X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=da33f3970476685f0677c523d2a15dac080ed5c0;hb=7664ccad29d55ad2355d72feeac23d8bdd49a2a7;hp=8b33debd11d818a982d45f72215efbeef79c8224;hpb=20ee237bee8261a2e14299a90d97a88701d47733;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 8b33deb..da33f39 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,39 +20,60 @@ */ 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.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GPreferences; -import jalview.jbgui.GSequenceLink; -import jalview.schemes.ColourSchemeProperty; -import jalview.util.MessageManager; -import jalview.ws.sifts.SiftsSettings; - import java.awt.BorderLayout; import java.awt.Color; +import java.awt.Component; import java.awt.Dimension; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseEvent; import java.io.File; -import java.util.Collection; +import java.util.ArrayList; import java.util.List; -import java.util.StringTokenizer; -import java.util.Vector; import javax.help.HelpSetException; -import javax.swing.JColorChooser; +import javax.swing.JComboBox; import javax.swing.JFileChooser; import javax.swing.JInternalFrame; -import javax.swing.JOptionPane; import javax.swing.JPanel; +import javax.swing.ListSelectionModel; +import javax.swing.RowFilter; +import javax.swing.RowSorter; +import javax.swing.SortOrder; +import javax.swing.event.DocumentEvent; +import javax.swing.event.DocumentListener; +import javax.swing.event.ListSelectionEvent; +import javax.swing.event.ListSelectionListener; +import javax.swing.table.TableCellRenderer; +import javax.swing.table.TableColumn; +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! @@ -84,21 +105,37 @@ 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"; - public static final String HIDE_INTRONS = "HIDE_INTRONS"; + public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY"; + + public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START"; + + public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP"; + + public static final String GAP_COLOUR = "GAP_COLOUR"; + + public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR"; private static final int MIN_FONT_SIZE = 1; 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 $SEQUENCE_ID=/.possible | chars ./=$ */ - public static Vector sequenceURLLinks; + public static UrlProviderI sequenceUrlLinks; + + public static UrlLinkTableModel dataModel; /** * Holds name and link separated with | character. Sequence IDS and Sequences @@ -108,80 +145,82 @@ public class Preferences extends GPreferences * (TODO: proper escape for using | to separate ids or sequences */ - public static Vector groupURLLinks; + public static List groupURLLinks; static { - String string = Cache - .getDefault( - "SEQUENCE_LINKS", - "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"); - sequenceURLLinks = new Vector(); - - try + // get links selected to be in the menu (SEQUENCE_LINKS) + // and links entered by the user but not selected (STORED_LINKS) + String inMenuString = Cache.getDefault("SEQUENCE_LINKS", ""); + String notInMenuString = Cache.getDefault("STORED_LINKS", ""); + String defaultUrl = Cache.getDefault("DEFAULT_URL", + UrlConstants.DEFAULT_LABEL); + + // if both links lists are empty, add the DEFAULT_URL link + // otherwise we assume the default link is in one of the lists + if (inMenuString.isEmpty() && notInMenuString.isEmpty()) { - StringTokenizer st = new StringTokenizer(string, "|"); - while (st.hasMoreElements()) - { - String name = st.nextToken(); - String url = st.nextToken(); - // check for '|' within a regex - int rxstart = url.indexOf("$SEQUENCE_ID$"); - while (rxstart == -1 && url.indexOf("/=$") == -1) - { - url = url + "|" + st.nextToken(); - } - sequenceURLLinks.addElement(name + "|" + url); - } - } catch (Exception ex) - { - System.out.println(ex + "\nError parsing sequence links"); - } - { - // upgrade old SRS link - int srsPos = sequenceURLLinks - .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); - if (srsPos > -1) - { - sequenceURLLinks - .setElementAt( - "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$", - srsPos); - } + inMenuString = UrlConstants.DEFAULT_STRING; } + UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl, + inMenuString, notInMenuString); + sequenceUrlLinks = factory.createUrlProvider(); + dataModel = new UrlLinkTableModel(sequenceUrlLinks); /** * TODO: reformulate groupURL encoding so two or more can be stored in the * .properties file as '|' separated strings */ - groupURLLinks = new Vector(); + groupURLLinks = new ArrayList<>(); } - Vector nameLinks, urlLinks; - JInternalFrame frame; - DasSourceBrowser dasSource; - private WsPreferences wsPrefs; + private OptionsParam promptEachTimeOpt = new OptionsParam( + MessageManager.getString("label.prompt_each_time"), + "Prompt each time"); + + private OptionsParam lineArtOpt = new OptionsParam( + MessageManager.getString("label.lineart"), "Lineart"); + + private OptionsParam textOpt = new OptionsParam( + MessageManager.getString("action.text"), "Text"); + /** * Creates a new Preferences object. */ 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); - dasSource = new DasSourceBrowser(); - dasTab.add(dasSource, BorderLayout.CENTER); - wsPrefs = new WsPreferences(); - wsTab.add(wsPrefs, BorderLayout.CENTER); - int width = 500, height = 470; - if (new jalview.util.Platform().isAMac()) + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { + wsPrefs = new WsPreferences(); + wsTab.add(wsPrefs, BorderLayout.CENTER); + } + int width = 500, height = 450; + if (Platform.isAMacAndNotJS()) { width = 570; - height = 500; + height = 480; } Desktop.addInternalFrame(frame, @@ -202,18 +241,19 @@ public class Preferences extends GPreferences openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false)); showUnconserved .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false)); - showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", - false)); - showGroupConservation.setSelected(Cache.getDefault( - "SHOW_GROUP_CONSERVATION", false)); - showConsensHistogram.setSelected(Cache.getDefault( - "SHOW_CONSENSUS_HISTOGRAM", true)); - showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", - false)); - showNpTooltip.setSelected(Cache - .getDefault("SHOW_NPFEATS_TOOLTIP", true)); - showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", - true)); + showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false)); + showGroupConsensus + .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false)); + showGroupConservation.setSelected( + Cache.getDefault("SHOW_GROUP_CONSERVATION", false)); + showConsensHistogram.setSelected( + Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true)); + showConsensLogo + .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false)); + showNpTooltip + .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); + showDbRefTooltip + .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); String[] fonts = java.awt.GraphicsEnvironment .getLocalGraphicsEnvironment().getAvailableFontFamilyNames(); @@ -233,17 +273,16 @@ public class Preferences extends GPreferences fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif")); fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10")); - fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN - + "")); + fontStyleCB.setSelectedItem( + Cache.getDefault("FONT_STYLE", Font.PLAIN + "")); - smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false)); - scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, - false)); + smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true)); + scaleProteinToCdna + .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false)); idItalics.setSelected(Cache.getDefault("ID_ITALICS", true)); wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false)); - hideIntrons.setSelected(Cache.getDefault(HIDE_INTRONS, true)); gapSymbolCB.addItem("-"); gapSymbolCB.addItem("."); @@ -279,23 +318,42 @@ public class Preferences extends GPreferences /* * Set Colours tab defaults */ - for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++) + protColour.addItem(ResidueColourScheme.NONE); + nucColour.addItem(ResidueColourScheme.NONE); + for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes()) { - protColour.addItem(ColourSchemeProperty.getColourName(i)); - nucColour.addItem(ColourSchemeProperty.getColourName(i)); + String name = cs.getSchemeName(); + protColour.addItem(name); + nucColour.addItem(name); } - String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None"); + String oldProp = Cache.getDefault(DEFAULT_COLOUR, + ResidueColourScheme.NONE); String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null); protColour.setSelectedItem(newProp != null ? newProp : oldProp); newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null); nucColour.setSelectedItem(newProp != null ? newProp : oldProp); - minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", - Color.orange)); - maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", - Color.red)); + minColour.setBackground( + Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); + maxColour.setBackground( + Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); + + /* + * Set overview panel defaults + */ + 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, false)); /* - * Set Structure tab defaults. + * Set Structure tab defaults */ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false); structFromPdb.setSelected(structSelected); @@ -305,15 +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()); + } } }); @@ -332,22 +427,156 @@ public class Preferences extends GPreferences /* * Set Connections tab defaults */ - nameLinks = new Vector(); - urlLinks = new Vector(); - for (int i = 0; i < sequenceURLLinks.size(); i++) + + // set up sorting + linkUrlTable.setModel(dataModel); + final TableRowSorter sorter = new TableRowSorter<>( + linkUrlTable.getModel()); + linkUrlTable.setRowSorter(sorter); + List sortKeys = new ArrayList<>(); + + UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel(); + sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(), + SortOrder.DESCENDING)); + sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(), + SortOrder.DESCENDING)); + sortKeys.add( + new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING)); + + sorter.setSortKeys(sortKeys); + // BH 2018 setSortKeys will do the sort + // sorter.sort(); + + // set up filtering + ActionListener onReset; + onReset = new