X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=da33f3970476685f0677c523d2a15dac080ed5c0;hb=7664ccad29d55ad2355d72feeac23d8bdd49a2a7;hp=3070ca13b0a888e167427278ae51a4cd72ba12f4;hpb=09ec96d9ac0fd717d6cf32417d9916cca781d92c;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 3070ca1..da33f39 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,29 +20,6 @@ */ 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.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; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -56,7 +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; @@ -74,6 +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! @@ -107,6 +107,8 @@ public class Preferences extends GPreferences 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"; @@ -125,6 +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 $SEQUENCE_ID=/.possible | chars ./=$ @@ -189,14 +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; @@ -332,7 +353,7 @@ public class Preferences extends GPreferences .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); @@ -342,29 +363,51 @@ public class Preferences extends GPreferences addSecondaryStructure.setEnabled(structSelected); addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false)); 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()); structViewer.setSelectedItem(viewerType); - boolean isChimeraX = viewerType.equals(ViewerType.CHIMERAX.name()); - if (viewerType.equals(ViewerType.JMOL.name())) + String viewerPath = ""; + ViewerType type = null; + try { - chimeraPath.setText(""); - } - else + 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) { - chimeraPath.setText(Cache - .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, "")); + Cache.log.error("Unknown structure viewer type: " + viewerType + + ", defaulting to Jmol"); + type = ViewerType.JMOL; } - chimeraPath.addActionListener(new ActionListener() + structureViewerPath.setText(viewerPath); + + structureViewerPath.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - if (validateChimeraPath()) + if (validateViewerPath()) { Cache.setProperty(structViewer.getSelectedItem() .equals(ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH - : CHIMERA_PATH, chimeraPath.getText()); + : CHIMERA_PATH, structureViewerPath.getText()); } } }); @@ -401,7 +444,8 @@ public class Preferences extends GPreferences 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; @@ -418,7 +462,7 @@ public class Preferences extends GPreferences doReset.addActionListener(onReset); // filter to display only custom urls - final RowFilter customUrlFilter = new RowFilter<>() + final RowFilter customUrlFilter = new RowFilter() { @Override public boolean include( @@ -504,10 +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", "")); @@ -520,23 +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()); @@ -574,6 +629,39 @@ public class Preferences extends GPreferences } /** + * 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); + } + } + + /** * Save user selections on the Preferences tabs to the Cache and write out to * file. * @@ -697,12 +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()); - boolean isChimeraX = structViewer.getSelectedItem().toString() - .equals(ViewerType.CHIMERAX.name()); - Cache.setOrRemove(isChimeraX ? CHIMERAX_PATH : 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()); @@ -712,6 +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 @@ -746,23 +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()); + // Proxy settings + saveProxySettings(); - 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()) @@ -821,7 +909,10 @@ 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 @@ -856,6 +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. @@ -875,7 +983,7 @@ public class Preferences extends GPreferences @Override protected boolean validateStructure() { - return validateChimeraPath(); + return validateViewerPath(); } @@ -885,6 +993,7 @@ public class Preferences extends GPreferences @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); @@ -918,8 +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) { @@ -1058,17 +1170,25 @@ public class Preferences extends GPreferences @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.setText(chooser.getSelectedFile().getAbsolutePath()); + } } - } /* @@ -1093,27 +1213,17 @@ public class Preferences extends GPreferences @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 @@ -1121,28 +1231,18 @@ public class Preferences extends GPreferences { if (!useLegacyGap.isSelected()) { - Color col = JColorChooser.showDialog(this, + JalviewColourChooser.showColourChooser(this, MessageManager.getString("label.select_gap_colour"), - gapColour.getBackground()); - if (col != null) - { - gap.setBackground(col); - } - gap.repaint(); + gap); } } @Override public void hiddenColour_actionPerformed(JPanel hidden) { - Color col = JColorChooser.showDialog(this, + JalviewColourChooser.showColourChooser(this, MessageManager.getString("label.select_hidden_colour"), - hiddenColour.getBackground()); - if (col != null) - { - hidden.setBackground(col); - } - hidden.repaint(); + hidden); } @Override @@ -1190,12 +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(""); } } @@ -1207,19 +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; } @@ -1228,33 +1329,57 @@ public class Preferences extends GPreferences } /** - * If Chimera or ChimeraX 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.JMOL.name())) { - chimeraPath.setEnabled(false); - chimeraPathLabel.setEnabled(false); + structureViewerPath.setEnabled(false); + structureViewerPathLabel.setEnabled(false); return; } boolean found = false; - chimeraPath.setEnabled(true); - chimeraPathLabel.setEnabled(true); - chimeraPathLabel.setText(MessageManager - .formatMessage("label.chimera_path", selectedItem)); + 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 */ - boolean isChimeraX = selectedItem.equals(ViewerType.CHIMERAX.name()); - chimeraPath.setText(Cache - .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, "")); + 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); - List paths = StructureManager.getChimeraPaths(isChimeraX); - paths.add(0, chimeraPath.getText()); + paths.add(0, structureViewerPath.getText()); for (String path : paths) { if (new File(path.trim()).canExecute()) @@ -1263,12 +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)