*/
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.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 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;
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!
* @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;
- public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
-
- public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+ private String previousProxyType;
- public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
- .darker();
+ private static Preferences INSTANCE = null; // add "final"
/**
* Holds name and link separated with | character. Sequence ID must be
JInternalFrame frame;
- DasSourceBrowser dasSource;
-
private WsPreferences wsPrefs;
private OptionsParam promptEachTimeOpt = new OptionsParam(
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);
- dasSource = new DasSourceBrowser();
- dasTab.add(dasSource, BorderLayout.CENTER);
- 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;
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));
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, OVERVIEW_DEFAULT_GAP));
- hiddenColour.setBackground(
- Cache.getDefaultColour(HIDDEN_COLOUR,
- 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());
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);
+ 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);
- 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)
+ {
+ Console.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())
+ {
+ 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);
+ }
+ }
}
});
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;
}
}
- 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", ""));
-
- defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
+ 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);
+
+ 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
/*
* 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());
- Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+ Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
userIdWidth.setText(wi == null ? "" : wi.toString());
+ // TODO: refactor to use common enum via FormatAdapter and allow extension
+ // for new flat file formats
blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
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<Object> 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);
+ }
}
/**
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()));
- Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
- structViewer.getSelectedItem().toString());
- Cache.setOrRemove(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());
*/
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",
+ (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",
- 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("FIGURE_AUTOIDWIDTH",
Boolean.toString(autoIdWidth.isSelected()));
userIdWidth_actionPerformed();
- Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+ Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
userIdWidth.getText());
/*
Cache.applicationProperties.setProperty("PAD_GAPS",
Boolean.toString(padGaps.isSelected()));
- dasSource.saveProperties(Cache.applicationProperties);
- wsPrefs.updateAndRefreshWsMenuConfig(false);
+ 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());
+
+ /*
+ * 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.
@Override
protected boolean validateStructure()
{
- return validateChimeraPath();
+ return validateViewerPath();
}
@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);
{
try
{
- wsPrefs.updateWsMenuConfig(true);
- wsPrefs.refreshWs_actionPerformed(e);
+ if (!Platform.isJS())
+ {
+ wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
+ }
frame.setClosed(true);
} catch (Exception ex)
{
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
@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.getModel().setSelectedItem(
+ chooser.getSelectedFile().getAbsolutePath());
+ }
}
-
}
/*
@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
{
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
boolean enabled = useLegacyGap.isSelected();
if (enabled)
{
- gapColour.setBackground(OVERVIEW_DEFAULT_LEGACY_GAP);
+ gapColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
}
else
{
- gapColour.setBackground(OVERVIEW_DEFAULT_GAP);
+ gapColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
}
gapColour.setEnabled(!enabled);
gapLabel.setEnabled(!enabled);
{
useLegacyGap.setSelected(false);
useLegacyGaps_actionPerformed(null);
- showHiddenAtStart.setSelected(true);
- hiddenColour.setBackground(OVERVIEW_DEFAULT_HIDDEN);
+ showHiddenAtStart.setSelected(false);
+ hiddenColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
}
@Override
}
} 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("");
}
}
}
/**
- * 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)
{
+ 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