X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=b1206a229e7f448066b142c5be315e1622831456;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=93988b5615bf1ef2d5679f87bde4fdb3503c37e1;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 93988b5..b1206a2 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -24,32 +24,54 @@ 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.FileFormatI; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GPreferences; import jalview.jbgui.GSequenceLink; -import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemes; +import jalview.schemes.ResidueColourScheme; +import jalview.urls.UrlLinkTableModel; +import jalview.urls.api.UrlProviderFactoryI; +import jalview.urls.api.UrlProviderI; +import jalview.urls.desktop.DesktopUrlProviderFactory; +import jalview.util.BrowserLauncher; import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.UrlConstants; +import jalview.ws.sifts.SiftsSettings; 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; @@ -59,33 +81,139 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager; * @author $author$ * @version $Revision$ */ +@SuppressWarnings("serial") public class Preferences extends GPreferences { - public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; + public static final String ADD_SS_ANN = "ADD_SS_ANN"; - public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; + public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN"; + + public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING"; + + public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX"; + + public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN"; + + public static final String ANTI_ALIAS = "ANTI_ALIAS"; + + public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS"; + + public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS"; + + public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS"; + + public static final String CHIMERA_PATH = "CHIMERA_PATH"; + + public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR"; public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR"; + public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC"; + public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT"; - public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC"; + public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; - public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN"; + public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH"; - public static final String ADD_SS_ANN = "ADD_SS_ANN"; + public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH"; - public static final String USE_RNAVIEW = "USE_RNAVIEW"; + public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS"; + + public static final String FONT_NAME = "FONT_NAME"; + + public static final String FONT_SIZE = "FONT_SIZE"; + + public static final String FONT_STYLE = "FONT_STYLE"; + + public static final String GAP_COLOUR = "GAP_COLOUR"; + + public static final String GAP_SYMBOL = "GAP_SYMBOL"; + + public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR"; + + public static final String HIDE_INTRONS = "HIDE_INTRONS"; + + public static final String ID_ITALICS = "ID_ITALICS"; + + public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL"; + + public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS"; + + public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES"; + + public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO"; + + public static final String NORMALISE_LOGO = "NORMALISE_LOGO"; + + public static final String PAD_GAPS = "PAD_GAPS"; + + public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT"; + + public static final String QUESTIONNAIRE = "QUESTIONNAIRE"; + + public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING"; + + public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS"; + + public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; + + public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS"; + + public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE"; + + public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS"; + + public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM"; + + public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO"; + + public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION"; + + public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP"; + + public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS"; + + public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION"; + + public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX"; + + public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP"; + + 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 SHOW_OVERVIEW = "SHOW_OVERVIEW"; + + public static final String SHOW_QUALITY = "SHOW_QUALITY"; + + public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED"; + + public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT"; + + public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; + + public static final String SORT_BY_TREE = "SORT_BY_TREE"; public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB"; public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY"; - public static final String CHIMERA_PATH = "CHIMERA_PATH"; + public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS"; - public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; + public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN"; + + public static final String USE_FULL_SO = "USE_FULL_SO"; + + public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP"; + + public static final String USE_RNAVIEW = "USE_RNAVIEW"; + + public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS"; + + public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT"; - public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE"; private static final int MIN_FONT_SIZE = 1; @@ -95,7 +223,9 @@ public class Preferences extends GPreferences * 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; // must be nonfinal for test + + public final static UrlLinkTableModel dataModel; /** * Holds name and link separated with | character. Sequence IDS and Sequences @@ -105,63 +235,59 @@ public class Preferences extends GPreferences * (TODO: proper escape for using | to separate ids or sequences */ - public static Vector groupURLLinks; + public static final List groupURLLinks; // not implemented + + public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE"; + + public static final String SHOW_IDENTITY = "SHOW_IDENTITY"; + + public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN"; + + public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension( + 600, 600); + 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 - { - 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("/=$") == -1) - { - url = url + "|" + st.nextToken(); - } - sequenceURLLinks.addElement(name + "|" + url); - } - } catch (Exception ex) + // get links selected to be in the menu (SEQUENCE_LINKS) + // and links entered by the user but not selected (STORED_LINKS) + String inMenuString = Cache.getDefault("SEQUENCE_LINKS", ""); + String notInMenuString = Cache.getDefault("STORED_LINKS", ""); + String defaultUrl = Cache.getDefault("DEFAULT_URL", + UrlConstants.DEFAULT_LABEL); + + // if both links lists are empty, add the DEFAULT_URL link + // otherwise we assume the default link is in one of the lists + if (inMenuString.isEmpty() && notInMenuString.isEmpty()) { - System.out.println(ex + "\nError parsing sequence links"); - } - { - // upgrade old SRS link - int srsPos = sequenceURLLinks - .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$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<>(); // not implemented } - 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. */ @@ -170,15 +296,23 @@ public class Preferences extends GPreferences super(); 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 = 450; - if (new jalview.util.Platform().isAMac()) + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { + wsPrefs = new WsPreferences(); + wsTab.add(wsPrefs, BorderLayout.CENTER); + } + int width = 500, height = 510; // BH 2019.07.12 added 60 to height + // (structure panel was too small anyway, and I added a default dimension + // for Jmol + if (Platform.isAMacAndNotJS()) { width = 570; - height = 480; + height = 540; // BH 2019.07.12 added 30 } Desktop.addInternalFrame(frame, @@ -188,29 +322,30 @@ public class Preferences extends GPreferences /* * Set Visual tab defaults */ - seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true)); - rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false)); - fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false)); - annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true)); - - conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true)); - quality.setSelected(Cache.getDefault("SHOW_QUALITY", true)); - identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true)); - openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false)); + seqLimit.setSelected(Cache.getDefault(SHOW_JVSUFFIX, true)); + rightAlign.setSelected(Cache.getDefault(RIGHT_ALIGN_IDS, false)); + fullScreen.setSelected(Cache.getDefault(SHOW_FULLSCREEN, false)); + annotations.setSelected(Cache.getDefault(SHOW_ANNOTATIONS, true)); + + conservation.setSelected(Cache.getDefault(SHOW_CONSERVATION, true)); + quality.setSelected(Cache.getDefault(SHOW_QUALITY, true)); + identity.setSelected(Cache.getDefault(SHOW_IDENTITY, true)); + 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)); + .setSelected(Cache.getDefault(SHOW_UNCONSERVED, false)); + 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(); @@ -228,28 +363,28 @@ public class Preferences extends GPreferences fontStyleCB.addItem("bold"); fontStyleCB.addItem("italic"); - fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif")); - fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10")); - fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN - + "")); + fontNameCB.setSelectedItem(Cache.getDefault(FONT_NAME, "SansSerif")); + fontSizeCB.setSelectedItem(Cache.getDefault(FONT_SIZE, "10")); + 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, false)); + scaleProteinToCdna + .