ActionListener() { - String link = sequenceURLLinks.elementAt(i).toString(); - nameLinks.addElement(link.substring(0, link.indexOf("|"))); - urlLinks.addElement(link.substring(link.indexOf("|") + 1)); - } + @Override + public void actionPerformed(ActionEvent e) + { + filterTB.setText(""); + sorter.setRowFilter(RowFilter.regexFilter("")); + } + + }; + doReset.addActionListener(onReset); + + // filter to display only custom urls + final RowFilter customUrlFilter = new RowFilter() + { + @Override + public boolean include( + Entry entry) + { + return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry); + } + }; + + final TableRowSorter customSorter = new TableRowSorter<>( + linkUrlTable.getModel()); + customSorter.setRowFilter(customUrlFilter); + + ActionListener onCustomOnly; + onCustomOnly = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + filterTB.setText(""); + sorter.setRowFilter(customUrlFilter); + } + }; + userOnly.addActionListener(onCustomOnly); + + filterTB.getDocument().addDocumentListener(new DocumentListener() + { + String caseInsensitiveFlag = "(?i)"; + + @Override + public void changedUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter + .regexFilter(caseInsensitiveFlag + filterTB.getText())); + } - updateLinkData(); + @Override + public void removeUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter + .regexFilter(caseInsensitiveFlag + filterTB.getText())); + } - useProxy.setSelected(Cache.getDefault("USE_PROXY", false)); - proxyServerTB.setEnabled(useProxy.isSelected()); - proxyPortTB.setEnabled(useProxy.isSelected()); - proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", "")); - proxyPortTB.setText(Cache.getDefault("PROXY_PORT", "")); + @Override + public void insertUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter + .regexFilter(caseInsensitiveFlag + filterTB.getText())); + } + }); + + // set up list selection functionality + linkUrlTable.getSelectionModel() + .addListSelectionListener(new UrlListSelectionHandler()); + + // set up radio buttons + int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getPrimaryColumn(); + String onClickName = linkUrlTable.getColumnName(onClickCol); + linkUrlTable.getColumn(onClickName) + .setCellRenderer(new RadioButtonRenderer()); + linkUrlTable.getColumn(onClickName) + .setCellEditor(new RadioButtonEditor()); + + // get boolean columns and resize those to min possible + for (int column = 0; column < linkUrlTable.getColumnCount(); column++) + { + if (linkUrlTable.getModel().getColumnClass(column) + .equals(Boolean.class)) + { + TableColumn tableColumn = linkUrlTable.getColumnModel() + .getColumn(column); + int preferredWidth = tableColumn.getMinWidth(); + + TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0, + column); + Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column); + int cwidth = c.getPreferredSize().width + + linkUrlTable.getIntercellSpacing().width; + preferredWidth = Math.max(preferredWidth, cwidth); + + tableColumn.setPreferredWidth(preferredWidth); + } + } + + 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", "")); @@ -360,17 +589,16 @@ public class Preferences extends GPreferences /* * Set Output tab defaults */ - epsRendering - .addItem(MessageManager.getString("label.prompt_each_time")); - epsRendering.addItem(MessageManager.getString("label.lineart")); - epsRendering.addItem(MessageManager.getString("action.text")); - epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING", - "Prompt each time")); + 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)); @@ -379,19 +607,58 @@ public class Preferences extends GPreferences pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true)); pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true)); modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false)); - embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", - true)); + embbedBioJSON + .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true)); /* * Set Editing tab defaults */ - autoCalculateConsCheck.setSelected(Cache.getDefault( - "AUTO_CALC_CONSENSUS", true)); + autoCalculateConsCheck + .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true)); padGaps.setSelected(Cache.getDefault("PAD_GAPS", false)); sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false)); 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); + } } /** @@ -428,20 +695,22 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected())); - Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB - .getSelectedItem().toString()); + Cache.applicationProperties.setProperty("GAP_SYMBOL", + gapSymbolCB.getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB - .getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB - .getSelectedItem().toString()); - Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB - .getSelectedItem().toString()); + Cache.applicationProperties.setProperty("FONT_NAME", + fontNameCB.getSelectedItem().toString()); + Cache.applicationProperties.setProperty("FONT_STYLE", + fontStyleCB.getSelectedItem().toString()); + Cache.applicationProperties.setProperty("FONT_SIZE", + fontSizeCB.getSelectedItem().toString()); Cache.applicationProperties.setProperty("ID_ITALICS", Boolean.toString(idItalics.isSelected())); Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", Boolean.toString(showUnconserved.isSelected())); + Cache.applicationProperties.setProperty(SHOW_OCCUPANCY, + Boolean.toString(showOccupancy.isSelected())); Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", Boolean.toString(showGroupConsensus.isSelected())); Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION", @@ -461,16 +730,14 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected())); - Cache.applicationProperties.setProperty(HIDE_INTRONS, - Boolean.toString(hideIntrons.isSelected())); Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText()); Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected())); - Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby - .getSelectedItem().toString()); + Cache.applicationProperties.setProperty("SORT_ALIGNMENT", + sortby.getSelectedItem().toString()); // convert description of sort order to enum name for save SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder @@ -482,22 +749,32 @@ public class Preferences extends GPreferences } final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0; - Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean - .valueOf(showAutocalcFirst).toString()); + Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, + Boolean.valueOf(showAutocalcFirst).toString()); /* * Save Colours settings */ - Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour - .getSelectedItem().toString()); - Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour - .getSelectedItem().toString()); + Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, + protColour.getSelectedItem().toString()); + Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, + nucColour.getSelectedItem().toString()); Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground()); Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", maxColour.getBackground()); /* + * Save Overview settings + */ + Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground()); + Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground()); + Cache.applicationProperties.setProperty(USE_LEGACY_GAP, + Boolean.toString(useLegacyGap.isSelected())); + Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START, + Boolean.toString(showHiddenAtStart.isSelected())); + + /* * Save Structure settings */ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN, @@ -508,9 +785,22 @@ public class Preferences extends GPreferences 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()); @@ -518,15 +808,12 @@ public class Preferences extends GPreferences /* * Save Output settings */ - if (epsRendering.getSelectedItem().equals("Prompt each time")) - { - Cache.applicationProperties.remove("EPS_RENDERING"); - } - else - { - Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering - .getSelectedItem().toString()); - } + 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 @@ -535,44 +822,35 @@ public class Preferences extends GPreferences jalview.util.BrowserLauncher.resetBrowser(); - if (nameLinks.size() > 0) + // save user-defined and selected links + String menuLinks = sequenceUrlLinks.writeUrlsAsString(true); + if (menuLinks.isEmpty()) { - StringBuffer links = new StringBuffer(); - sequenceURLLinks = new Vector(); - for (int i = 0; i < nameLinks.size(); i++) - { - sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" - + urlLinks.elementAt(i)); - links.append(sequenceURLLinks.elementAt(i).toString()); - links.append("|"); - } - // remove last "|" - links.setLength(links.length() - 1); - Cache.applicationProperties.setProperty("SEQUENCE_LINKS", - links.toString()); + Cache.applicationProperties.remove("SEQUENCE_LINKS"); } else { - Cache.applicationProperties.remove("SEQUENCE_LINKS"); + Cache.applicationProperties.setProperty("SEQUENCE_LINKS", + menuLinks.toString()); } - Cache.applicationProperties.setProperty("USE_PROXY", - Boolean.toString(useProxy.isSelected())); - - Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText()); - - Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText()); - - if (useProxy.isSelected()) + String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false); + if (nonMenuLinks.isEmpty()) { - System.setProperty("http.proxyHost", proxyServerTB.getText()); - System.setProperty("http.proxyPort", proxyPortTB.getText()); + Cache.applicationProperties.remove("STORED_LINKS"); } else { - System.setProperty("http.proxyHost", ""); - System.setProperty("http.proxyPort", ""); + Cache.applicationProperties.setProperty("STORED_LINKS", + nonMenuLinks.toString()); } + + Cache.applicationProperties.setProperty("DEFAULT_URL", + sequenceUrlLinks.getPrimaryUrlId()); + + // Proxy settings + saveProxySettings(); + Cache.setProperty("VERSION_CHECK", Boolean.toString(versioncheck.isSelected())); if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected()) @@ -618,7 +896,7 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", Boolean.toString(autoIdWidth.isSelected())); userIdWidth_actionPerformed(); - Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH", + Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH", userIdWidth.getText()); /* @@ -631,8 +909,34 @@ public class Preferences extends GPreferences 