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 ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
+import jalview.bin.MemorySetting;
import jalview.ext.pymol.PymolManager;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
* @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 $SEQUENCE_ID=/.possible | chars ./=$
/**
* Holds name and link separated with | character. Sequence IDS and Sequences
- * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
- * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
- * for first and second token specified after a pipe character at end |,|.
- * (TODO: proper escape for using | to separate ids or sequences
+ * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$
+ * or $SEQUENCES=/.possible | chars ./=$ and separation character for first and
+ * second token specified after a pipe character at end |,|. (TODO: proper
+ * escape for using | to separate ids or sequences
*/
public static List<String> groupURLLinks;
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 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);
/*
{
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)
+ {
+ Cache.log.error("Failed to set path - unknown viewer type",x);
+ }
}
}
});
}
}
- 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:
+ Cache.log.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", ""));
* Set Backups tab defaults
*/
loadLastSavedBackupsOptions();
+
+ /*
+ * Set Startup tab defaults
+ */
+
}
/**
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();
/*
* Save Connections settings
*/
+ // Proxy settings set first (to catch web services)
+
Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
jalview.util.BrowserLauncher.resetBrowser();
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())
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.
+ * Do any necessary validation before saving settings. Return focus to the first
+ * tab which fails validation.
*
* @return
*/
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
@Override
public void cancel_actionPerformed(ActionEvent e)
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
@Override
public void annotations_actionPerformed(ActionEvent e)
}
/**
- * 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
+ * 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 validateViewerPath()
}
/**
- * 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
+ * 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)
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