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false)); - idItalics.setSelected(Cache.getDefault("ID_ITALICS", true)); + idItalics.setSelected(Cache.getDefault(ID_ITALICS, true)); - wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false)); + wrap.setSelected(Cache.getDefault(WRAP_ALIGNMENT, false)); gapSymbolCB.addItem("-"); gapSymbolCB.addItem("."); - gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-")); + gapSymbolCB.setSelectedItem(Cache.getDefault(GAP_SYMBOL, "-")); sortby.addItem("No sort"); sortby.addItem("Id"); sortby.addItem("Pairwise Identity"); - sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort")); + sortby.setSelectedItem(Cache.getDefault(SORT_ALIGNMENT, "No sort")); sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString()); sortAnnBy @@ -275,20 +410,39 @@ 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. @@ -301,8 +455,12 @@ 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())); + structViewer.setSelectedItem( + Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name())); + Dimension d = Cache.getDefaultDim(STRUCTURE_DIMENSIONS, + DEFAULT_STRUCTURE_DIMENSIONS); + String s = d.width + "," + d.height; + structureDimensions.setText(s); chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, "")); chimeraPath.addActionListener(new ActionListener() { @@ -313,23 +471,144 @@ public class Preferences extends GPreferences } }); + if (Cache.getDefault(MAP_WITH_SIFTS, false)) + { + siftsMapping.setSelected(true); + } + else + { + nwMapping.setSelected(true); + } + + SiftsSettings + .setMapWithSifts(Cache.getDefault(MAP_WITH_SIFTS, false)); + /* * 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("")); + } - updateLinkData(); + }; + 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())); + } + + @Override + public void removeUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter + .regexFilter(caseInsensitiveFlag + filterTB.getText())); + } + + @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); + } + } useProxy.setSelected(Cache.getDefault("USE_PROXY", false)); - proxyServerTB.setEnabled(useProxy.isSelected()); - proxyPortTB.setEnabled(useProxy.isSelected()); + useProxy_actionPerformed(); // make sure useProxy is correctly initialised proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", "")); proxyPortTB.setText(Cache.getDefault("PROXY_PORT", "")); @@ -338,23 +617,22 @@ public class Preferences extends GPreferences usagestats.setSelected(Cache.getDefault("USAGESTATS", false)); // note antisense here: default is true questionnaire - .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); + .setSelected(Cache.getProperty(NOQUESTIONNAIRES) == null); versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); /* * 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")); - autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); + 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)); @@ -363,19 +641,58 @@ 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)); - padGaps.setSelected(Cache.getDefault("PAD_GAPS", false)); - sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false)); + 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); + } } /** @@ -384,6 +701,7 @@ public class Preferences extends GPreferences * * @param e */ + @Override public void ok_actionPerformed(ActionEvent e) { if (!validateSettings()) @@ -394,147 +712,170 @@ public class Preferences extends GPreferences /* * Save Visual settings */ - Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", + Cache.setPropertyNoSave(SHOW_JVSUFFIX, Boolean.toString(seqLimit.isSelected())); - Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", + Cache.setPropertyNoSave(RIGHT_ALIGN_IDS, Boolean.toString(rightAlign.isSelected())); - Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", + Cache.setPropertyNoSave(SHOW_FULLSCREEN, Boolean.toString(fullScreen.isSelected())); - Cache.applicationProperties.setProperty("SHOW_OVERVIEW", + Cache.setPropertyNoSave(SHOW_OVERVIEW, Boolean.toString(openoverv.isSelected())); - Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", + Cache.setPropertyNoSave(SHOW_ANNOTATIONS, Boolean.toString(annotations.isSelected())); - Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Cache.setPropertyNoSave(SHOW_CONSERVATION, Boolean.toString(conservation.isSelected())); - Cache.applicationProperties.setProperty("SHOW_QUALITY", + Cache.setPropertyNoSave(SHOW_QUALITY, Boolean.toString(quality.isSelected())); - Cache.applicationProperties.setProperty("SHOW_IDENTITY", + Cache.setPropertyNoSave(SHOW_IDENTITY, Boolean.toString(identity.isSelected())); - Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB - .getSelectedItem().toString()); + Cache.setPropertyNoSave(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.setPropertyNoSave(FONT_NAME, + fontNameCB.getSelectedItem().toString()); + Cache.setPropertyNoSave(FONT_STYLE, + fontStyleCB.getSelectedItem().toString()); + Cache.setPropertyNoSave(FONT_SIZE, + fontSizeCB.getSelectedItem().toString()); - Cache.applicationProperties.setProperty("ID_ITALICS", + Cache.setPropertyNoSave(ID_ITALICS, Boolean.toString(idItalics.isSelected())); - Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", + Cache.setPropertyNoSave(SHOW_UNCONSERVED, Boolean.toString(showUnconserved.isSelected())); - Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", + Cache.setPropertyNoSave(SHOW_OCCUPANCY, + Boolean.toString(showOccupancy.isSelected())); + Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, Boolean.toString(showGroupConsensus.isSelected())); - Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION", + Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, Boolean.toString(showGroupConservation.isSelected())); - Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM", + Cache.setPropertyNoSave(SHOW_CONSENSUS_HISTOGRAM, Boolean.toString(showConsensHistogram.isSelected())); - Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", + Cache.setPropertyNoSave(SHOW_CONSENSUS_LOGO, Boolean.toString(showConsensLogo.isSelected())); - Cache.applicationProperties.setProperty("ANTI_ALIAS", + Cache.setPropertyNoSave(ANTI_ALIAS, Boolean.toString(smoothFont.isSelected())); - Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA, + Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA, Boolean.toString(scaleProteinToCdna.isSelected())); - Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", + Cache.setPropertyNoSave(SHOW_NPFEATS_TOOLTIP, Boolean.toString(showNpTooltip.isSelected())); - Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", + Cache.setPropertyNoSave(SHOW_DBREFS_TOOLTIP, Boolean.toString(showDbRefTooltip.isSelected())); - Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", + Cache.setPropertyNoSave(WRAP_ALIGNMENT, Boolean.toString(wrap.isSelected())); - Cache.applicationProperties.setProperty("STARTUP_FILE", + Cache.setPropertyNoSave("STARTUP_FILE", startupFileTextfield.getText()); - Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", + Cache.setPropertyNoSave("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected())); - Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby - .getSelectedItem().toString()); + Cache.setPropertyNoSave(SORT_ALIGNMENT, + sortby.getSelectedItem().toString()); // convert description of sort order to enum name for save SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder .forDescription(sortAnnBy.getSelectedItem().toString()); if (annSortOrder != null) { - Cache.applicationProperties.setProperty(SORT_ANNOTATIONS, + Cache.setPropertyNoSave(SORT_ANNOTATIONS, annSortOrder.name()); } final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0; - Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean - .valueOf(showAutocalcFirst).toString()); + Cache.setPropertyNoSave(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.setColourProperty("ANNOTATIONCOLOUR_MIN", + Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT, + protColour.getSelectedItem().toString()); + Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC, + nucColour.getSelectedItem().toString()); + Cache.setColourProperty(ANNOTATIONCOLOUR_MIN, minColour.getBackground()); - Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", + Cache.setColourProperty(ANNOTATIONCOLOUR_MAX, maxColour.getBackground()); /* + * Save Overview settings + */ + Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground()); + Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground()); + Cache.setPropertyNoSave(USE_LEGACY_GAP, + Boolean.toString(useLegacyGap.isSelected())); + Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START, + Boolean.toString(showHiddenAtStart.isSelected())); + + /* * Save Structure settings */ - Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN, + Cache.setPropertyNoSave(ADD_TEMPFACT_ANN, Boolean.toString(addTempFactor.isSelected())); - Cache.applicationProperties.setProperty(ADD_SS_ANN, + Cache.setPropertyNoSave(ADD_SS_ANN, Boolean.toString(addSecondaryStructure.isSelected())); - Cache.applicationProperties.setProperty(USE_RNAVIEW, + Cache.setPropertyNoSave(USE_RNAVIEW, Boolean.toString(useRnaView.isSelected())); - Cache.applicationProperties.setProperty(STRUCT_FROM_PDB, + Cache.setPropertyNoSave(STRUCT_FROM_PDB, Boolean.toString(structFromPdb.isSelected())); - Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer - .getSelectedItem().toString()); + Cache.setPropertyNoSave(STRUCTURE_DISPLAY, + structViewer.getSelectedItem().toString()); + Cache.setPropertyNoSave(STRUCTURE_DIMENSIONS, + structureDimensions.getText()); // BH 2019.07.12 Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText()); + Cache.setPropertyNoSave(MAP_WITH_SIFTS, + Boolean.toString(siftsMapping.isSelected())); + SiftsSettings.setMapWithSifts(siftsMapping.isSelected()); /* * Save Output settings */ - if (epsRendering.getSelectedItem().equals("Prompt each time")) + Cache.setPropertyNoSave("EPS_RENDERING", + ((OptionsParam) epsRendering.getSelectedItem()).getCode()); + Cache.setPropertyNoSave("HTML_RENDERING", + ((OptionsParam) htmlRendering.getSelectedItem()).getCode()); + Cache.setPropertyNoSave("SVG_RENDERING", + ((OptionsParam) svgRendering.getSelectedItem()).getCode()); + + if (!Platform.isJS()) + /** + * @j2sNative + */ + { + // Java only + // Save Connections settings + Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText()); + BrowserLauncher.resetBrowser(); + } + + // save user-defined and selected links + String menuLinks = sequenceUrlLinks.writeUrlsAsString(true); + if (menuLinks.isEmpty()) { - Cache.applicationProperties.remove("EPS_RENDERING"); + Cache.removePropertyNoSave("SEQUENCE_LINKS"); } else { - Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering - .getSelectedItem().toString()); + Cache.setPropertyNoSave("SEQUENCE_LINKS", + menuLinks.toString()); } - /* - * Save Connections settings - */ - Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText()); - - jalview.util.BrowserLauncher.resetBrowser(); - - if (nameLinks.size() > 0) + String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false); + if (nonMenuLinks.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.removePropertyNoSave("STORED_LINKS"); } else { - Cache.applicationProperties.remove("SEQUENCE_LINKS"); + Cache.setPropertyNoSave("STORED_LINKS", + nonMenuLinks.toString()); } - Cache.applicationProperties.setProperty("USE_PROXY", + Cache.setPropertyNoSave("DEFAULT_URL", + sequenceUrlLinks.getPrimaryUrlId()); + + Cache.setPropertyNoSave("USE_PROXY", Boolean.toString(useProxy.isSelected())); Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText()); @@ -561,58 +902,79 @@ public class Preferences extends GPreferences } if (!questionnaire.isSelected()) { - Cache.setProperty("NOQUESTIONNAIRES", "true"); + Cache.setProperty(NOQUESTIONNAIRES, "true"); } else { // special - made easy to edit a property file to disable questionnaires // by just adding the given line - Cache.removeProperty("NOQUESTIONNAIRES"); + Cache.removeProperty(NOQUESTIONNAIRES); } /* * Save Output settings */ - Cache.applicationProperties.setProperty("BLC_JVSUFFIX", + Cache.setPropertyNoSave("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected())); - Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", + Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected())); - Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", + Cache.setPropertyNoSave("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected())); - Cache.applicationProperties.setProperty("MSF_JVSUFFIX", + Cache.setPropertyNoSave("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected())); - Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", + Cache.setPropertyNoSave("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected())); - Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", + Cache.setPropertyNoSave("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected())); - Cache.applicationProperties.setProperty("PIR_JVSUFFIX", + Cache.setPropertyNoSave("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected())); - Cache.applicationProperties.setProperty("PIR_MODELLER", + Cache.setPropertyNoSave("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected())); - Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON", + Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON", Boolean.toString(embbedBioJSON.isSelected())); - jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected(); - - Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", + Cache.setPropertyNoSave(FIGURE_AUTOIDWIDTH, Boolean.toString(autoIdWidth.isSelected())); userIdWidth_actionPerformed(); - Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH", + Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH", userIdWidth.getText()); /* * Save Editing settings */ - Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", + Cache.setPropertyNoSave(AUTO_CALC_CONSENSUS, Boolean.toString(autoCalculateConsCheck.isSelected())); - Cache.applicationProperties.setProperty("SORT_BY_TREE", + Cache.setPropertyNoSave(SORT_BY_TREE, Boolean.toString(sortByTree.isSelected())); - Cache.applicationProperties.setProperty("PAD_GAPS", + Cache.setPropertyNoSave(PAD_GAPS, Boolean.toString(padGaps.isSelected())); - dasSource.saveProperties(Cache.applicationProperties); - wsPrefs.updateAndRefreshWsMenuConfig(false); + if (!Platform.isJS()) + { + wsPrefs.updateAndRefreshWsMenuConfig(false); + } + + /* + * Save Backups settings + */ + Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD, + Boolean.toString(backupfilesConfirmDelete.isSelected())); + Cache.setPropertyNoSave(BackupFiles.ENABLED, + Boolean.toString(enableBackupFiles.isSelected())); + Cache.setPropertyNoSave(BackupFiles.NO_MAX, + Boolean.toString(backupfilesKeepAll.isSelected())); + Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER, + Boolean.toString(suffixReverse.isSelected())); + Cache.setPropertyNoSave(BackupFiles.SUFFIX, + suffixTemplate.getText()); + Cache.setPropertyNoSave(BackupFiles.ROLL_MAX, + Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4))); + Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS, + Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3))); + Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET", + Integer.toString(getComboIntStringKey(backupfilesPresetsCombo))); + Cache.saveProperties(); - Desktop.instance.doConfigureStructurePrefs(); + Desktop.getInstance().doConfigureStructurePrefs(); try { frame.setClosed(true); @@ -621,6 +983,43 @@ public class Preferences extends GPreferences } } + public static void setAppletDefaults() + { + + // http://www.jalview.org/old/v2_8/examples/appletParameters.html + + // showConservation true or false Default is true. + // showQuality true or false Default is true. + // showConsensus true or false Default is true. + // showFeatureSettings true or false Shows the feature settings window when + // startin + // showTreeBootstraps true or false (default is true) show or hide branch + // bootstraps + // showTreeDistances true or false (default is true) show or hide branch + // lengths + // showUnlinkedTreeNodes true or false (default is false) indicate if + // unassociated nodes should be highlighted in the tree view + // showUnconserved true of false (default is false) When true, only gaps and + // symbols different to the consensus sequence ions of the alignment + // showGroupConsensus true of false (default is false) When true, shows + // consensus annotation row for any groups on the alignment. (since 2.7) + // showGroupConservation true of false (default is false) When true, shows + // amino-acid property conservation annotation row for any groups on the + // showConsensusHistogram true of false (default is true) When true, shows + // the percentage occurence of the consensus symbol for each column as a + // showSequenceLogo true of false (default is false) When true, shows a + // sequence logo above the consensus sequence (overlaid above the Consensus + + Cache.setPropertyNoSave(SHOW_CONSERVATION, "true"); + Cache.setPropertyNoSave(SHOW_QUALITY, "false"); + Cache.setPropertyNoSave(SHOW_CONSENSUS, "true"); + Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false"); + Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false"); + Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false"); + + // TODO -- just a start here + } + /** * Do any necessary validation before saving settings. Return focus to the * first tab which fails validation. @@ -647,26 +1046,29 @@ public class Preferences extends GPreferences /** * DOCUMENT ME! */ + @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.setPropertyNoSave("DEFAULT_FILE_FORMAT", + format.getName()); + } + startupFileTextfield + .setText(chooser.getSelectedFile().getAbsolutePath()); } } @@ -676,12 +1078,16 @@ public class Preferences extends GPreferences * @param e * DOCUMENT ME! */ + @Override public void cancel_actionPerformed(ActionEvent e) { try { - wsPrefs.updateWsMenuConfig(true); - wsPrefs.refreshWs_actionPerformed(e); + if (!Platform.isJS()) + { + wsPrefs.updateWsMenuConfig(true); + wsPrefs.refreshWs_actionPerformed(e); + } frame.setClosed(true); } catch (Exception ex) { @@ -694,11 +1100,13 @@ public class Preferences extends GPreferences * @param e * DOCUMENT ME! */ + @Override public void annotations_actionPerformed(ActionEvent e) { 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() @@ -707,23 +1115,32 @@ public class Preferences extends GPreferences && (identity.isSelected() || showGroupConsensus.isSelected())); } + @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.getDesktopPane(), 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 @@ -733,40 +1150,52 @@ public class Preferences extends GPreferences } } + @Override public void editLink_actionPerformed(ActionEvent e) { 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.getDesktopPane(), 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; @@ -774,41 +1203,48 @@ 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()); + } } - } /* @@ -818,13 +1254,19 @@ public class Preferences extends GPreferences * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event * .ActionEvent) */ + @Override protected void showunconserved_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub super.showunconserved_actionPerformed(e); } - public static Collection getGroupURLLinks() + /** + * not implemented -- returns empty list + * + * @return + */ + public static List getGroupURLLinks() { return groupURLLinks; } @@ -832,27 +1274,64 @@ 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()) { - panel.setBackground(col); + JalviewColourChooser.showColourChooser(this, + MessageManager.getString("label.select_gap_colour"), + gap); } - panel.repaint(); + } + + @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 + { + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + } + 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 @@ -872,11 +1351,12 @@ 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.getDesktopPane(), + MessageManager + .getString("warn.user_defined_width_requirements"), + MessageManager.getString("label.invalid_id_column_width"), + JvOptionPane.WARNING_MESSAGE); } } @@ -891,17 +1371,17 @@ public class Preferences extends GPreferences * Returns true if chimera path is to a valid executable, else show an error * dialog. */ - private boolean validateChimeraPath() + protected boolean validateChimeraPath() { if (chimeraPath.getText().trim().length() > 0) { File f = new File(chimeraPath.getText()); if (!f.canExecute()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.invalid_chimera_path"), MessageManager.getString("label.invalid_name"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); return false; } } @@ -937,13 +1417,12 @@ public class Preferences extends GPreferences if (!found) { String[] options = { "OK", "Help" }; - int showHelp = JOptionPane.showInternalOptionDialog( - Desktop.desktop, + int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(), JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.chimera_missing")), - "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE, + "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, null, options, options[0]); - if (showHelp == JOptionPane.NO_OPTION) + if (showHelp == JvOptionPane.NO_OPTION) { try { @@ -956,4 +1435,99 @@ 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(); + } + } + + protected 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); + } + } + } }