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()); + Cache.saveProperties(); Desktop.instance.doConfigureStructurePrefs(); try @@ -643,6 +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. @@ -662,7 +983,7 @@ public class Preferences extends GPreferences @Override protected boolean validateStructure() { - return validateChimeraPath(); + return validateViewerPath(); } @@ -672,24 +993,26 @@ public class Preferences extends GPreferences @Override public void startupFileTextfield_mouseClicked() { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { - "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", - "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF", - "PIR", "BLC", "Jalview" }, - jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); + // TODO: JAL-3048 not needed for Jalview-JS + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser chooser = JalviewFileChooser + .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.select_startup_file")); + chooser.setDialogTitle( + MessageManager.getString("label.select_startup_file")); int value = chooser.showOpenDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { - jalview.bin.Cache.applicationProperties.setProperty( - "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat()); - startupFileTextfield.setText(chooser.getSelectedFile() - .getAbsolutePath()); + FileFormatI format = chooser.getSelectedFormat(); + if (format != null) + { + Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT", + format.getName()); + } + startupFileTextfield + .setText(chooser.getSelectedFile().getAbsolutePath()); } } @@ -704,8 +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) { @@ -724,6 +1050,7 @@ public class Preferences extends GPreferences conservation.setEnabled(annotations.isSelected()); quality.setEnabled(annotations.isSelected()); identity.setEnabled(annotations.isSelected()); + showOccupancy.setEnabled(annotations.isSelected()); showGroupConsensus.setEnabled(annotations.isSelected()); showGroupConservation.setEnabled(annotations.isSelected()); showConsensHistogram.setEnabled(annotations.isSelected() @@ -735,21 +1062,29 @@ public class Preferences extends GPreferences @Override public void newLink_actionPerformed(ActionEvent e) { - GSequenceLink link = new GSequenceLink(); boolean valid = false; while (!valid) { - if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, MessageManager.getString("label.new_sequence_url_link"), - JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION, -1, + null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { - nameLinks.addElement(link.getName()); - urlLinks.addElement(link.getURL()); - updateLinkData(); - valid = true; + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isUniqueName(link.getName())) + { + ((UrlLinkTableModel) linkUrlTable.getModel()) + .insertRow(link.getName(), link.getURL()); + valid = true; + } + else + { + link.notifyDuplicate(); + continue; + } } } else @@ -764,36 +1099,47 @@ public class Preferences extends GPreferences { GSequenceLink link = new GSequenceLink(); - int index = linkNameList.getSelectedIndex(); + int index = linkUrlTable.getSelectedRow(); if (index == -1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.no_link_selected"), - MessageManager.getString("label.no_link_selected"), - JOptionPane.WARNING_MESSAGE); + // button no longer enabled if row is not selected + Cache.log.debug("Edit with no row selected in linkUrlTable"); return; } - link.setName(nameLinks.elementAt(index).toString()); - link.setURL(urlLinks.elementAt(index).toString()); + int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getNameColumn(); + int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getUrlColumn(); + String oldName = linkUrlTable.getValueAt(index, nameCol).toString(); + link.setName(oldName); + link.setURL(linkUrlTable.getValueAt(index, urlCol).toString()); boolean valid = false; while (!valid) { - - if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link, - MessageManager.getString("label.new_sequence_url_link"), - JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION) + if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + MessageManager.getString("label.edit_sequence_url_link"), + JvOptionPane.OK_CANCEL_OPTION, -1, + null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { - nameLinks.setElementAt(link.getName(), index); - urlLinks.setElementAt(link.getURL(), index); - updateLinkData(); - valid = true; + if ((oldName.equals(link.getName())) + || (((UrlLinkTableModel) linkUrlTable.getModel()) + .isUniqueName(link.getName()))) + { + linkUrlTable.setValueAt(link.getName(), index, nameCol); + linkUrlTable.setValueAt(link.getURL(), index, urlCol); + valid = true; + } + else + { + link.notifyDuplicate(); + continue; + } } } - else { break; @@ -804,40 +1150,45 @@ public class Preferences extends GPreferences @Override public void deleteLink_actionPerformed(ActionEvent e) { - int index = linkNameList.getSelectedIndex(); + int index = linkUrlTable.getSelectedRow(); + int modelIndex = -1; if (index == -1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.no_link_selected"), - MessageManager.getString("label.no_link_selected"), - JOptionPane.WARNING_MESSAGE); + // button no longer enabled if row is not selected + Cache.log.debug("Delete with no row selected