X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=00b2a38122f1313111427088f9e1ae0386077878;hb=0fcc08f1f633aa9eae854ebe0c78b5fb75471898;hp=67e0f831b676d133a07b9363cc6b0c2ccd629803;hpb=43a0d0608b026a8a1dac00d9d8b28c0bf2153621;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 67e0f83..00b2a38 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,39 +20,57 @@ */ package jalview.gui; +import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; +import jalview.bin.Cache; +import jalview.gui.Help.HelpId; +import jalview.gui.StructureViewer.ViewerType; +import jalview.io.FileFormatI; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.jbgui.GPreferences; +import jalview.jbgui.GSequenceLink; +import jalview.schemes.ColourSchemeProperty; +import jalview.urls.UrlLinkTableModel; +import jalview.urls.api.UrlProviderFactoryI; +import jalview.urls.api.UrlProviderI; +import jalview.urls.desktop.DesktopUrlProviderFactory; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.UrlConstants; +import jalview.ws.sifts.SiftsSettings; + import java.awt.BorderLayout; import java.awt.Color; +import java.awt.Component; 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.JFileChooser; import javax.swing.JInternalFrame; -import javax.swing.JOptionPane; import javax.swing.JPanel; +import javax.swing.ListSelectionModel; +import javax.swing.RowFilter; +import javax.swing.RowSorter; +import javax.swing.SortOrder; +import javax.swing.event.DocumentEvent; +import javax.swing.event.DocumentListener; +import javax.swing.event.ListSelectionEvent; +import javax.swing.event.ListSelectionListener; +import javax.swing.table.TableCellRenderer; +import javax.swing.table.TableColumn; +import javax.swing.table.TableModel; +import javax.swing.table.TableRowSorter; import ext.edu.ucsf.rbvi.strucviz2.StructureManager; -import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.bin.Cache; -import jalview.gui.Help.HelpId; -import jalview.gui.StructureViewer.ViewerType; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GPreferences; -import jalview.jbgui.GSequenceLink; -import jalview.schemes.ColourSchemeProperty; -import jalview.util.MessageManager; - /** * DOCUMENT ME! * @@ -95,7 +113,9 @@ 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; + + public static UrlLinkTableModel dataModel; /** * Holds name and link separated with | character. Sequence IDS and Sequences @@ -105,63 +125,51 @@ public class Preferences extends GPreferences * (TODO: proper escape for using | to separate ids or sequences */ - public static Vector groupURLLinks; + public static List groupURLLinks; static { - String string = Cache - .getDefault( - "SEQUENCE_LINKS", - "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"); - sequenceURLLinks = new Vector(); - - try - { - 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("/=$") == -1) - { - url = url + "|" + st.nextToken(); - } - sequenceURLLinks.addElement(name + "|" + url); - } - } catch (Exception ex) - { - System.out.println(ex + "\nError parsing sequence links"); - } + // get links selected to be in the menu (SEQUENCE_LINKS) + // and links entered by the user but not selected (STORED_LINKS) + String inMenuString = Cache.getDefault("SEQUENCE_LINKS", ""); + String notInMenuString = Cache.getDefault("STORED_LINKS", ""); + String defaultUrl = Cache.getDefault("DEFAULT_URL", + UrlConstants.DEFAULT_LABEL); + + // if both links lists are empty, add the DEFAULT_URL link + // otherwise we assume the default link is in one of the lists + if (inMenuString.isEmpty() && notInMenuString.isEmpty()) { - // upgrade old SRS link - int srsPos = sequenceURLLinks - .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); - if (srsPos > -1) - { - sequenceURLLinks - .setElementAt( - "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$", - srsPos); - } + inMenuString = UrlConstants.DEFAULT_STRING; } + UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl, + inMenuString, notInMenuString); + sequenceUrlLinks = factory.createUrlProvider(); + dataModel = new UrlLinkTableModel(sequenceUrlLinks); /** * TODO: reformulate groupURL encoding so two or more can be stored in the * .properties file as '|' separated strings */ - groupURLLinks = new Vector(); + groupURLLinks = new ArrayList(); } - Vector nameLinks, urlLinks; - JInternalFrame frame; DasSourceBrowser dasSource; private WsPreferences wsPrefs; + private OptionsParam promptEachTimeOpt = new OptionsParam( + MessageManager.getString("label.prompt_each_time"), + "Prompt each time"); + + private OptionsParam lineArtOpt = new OptionsParam( + MessageManager.getString("label.lineart"), "Lineart"); + + private OptionsParam textOpt = new OptionsParam( + MessageManager.getString("action.text"), "Text"); + /** * Creates a new Preferences object. */ @@ -175,7 +183,8 @@ public class Preferences extends GPreferences wsPrefs = new WsPreferences(); wsTab.add(wsPrefs, BorderLayout.CENTER); int width = 500, height = 450; - if (new jalview.util.Platform().isAMac()) + new jalview.util.Platform(); + if (Platform.isAMac()) { width = 570; height = 480; @@ -263,8 +272,7 @@ public class Preferences extends GPreferences sortAutocalc.addItem("Autocalculated first"); sortAutocalc.addItem("Autocalculated last"); - final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, - true); + final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true); sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0) : sortAutocalc.getItemAt(1)); startupCheckbox @@ -298,8 +306,7 @@ public class Preferences extends GPreferences