X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=da33f3970476685f0677c523d2a15dac080ed5c0;hb=7664ccad29d55ad2355d72feeac23d8bdd49a2a7;hp=473e3fc7acb4f4e6a495f6e538d6dc223ab6a92a;hpb=468328551c99e1bb06a6eccd8e564885fc251ac6;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 473e3fc..da33f39 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,28 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.bin.Cache; -import jalview.gui.Help.HelpId; -import jalview.gui.JalviewColourChooser.ColourChooserListener; -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; @@ -55,7 +33,7 @@ import java.util.ArrayList; import java.util.List; import javax.help.HelpSetException; -import javax.swing.JColorChooser; +import javax.swing.JComboBox; import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JPanel; @@ -73,6 +51,29 @@ import javax.swing.table.TableModel; 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! @@ -104,6 +105,10 @@ public class Preferences extends GPreferences 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"; @@ -122,6 +127,8 @@ public class Preferences extends GPreferences private static final int MAX_FONT_SIZE = 30; + private String previousProxyType; + /** * Holds name and link separated with | character. Sequence ID must be * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$ @@ -186,14 +193,31 @@ public class Preferences extends GPreferences */ public Preferences() { - super(); + new Preferences(0); + } + + public Preferences(int selectTab) + { + new Preferences(selectTab, null); + } + + public Preferences(int selectTab, String message) + { + super(selectTab, message); frame = new JInternalFrame(); frame.setContentPane(this); - 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; @@ -252,7 +276,7 @@ public class Preferences extends GPreferences 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)); @@ -326,10 +350,10 @@ public class Preferences extends GPreferences 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); @@ -339,15 +363,52 @@ public class Preferences extends GPreferences 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()); + } } }); @@ -487,10 +548,35 @@ public class Preferences extends GPreferences } } - 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 + proxyAuthPasswordTB.setText(Cache.proxyAuthPassword == null ? "" + : new String(Cache.proxyAuthPassword)); + setCustomProxyEnabled(); defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", "")); @@ -503,23 +589,9 @@ public class Preferences extends GPreferences /* * 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()); @@ -548,6 +620,45 @@ public class Preferences extends GPreferences annotations_actionPerformed(null); // update the display of the annotation // settings + + + /* + * Set Backups tab defaults + */ + loadLastSavedBackupsOptions(); + } + + /** + * 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 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); + } } /** @@ -674,9 +785,22 @@ public class Preferences extends GPreferences 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()); @@ -686,6 +810,10 @@ public class Preferences extends GPreferences */ 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 @@ -720,23 +848,9 @@ public class Preferences extends GPreferences 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()); + // Proxy settings + saveProxySettings(); - 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()) @@ -795,7 +909,34 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("PAD_GAPS", Boolean.toString(padGaps.isSelected())); - 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()); + Cache.saveProperties(); Desktop.instance.doConfigureStructurePrefs(); try @@ -806,6 +947,23 @@ public class Preferences extends GPreferences } } + public void saveProxySettings() + { + Cache.applicationProperties.setProperty("USE_PROXY", + customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM + : noProxy.isSelected() ? Cache.PROXYTYPE_NONE + : Cache.PROXYTYPE_SYSTEM); + 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 = proxyAuthPasswordTB.getPassword(); + Cache.setProxyPropertiesFromPreferences(previousProxyType); + } + /** * Do any necessary validation before saving settings. Return focus to the * first tab which fails validation. @@ -825,7 +983,7 @@ public class Preferences extends GPreferences @Override protected boolean validateStructure() { - return validateChimeraPath(); + return validateViewerPath(); } @@ -869,8 +1027,11 @@ public class Preferences extends GPreferences { try { - wsPrefs.updateWsMenuConfig(true); - wsPrefs.refreshWs_actionPerformed(e); + if (!Platform.isJS()) + { + wsPrefs.updateWsMenuConfig(true); + wsPrefs.refreshWs_actionPerformed(e); + } frame.setClosed(true); } catch (Exception ex) { @@ -1010,8 +1171,11 @@ public class Preferences extends GPreferences 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("."); @@ -1104,7 +1268,7 @@ public class Preferences extends GPreferences { useLegacyGap.setSelected(false); useLegacyGaps_actionPerformed(null); - showHiddenAtStart.setSelected(true); + showHiddenAtStart.setSelected(false); hiddenColour.setBackground( jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); } @@ -1126,12 +1290,12 @@ public class Preferences extends GPreferences } } 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(""); } } @@ -1143,19 +1307,20 @@ public class Preferences extends GPreferences } /** - * 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; } @@ -1164,23 +1329,57 @@ public class Preferences extends GPreferences } /** - * 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 paths = StructureManager.getChimeraPaths(); - paths.add(0, chimeraPath.getText()); + String viewerPath = ""; + List 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()) @@ -1189,12 +1388,13 @@ public class Preferences extends GPreferences 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)