in linkUrlTable"); return; } - nameLinks.removeElementAt(index); - urlLinks.removeElementAt(index); - updateLinkData(); - } + else + { + modelIndex = linkUrlTable.convertRowIndexToModel(index); + } - void updateLinkData() - { - linkNameList.setListData(nameLinks); - linkURLList.setListData(urlLinks); + // make sure we use the model index to delete, and not the table index + ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex); } @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()); + } } - } /* @@ -854,7 +1205,7 @@ public class Preferences extends GPreferences super.showunconserved_actionPerformed(e); } - public static Collection getGroupURLLinks() + public static List getGroupURLLinks() { return groupURLLinks; } @@ -862,27 +1213,64 @@ 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); + } + + @Override + public void gapColour_actionPerformed(JPanel gap) + { + if (!useLegacyGap.isSelected()) + { + JalviewColourChooser.showColourChooser(this, + MessageManager.getString("label.select_gap_colour"), + gap); + } + } + + @Override + public void hiddenColour_actionPerformed(JPanel hidden) + { + JalviewColourChooser.showColourChooser(this, + MessageManager.getString("label.select_hidden_colour"), + hidden); + } + + @Override + protected void useLegacyGaps_actionPerformed(ActionEvent e) + { + boolean enabled = useLegacyGap.isSelected(); + if (enabled) + { + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP); + } + else { - panel.setBackground(col); + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); } - panel.repaint(); + gapColour.setEnabled(!enabled); + gapLabel.setEnabled(!enabled); + } + + @Override + protected void resetOvDefaults_actionPerformed(ActionEvent e) + { + useLegacyGap.setSelected(false); + useLegacyGaps_actionPerformed(null); + showHiddenAtStart.setSelected(false); + hiddenColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); } @Override @@ -902,11 +1290,12 @@ public class Preferences extends GPreferences } } catch (NumberFormatException x) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager - .getString("warn.user_defined_width_requirements"), - MessageManager.getString("label.invalid_id_column_width"), - JOptionPane.WARNING_MESSAGE); userIdWidth.setText(""); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager + .getString("warn.user_defined_width_requirements"), + MessageManager.getString("label.invalid_id_column_width"), + JvOptionPane.WARNING_MESSAGE); } } @@ -918,20 +1307,21 @@ 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()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.invalid_chimera_path"), - MessageManager.getString("label.invalid_name"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.invalid_viewer_path"), + MessageManager.getString("label.invalid_viewer_path"), + JvOptionPane.ERROR_MESSAGE); return false; } } @@ -939,23 +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()) @@ -964,16 +1388,16 @@ public class Preferences extends GPreferences break; } } + if (!found) { String[] options = { "OK", "Help" }; - int showHelp = JOptionPane.showInternalOptionDialog( - Desktop.desktop, + int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop, JvSwingUtils.wrapTooltip(true, - MessageManager.getString("label.chimera_missing")), - "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE, + MessageManager.getString("label.viewer_missing")), + "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, null, options, options[0]); - if (showHelp == JOptionPane.NO_OPTION) + if (showHelp == JvOptionPane.NO_OPTION) { try { @@ -986,4 +1410,99 @@ public class Preferences extends GPreferences } } + public class OptionsParam + { + private String name; + + private String code; + + public OptionsParam(String name, String code) + { + this.name = name; + this.code = code; + } + + public String getName() + { + return name; + } + + public void setName(String name) + { + this.name = name; + } + + public String getCode() + { + return code; + } + + public void setCode(String code) + { + this.code = code; + } + + @Override + public String toString() + { + return name; + } + + @Override + public boolean equals(Object that) + { + if (!(that instanceof OptionsParam)) + { + return false; + } + return this.code.equalsIgnoreCase(((OptionsParam) that).code); + } + + @Override + public int hashCode() + { + return name.hashCode() + code.hashCode(); + } + } + + private class UrlListSelectionHandler implements ListSelectionListener + { + + @Override + public void valueChanged(ListSelectionEvent e) + { + ListSelectionModel lsm = (ListSelectionModel) e.getSource(); + + int index = lsm.getMinSelectionIndex(); + if (index == -1) + { + // no selection, so disable delete/edit buttons + editLink.setEnabled(false); + deleteLink.setEnabled(false); + return; + } + int modelIndex = linkUrlTable.convertRowIndexToModel(index); + + // enable/disable edit and delete link buttons + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isRowDeletable(modelIndex)) + { + deleteLink.setEnabled(true); + } + else + { + deleteLink.setEnabled(false); + } + + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isRowEditable(modelIndex)) + { + editLink.setEnabled(true); + } + else + { + editLink.setEnabled(false); + } + } + } }