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.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.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;
* @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";
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 $SEQUENCE_ID=/.possible | chars ./=$
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();
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
/*
* 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());
/*
* 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;
}
} catch (IllegalArgumentException e)
{
- Cache.log.error("Unknown structure viewer type: " + viewerType
+ Console.error("Unknown structure viewer type: " + viewerType
+ ", defaulting to Jmol");
type = ViewerType.JMOL;
}
{
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);
+ }
}
}
});
}
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);
+
+ String browserPref = Cache.getDefault("DEFAULT_BROWSER", "");
+ if (browserPref != null)
+ {
+ defaultBrowser.getModel().setSelectedItem(browserPref);
+ }
usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
// note antisense here: default is true
annotations_actionPerformed(null); // update the display of the annotation
// settings
-
-
+
/*
* Set Backups tab defaults
*/
loadLastSavedBackupsOptions();
+
+ /*
+ * Set Startup tab defaults
+ */
+
}
/**
comboBox.addItem(promptEachTimeOpt);
comboBox.addItem(lineArtOpt);
comboBox.addItem(textOpt);
-
+
/*
* JalviewJS doesn't support Lineart so force it to Text
*/
return;
}
+ /*
+ * Set proxy settings first (to be before web services refresh)
+ */
+ saveProxySettings();
+
/*
* Save Visual settings
*/
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);
/*
* 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",
+ (String) defaultBrowser.getSelectedItem());
+ 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);
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())
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
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
}
}
+ 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.
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;
}
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
if (value == JFileChooser.APPROVE_OPTION)
{
- defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+ defaultBrowser.getModel().setSelectedItem(
+ chooser.getSelectedFile().getAbsolutePath());
}
}
}
if (!useLegacyGap.isSelected())
{
JalviewColourChooser.showColourChooser(this,
- MessageManager.getString("label.select_gap_colour"),
- gap);
+ MessageManager.getString("label.select_gap_colour"), gap);
}
}
public void hiddenColour_actionPerformed(JPanel hidden)
{
JalviewColourChooser.showColourChooser(this,
- MessageManager.getString("label.select_hidden_colour"),
- hidden);
+ MessageManager.getString("label.select_hidden_colour"), hidden);
}
@Override
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);
e.printStackTrace();
}
}
+ else if (showHelp == JvOptionPane.OK_OPTION)
+ {
+ this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
+ CompletableFuture<Void> 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)
+ {
+ }
+ });
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff