*/
package jalview.gui;
-import static jalview.util.UrlConstants.EMBLEBI_STRING;
-import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static jalview.util.UrlConstants.SRS_STRING;
-
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.io.File;
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;
* @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 BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
+
+ 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_FULLSCREEN = "SHOW_FULLSCREEN";
+
+ 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_IDENTITY = "SHOW_IDENTITY";
+
+ 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;
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
*/
- public static Vector<String> 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
* (TODO: proper escape for using | to separate ids or sequences
*/
- public static List<String> groupURLLinks;
+ public static final List<String> groupURLLinks; // not implemented
+
+ public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
+ 600, 600);
+
static
{
- String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
- sequenceURLLinks = new Vector<String>();
-
- 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_STRING);
- if (srsPos > -1)
- {
- sequenceURLLinks.setElementAt(EMBLEBI_STRING, 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 ArrayList<String>();
+ groupURLLinks = new ArrayList<>(); // not implemented
}
- Vector<String> nameLinks, urlLinks;
-
JInternalFrame frame;
- DasSourceBrowser dasSource;
-
private WsPreferences wsPrefs;
private OptionsParam promptEachTimeOpt = new OptionsParam(
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;
- new jalview.util.Platform();
- if (Platform.isAMac())
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ wsPrefs = new WsPreferences();
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
+ }
+ int width = 700, height = 510; // BH 2019.07.12 added 60 to height and 40 to
+ // width (for Visual check boxes and Links
+ // "Double Click" header)
+ // BH 2019.09.24 added 20 to width
+ // (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,
/*
* 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();
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
/*
* 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.
addSecondaryStructure.setEnabled(structSelected);
addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
addTempFactor.setEnabled(structSelected);
- structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
- ViewerType.JMOL.name()));
+ if (!Platform.isJS())
+ {
+ 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()
{
}
});
- if (Cache.getDefault("MAP_WITH_SIFTS", false))
+ if (Cache.getDefault(MAP_WITH_SIFTS, false))
{
siftsMapping.setSelected(true);
}
}
SiftsSettings
- .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+ .setMapWithSifts(Cache.getDefault(MAP_WITH_SIFTS, false));
/*
* Set Connections tab defaults
*/
- nameLinks = new Vector<String>();
- urlLinks = new Vector<String>();
- for (int i = 0; i < sequenceURLLinks.size(); i++)
+
+ // set up sorting
+ linkUrlTable.setModel(dataModel);
+ final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
+ linkUrlTable.getModel());
+ linkUrlTable.setRowSorter(sorter);
+ List<RowSorter.SortKey> 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<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
+ {
+ @Override
+ public boolean include(
+ Entry<? extends TableModel, ? extends Object> entry)
+ {
+ return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
+ }
+ };
+
+ final TableRowSorter<TableModel> 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", ""));
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(promptEachTimeOpt);
- epsRendering.addItem(lineArtOpt);
- epsRendering.addItem(textOpt);
- String defaultEPS = Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
- if (defaultEPS.equalsIgnoreCase("Text"))
- {
- epsRendering.setSelectedItem(textOpt);
- }
- else if (defaultEPS.equalsIgnoreCase("Lineart"))
- {
- epsRendering.setSelectedItem(lineArtOpt);
- }
- else
- {
- epsRendering.setSelectedItem(promptEachTimeOpt);
- }
- 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));
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
+ */
+ if (!Platform.isJS())
+ {
+ 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<Object> comboBox,
+ String propertyKey)
+ {
+ comboBox.addItem(promptEachTimeOpt);
+ comboBox.addItem(lineArtOpt);
+ comboBox.addItem(textOpt);
+
+ /*
+ * JalviewJS doesn't support Lineart so force it to Text
+ */
+ String defaultOption = Platform.isJS() ? "Text"
+ : Cache.getDefault(propertyKey, "Prompt each time");
+ if (defaultOption.equalsIgnoreCase("Text"))
+ {
+ comboBox.setSelectedItem(textOpt);
+ }
+ else if (defaultOption.equalsIgnoreCase("Lineart"))
+ {
+ comboBox.setSelectedItem(lineArtOpt);
+ }
+ else
+ {
+ comboBox.setSelectedItem(promptEachTimeOpt);
+ }
}
/**
/*
* Save 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",
- startupFileTextfield.getText());
- Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
+ Cache.setPropertyNoSave("STARTUP_FILE", startupFileTextfield.getText());
+ 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,
- annSortOrder.name());
+ 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.setColourPropertyNoSave(ANNOTATIONCOLOUR_MIN,
minColour.getBackground());
- Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ Cache.setColourPropertyNoSave(ANNOTATIONCOLOUR_MAX,
maxColour.getBackground());
/*
+ * Save Overview settings
+ */
+ Cache.setColourPropertyNoSave(GAP_COLOUR, gapColour.getBackground());
+ Cache.setColourPropertyNoSave(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.applicationProperties.setProperty("MAP_WITH_SIFTS",
+ Cache.setPropertyNoSave(MAP_WITH_SIFTS,
Boolean.toString(siftsMapping.isSelected()));
SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
/*
* Save Output settings
*/
- Cache.applicationProperties.setProperty("EPS_RENDERING",
+ Cache.setPropertyNoSave("EPS_RENDERING",
((OptionsParam) epsRendering.getSelectedItem()).getCode());
+ Cache.setPropertyNoSave("HTML_RENDERING",
+ ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
+ Cache.setPropertyNoSave("SVG_RENDERING",
+ ((OptionsParam) svgRendering.getSelectedItem()).getCode());
- /*
- * Save Connections settings
+ if (!Platform.isJS())
+ /**
+ * @j2sNative
*/
- Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+ {
+ // Java only
+ // Save Connections settings
+ Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+ BrowserLauncher.resetBrowser();
+ }
- jalview.util.BrowserLauncher.resetBrowser();
+ // save user-defined and selected links
+ String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
+ if (menuLinks.isEmpty())
+ {
+ Cache.removePropertyNoSave("SEQUENCE_LINKS");
+ }
+ else
+ {
+ Cache.setPropertyNoSave("SEQUENCE_LINKS", menuLinks.toString());
+ }
- if (nameLinks.size() > 0)
+ String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
+ if (nonMenuLinks.isEmpty())
{
- StringBuffer links = new StringBuffer();
- sequenceURLLinks = new Vector<String>();
- 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());
}
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",
- userIdWidth.getText());
+ 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);
}
}
+ 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.
}
/**
- * DOCUMENT ME!
+ * Opens a file browser, and if a file is chosen, sets its path as the text of
+ * the 'startup file' text field
*/
@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)
+ {
+ /*
+ * saving properties to file is deferred to the 'OK' action
+ */
+ Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT", format.getName());
+ }
+ startupFileTextfield
+ .setText(chooser.getSelectedFile().getAbsolutePath());
}
}
{
try
{
- wsPrefs.updateWsMenuConfig(true);
- wsPrefs.refreshWs_actionPerformed(e);
+ if (!Platform.isJS())
+ {
+ wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
+ }
frame.setClosed(true);
} catch (Exception ex)
{
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()
@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
{
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;
@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());
+ }
}
-
}
/*
super.showunconserved_actionPerformed(e);
}
+ /**
+ * not implemented -- returns empty list
+ *
+ * @return
+ */
public static List<String> getGroupURLLinks()
{
return groupURLLinks;
@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
}
} 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);
}
}
* 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;
}
}
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
{
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);
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff