X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=c4dcc6c68309f5c91011afd0259ac2a29b678ea6;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=d0f6cdbc3acff5baf472e4a188d028f0828bc039;hpb=42f4227ed213d422a87d3b22fc9e85d14ffaf53f;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index d0f6cdb..c4dcc6c 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! @@ -194,11 +194,18 @@ public class Preferences extends GPreferences super(); 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; @@ -334,7 +341,7 @@ 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); @@ -344,24 +351,46 @@ 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 { - structureViewerPath.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) { - structureViewerPath.setText(Cache - .getDefault(isChimeraX ? CHIMERAX_PATH : CHIMERA_PATH, "")); + 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) { - if (validateChimeraPath()) + if (validateViewerPath()) { Cache.setProperty(structViewer.getSelectedItem() .equals(ViewerType.CHIMERAX.name()) @@ -403,7 +432,8 @@ 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; @@ -522,23 +552,9 @@ 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()); @@ -576,6 +592,39 @@ 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. * @@ -724,6 +773,10 @@ 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 @@ -833,7 +886,10 @@ 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 @@ -887,7 +943,7 @@ public class Preferences extends GPreferences @Override protected boolean validateStructure() { - return validateChimeraPath(); + return validateViewerPath(); } @@ -897,6 +953,7 @@ 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); @@ -930,8 +987,11 @@ 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) { @@ -1070,17 +1130,25 @@ 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()); + } } - } /* @@ -1105,27 +1173,17 @@ 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 @@ -1133,28 +1191,18 @@ 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 @@ -1202,12 +1250,12 @@ 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(""); } } @@ -1219,10 +1267,11 @@ 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 (structureViewerPath.getText().trim().length() > 0) { @@ -1230,8 +1279,8 @@ public class Preferences extends GPreferences 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; } @@ -1256,16 +1305,40 @@ public class Preferences extends GPreferences structureViewerPath.setEnabled(true); structureViewerPathLabel.setEnabled(true); structureViewerPathLabel.setText(MessageManager - .formatMessage("label.chimera_path", selectedItem)); + .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()); - structureViewerPath.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, structureViewerPath.getText()); for (String path : paths) { @@ -1275,12 +1348,13 @@ 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)