X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=c4f32c39f8acd7525386774a9cd73cc82d158595;hb=65ed1da9a1710a9ce132c7edfce54955dc1ddf99;hp=f337898415aeae7010b9338a52fa35093039faed;hpb=a934d28336923f2966aeac29f7d1a877e5db1cec;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index f337898..c4f32c3 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -27,14 +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.JComboBox; -import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JPanel; import javax.swing.ListSelectionModel; @@ -50,9 +49,12 @@ 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; @@ -81,6 +83,10 @@ import jalview.ws.sifts.SiftsSettings; * @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"; @@ -127,6 +133,10 @@ 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 $SEQUENCE_ID=/.possible | chars ./=$ @@ -146,6 +156,9 @@ public class Preferences extends GPreferences public static List groupURLLinks; static { + // don't populate with session properties + Cache.disableSessionProperties(); + // get links selected to be in the menu (SEQUENCE_LINKS) // and links entered by the user but not selected (STORED_LINKS) String inMenuString = Cache.getDefault("SEQUENCE_LINKS", ""); @@ -170,6 +183,9 @@ public class Preferences extends GPreferences */ groupURLLinks = new ArrayList<>(); + + // reenable + Cache.enableSessionProperties(); } JInternalFrame frame; @@ -178,7 +194,7 @@ public class Preferences extends GPreferences private OptionsParam promptEachTimeOpt = new OptionsParam( MessageManager.getString("label.prompt_each_time"), - "Prompt each time"); + LineartOptions.PROMPT_EACH_TIME); private OptionsParam lineArtOpt = new OptionsParam( MessageManager.getString("label.lineart"), "Lineart"); @@ -186,13 +202,63 @@ 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(); + // don't populate with session properties + Cache.disableSessionProperties(); + frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(this); if (!Platform.isJS()) /** @@ -300,8 +366,8 @@ 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 @@ -328,12 +394,10 @@ 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, + OverviewCanvas.OVERVIEW_DEFAULT_GAP)); + hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR, + OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN)); useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false)); gapLabel.setEnabled(!useLegacyGap.isSelected()); gapColour.setEnabled(!useLegacyGap.isSelected()); @@ -343,20 +407,19 @@ public class Preferences extends GPreferences /* * 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); /* * 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()); + String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, + ViewerType.JMOL.name()); structViewer.setSelectedItem(viewerType); String viewerPath = ""; ViewerType type = null; @@ -379,7 +442,7 @@ public class Preferences extends GPreferences } } catch (IllegalArgumentException e) { - Cache.log.error("Unknown structure viewer type: " + viewerType + Console.error("Unknown structure viewer type: " + viewerType + ", defaulting to Jmol"); type = ViewerType.JMOL; } @@ -392,10 +455,28 @@ public class Preferences extends GPreferences { if (validateViewerPath()) { - Cache.setProperty(structViewer.getSelectedItem() - .equals(ViewerType.CHIMERAX.name()) - ? CHIMERAX_PATH - : CHIMERA_PATH, structureViewerPath.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); + } } } }); @@ -537,28 +618,35 @@ public class Preferences extends GPreferences } String proxyTypeString = Cache.getDefault("USE_PROXY", "false"); + previousProxyType = proxyTypeString; switch (proxyTypeString) { - case "none": + case Cache.PROXYTYPE_NONE: proxyType.setSelected(noProxy.getModel(), true); break; - case "false": + case Cache.PROXYTYPE_SYSTEM: proxyType.setSelected(systemProxy.getModel(), true); break; - case "true": + case Cache.PROXYTYPE_CUSTOM: proxyType.setSelected(customProxy.getModel(), true); break; default: - String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): " - + proxyTypeString; - Cache.log.warn(message); + 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", "")); - - defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", "")); + 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 @@ -600,12 +688,18 @@ public class Preferences extends GPreferences annotations_actionPerformed(null); // update the display of the annotation // settings - - + /* * Set Backups tab defaults */ loadLastSavedBackupsOptions(); + + /* + * Set Startup tab defaults + */ + + // re-enable + Cache.enableSessionProperties(); } /** @@ -618,10 +712,12 @@ public class Preferences extends GPreferences protected void setupOutputCombo(JComboBox comboBox, String propertyKey) { + Cache.disableSessionProperties(); + comboBox.addItem(promptEachTimeOpt); comboBox.addItem(lineArtOpt); comboBox.addItem(textOpt); - + /* * JalviewJS doesn't support Lineart so force it to Text */ @@ -639,6 +735,8 @@ public class Preferences extends GPreferences { comboBox.setSelectedItem(promptEachTimeOpt); } + + Cache.enableSessionProperties(); } /** @@ -650,14 +748,22 @@ public class Preferences extends GPreferences @Override public void ok_actionPerformed(ActionEvent e) { + Cache.disableSessionProperties(); + if (!validateSettings()) { return; } + /* + * Set proxy settings first (to be before web services refresh) + */ + saveProxySettings(); + /* * Save Visual settings */ + Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected())); Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", @@ -761,14 +867,11 @@ 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())); String viewer = structViewer.getSelectedItem().toString(); String viewerPath = structureViewerPath.getText(); - Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, - viewer); + Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer); if (viewer.equals(ViewerType.CHIMERA.name())) { Cache.setOrRemove(CHIMERA_PATH, viewerPath); @@ -798,9 +901,7 @@ public class Preferences extends GPreferences /* * 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); @@ -828,36 +929,6 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("DEFAULT_URL", sequenceUrlLinks.getPrimaryUrlId()); - Cache.applicationProperties.setProperty("USE_PROXY", - customProxy.isSelected() ? "true" - : noProxy.isSelected() ? "none" : "false"); - - 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()); - - if (noProxy.isSelected()) - { - Cache.log.warn("Setting no proxy settings"); - Cache.setProxyProperties(null, null, null, null); - } - else if (customProxy.isSelected()) - { - Cache.log.warn("Setting custom proxy settings"); - Cache.setProxyProperties(proxyServerHttpTB.getText(), - proxyPortHttpTB.getText(), proxyServerHttpsTB.getText(), - proxyPortHttpsTB.getText()); - } - else // systemProxy should be selected and is sensible default - { - Cache.log.warn("Setting system proxy settings"); - Cache.resetProxyProperties(); - } - Cache.setProperty("VERSION_CHECK", Boolean.toString(versioncheck.isSelected())); if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected()) @@ -927,16 +998,16 @@ 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 @@ -944,6 +1015,21 @@ 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 @@ -952,6 +1038,36 @@ public class Preferences extends GPreferences } catch (Exception ex) { } + + Cache.enableSessionProperties(); + } + + public void saveProxySettings() + { + Cache.disableSessionProperties(); + + 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; + + Cache.enableSessionProperties(); } /** @@ -983,6 +1099,8 @@ public class Preferences extends GPreferences @Override public void startupFileTextfield_mouseClicked() { + Cache.disableSessionProperties(); + // TODO: JAL-3048 not needed for Jalview-JS String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser chooser = JalviewFileChooser @@ -1004,6 +1122,8 @@ public class Preferences extends GPreferences startupFileTextfield .setText(chooser.getSelectedFile().getAbsolutePath()); } + + Cache.enableSessionProperties(); } /** @@ -1093,7 +1213,7 @@ 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; } @@ -1145,7 +1265,7 @@ 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 @@ -1157,30 +1277,6 @@ public class Preferences extends GPreferences ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex); } - @Override - public void defaultBrowser_mouseClicked(MouseEvent e) - { - // 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); - - if (value == JFileChooser.APPROVE_OPTION) - { - defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath()); - } - } - } - /* * (non-Javadoc) * @@ -1222,8 +1318,7 @@ public class Preferences extends GPreferences if (!useLegacyGap.isSelected()) { JalviewColourChooser.showColourChooser(this, - MessageManager.getString("label.select_gap_colour"), - gap); + MessageManager.getString("label.select_gap_colour"), gap); } } @@ -1231,8 +1326,7 @@ public class Preferences extends GPreferences public void hiddenColour_actionPerformed(JPanel hidden) { JalviewColourChooser.showColourChooser(this, - MessageManager.getString("label.select_hidden_colour"), - hidden); + MessageManager.getString("label.select_hidden_colour"), hidden); } @Override @@ -1241,13 +1335,11 @@ public class Preferences extends GPreferences boolean enabled = useLegacyGap.isSelected(); if (enabled) { - gapColour.setBackground( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP); + gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP); } else { - gapColour.setBackground( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP); } gapColour.setEnabled(!enabled); gapLabel.setEnabled(!enabled); @@ -1259,8 +1351,7 @@ public class Preferences extends GPreferences useLegacyGap.setSelected(false); useLegacyGaps_actionPerformed(null); showHiddenAtStart.setSelected(false); - hiddenColour.setBackground( - jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); + hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN); } @Override @@ -1342,6 +1433,7 @@ public class Preferences extends GPreferences */ String viewerPath = ""; List paths = null; + Cache.disableSessionProperties(); try { ViewerType viewerType = ViewerType.valueOf(selectedItem); @@ -1367,6 +1459,7 @@ public class Preferences extends GPreferences { // only valid entries should be in the drop-down } + Cache.enableSessionProperties(); structureViewerPath.setText(viewerPath); paths.add(0, structureViewerPath.getText()); @@ -1387,8 +1480,10 @@ public class Preferences extends GPreferences 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); @@ -1397,6 +1492,24 @@ 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) + { + } + }); + } } }