*/
package jalview.gui;
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-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.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;
import javax.swing.table.TableRowSorter;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+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!
* @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";
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";
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(0, null);
+ }
+
+ public static void openPreferences(int selectTab, String message)
+ {
+ Preferences p = getInstance();
+ p.selectTab(selectTab);
+ p.setMessage(message);
+ p.frame.show();
+ p.frame.moveToFront();
+ p.frame.grabFocus();
+ }
+
/**
* Creates a new Preferences object.
*/
- public Preferences()
+ private Preferences()
{
super();
frame = new JInternalFrame();
frame.setContentPane(this);
- if (!Jalview.isJS())
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
wsPrefs = new WsPreferences();
wsTab.add(wsPrefs, BorderLayout.CENTER);
fontStyleCB.setSelectedItem(
Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
- smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+ smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
scaleProteinToCdna
.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
gapLabel.setEnabled(!useLegacyGap.isSelected());
gapColour.setEnabled(!useLegacyGap.isSelected());
showHiddenAtStart
- .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
+ .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);
structFromPdb.setSelected(structSelected);
addSecondaryStructure.setEnabled(structSelected);
addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
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)
+ {
+ Cache.log.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())
+ {
+ Cache.setProperty(structViewer.getSelectedItem()
+ .equals(ViewerType.CHIMERAX.name())
+ ? CHIMERAX_PATH
+ : CHIMERA_PATH, structureViewerPath.getText());
+ }
}
});
}
}
- 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", ""));
annotations_actionPerformed(null); // update the display of the annotation
// settings
+
+
+ /*
+ * Set Backups tab defaults
+ */
+ loadLastSavedBackupsOptions();
}
/**
/*
* JalviewJS doesn't support Lineart so force it to Text
*/
- String defaultOption = Jalview.isJS() ? "Text"
+ String defaultOption = Platform.isJS() ? "Text"
: Cache.getDefault(propertyKey, "Prompt each time");
if (defaultOption.equalsIgnoreCase("Text"))
{
return;
}
+ /*
+ * Set proxy settings first (to be before web services refresh)
+ */
+ saveProxySettings();
+
/*
* Save Visual settings
*/
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,
- structViewer.getSelectedItem().toString());
- Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+ 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());
/*
* 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("PAD_GAPS",
Boolean.toString(padGaps.isSelected()));
- if (!Jalview.isJS())
+ 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());
+
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.
@Override
protected boolean validateStructure()
{
- return validateChimeraPath();
+ return validateViewerPath();
}
{
try
{
- if (!Jalview.isJS())
+ if (!Platform.isJS())
{
wsPrefs.updateWsMenuConfig(true);
wsPrefs.refreshWs_actionPerformed(e);
public void defaultBrowser_mouseClicked(MouseEvent e)
{
// TODO: JAL-3048 not needed for j2s
- /*
- * @j2sNative
+ if (!Platform.isJS()) // BH 2019
+ /**
+ * Java only
+ *
+ * @j2sIgnore
*/
{
JFileChooser chooser = new JFileChooser(".");
{
useLegacyGap.setSelected(false);
useLegacyGaps_actionPerformed(null);
- showHiddenAtStart.setSelected(true);
+ showHiddenAtStart.setSelected(false);
hiddenColour.setBackground(
jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
}
}
/**
- * 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;
}
}
/**
- * 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<String> paths = StructureManager.getChimeraPaths();
- paths.add(0, chimeraPath.getText());
+ String viewerPath = "";
+ List<String> 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())
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)
git://source.jalview.org / jalview.git / blobdiff