +1038,30 @@ 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. @@ -875,7 +1081,7 @@ public class Preferences extends GPreferences @Override protected boolean validateStructure() { - return validateChimeraPath(); + return validateViewerPath(); } @@ -885,6 +1091,7 @@ 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); @@ -918,8 +1125,11 @@ 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) { @@ -991,7 +1201,7 @@ 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; } @@ -1043,7 +1253,7 @@ 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 @@ -1058,17 +1268,25 @@ 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()); + } } - } /* @@ -1093,27 +1311,17 @@ 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 @@ -1121,28 +1329,16 @@ public class Preferences extends GPreferences { if (!useLegacyGap.isSelected()) { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_gap_colour"), - gapColour.getBackground()); - if (col != null) - { - gap.setBackground(col); - } - gap.repaint(); + JalviewColourChooser.showColourChooser(this, + MessageManager.getString("label.select_gap_colour"), gap); } } @Override public void hiddenColour_actionPerformed(JPanel hidden) { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_hidden_colour"), - hiddenColour.getBackground()); - if (col != null) - { - hidden.setBackground(col); - } - hidden.repaint(); + JalviewColourChooser.showColourChooser(this, + MessageManager.getString("label.select_hidden_colour"), hidden); } @Override @@ -1190,12 +1386,12 @@ public class Preferences extends GPreferences } } catch (NumberFormatException x) { + 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(""); } } @@ -1207,19 +1403,20 @@ 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; } @@ -1228,33 +1425,57 @@ public class Preferences extends GPreferences } /** - * If Chimera or ChimeraX 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.JMOL.name())) { - chimeraPath.setEnabled(false); - chimeraPathLabel.setEnabled(false); + structureViewerPath.setEnabled(false); + structureViewerPathLabel.setEnabled(false); return; } boolean found = false; - chimeraPath.setEnabled(true); - chimeraPathLabel.setEnabled(true); - chimeraPathLabel.setText(MessageManager - .formatMessage("label.chimera_path", selectedItem)); + 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 */ - boolean isChimeraX = selectedItem.equals(ViewerType.CHIMERAX.name()); - chimeraPath.setText(Cache - .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, "")); + 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); - List paths = StructureManager.getChimeraPaths(isChimeraX); - paths.add(0, chimeraPath.getText()); + paths.add(0, structureViewerPath.getText()); for (String path : paths) { if (new File(path.trim()).canExecute()) @@ -1263,16 +1484,19 @@ public class Preferences extends GPreferences break; } } + if (!found) { String[] options = { "OK", "Help" }; 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); @@ -1281,6 +1505,24 @@ 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) + { + } + }); + } } }