structFromPdb.setSelected(structSelected); useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false)); useRnaView.setEnabled(structSelected); - addSecondaryStructure - .setSelected(Cache.getDefault(ADD_SS_ANN, false)); + addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false)); addSecondaryStructure.setEnabled(structSelected); addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false)); addTempFactor.setEnabled(structSelected); @@ -315,21 +322,143 @@ 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.getDefaultColumn(), + SortOrder.DESCENDING)); + sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(), + SortOrder.DESCENDING)); + sortKeys.add(new RowSorter.SortKey(m.getNameColumn(), + SortOrder.ASCENDING)); + + sorter.setSortKeys(sortKeys); + sorter.sort(); + + // set up filtering + ActionListener onReset; + onReset = new ActionListener() { - String link = sequenceURLLinks.elementAt(i).toString(); - nameLinks.addElement(link.substring(0, link.indexOf("|"))); - urlLinks.addElement(link.substring(link.indexOf("|") + 1)); - } + @Override + public void actionPerformed(ActionEvent e) + { + filterTB.setText(""); + sorter.setRowFilter(RowFilter.regexFilter("")); + } + + }; + doReset.addActionListener(onReset); + + // filter to display only custom urls + final RowFilter customUrlFilter = new RowFilter() + { + @Override + public boolean include( + Entry entry) + { + return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry); + } + }; + + final TableRowSorter customSorter = new TableRowSorter<>( + linkUrlTable.getModel()); + customSorter.setRowFilter(customUrlFilter); + + ActionListener onCustomOnly; + onCustomOnly = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + filterTB.setText(""); + sorter.setRowFilter(customUrlFilter); + } + }; + userOnly.addActionListener(onCustomOnly); + + filterTB.getDocument().addDocumentListener(new DocumentListener() + { + String caseInsensitiveFlag = "(?i)"; + + @Override + public void changedUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag + + filterTB.getText())); + } + + @Override + public void removeUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag + + filterTB.getText())); + } - updateLinkData(); + @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()) + .getDefaultColumn(); + 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)); + useProxy_actionPerformed(); // make sure useProxy is correctly initialised proxyServerTB.setEnabled(useProxy.isSelected()); proxyPortTB.setEnabled(useProxy.isSelected()); proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", "")); @@ -346,15 +475,26 @@ public class Preferences extends GPreferences /* * Set Output tab defaults */ - epsRendering - .addItem(MessageManager.getString("label.prompt_each_time")); - epsRendering.addItem(MessageManager.getString("label.lineart")); - epsRendering.addItem(MessageManager.getString("action.text")); - epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING", - "Prompt each time")); + 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)); - userIdWidth.setEnabled(autoIdWidth.isSelected()); - userIdWidthlabel.setEnabled(autoIdWidth.isSelected()); + userIdWidth.setEnabled(!autoIdWidth.isSelected()); + userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH"); userIdWidth.setText(wi == null ? "" : wi.toString()); blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true)); @@ -365,6 +505,8 @@ 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)); /* * Set Editing tab defaults @@ -384,6 +526,7 @@ public class Preferences extends GPreferences * * @param e */ + @Override public void ok_actionPerformed(ActionEvent e) { if (!validateSettings()) @@ -463,8 +606,8 @@ public class Preferences extends GPreferences } final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0; - Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, - Boolean.valueOf(showAutocalcFirst).toString()); + Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean + .valueOf(showAutocalcFirst).toString()); /* * Save Colours settings @@ -492,19 +635,15 @@ public class Preferences extends GPreferences Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer .getSelectedItem().toString()); Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText()); + Cache.applicationProperties.setProperty("MAP_WITH_SIFTS", + Boolean.toString(siftsMapping.isSelected())); + SiftsSettings.setMapWithSifts(siftsMapping.isSelected()); /* * Save Output settings */ - if (epsRendering.getSelectedItem().equals("Prompt each time")) - { - Cache.applicationProperties.remove("EPS_RENDERING"); - } - else - { - Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering - .getSelectedItem().toString()); - } + Cache.applicationProperties.setProperty("EPS_RENDERING", + ((OptionsParam) epsRendering.getSelectedItem()).getCode()); /* * Save Connections settings @@ -513,27 +652,32 @@ public class Preferences extends GPreferences jalview.util.BrowserLauncher.resetBrowser(); - if (nameLinks.size() > 0) + // save user-defined and selected links + String menuLinks = sequenceUrlLinks.writeUrlsAsString(true); + if (menuLinks.isEmpty()) + { + Cache.applicationProperties.remove("SEQUENCE_LINKS"); + } + else { - 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()); + menuLinks.toString()); + } + + String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false); + if (nonMenuLinks.isEmpty()) + { + Cache.applicationProperties.remove("STORED_LINKS"); } else { - Cache.applicationProperties.remove("SEQUENCE_LINKS"); + Cache.applicationProperties.setProperty("STORED_LINKS", + nonMenuLinks.toString()); } + Cache.applicationProperties.setProperty("DEFAULT_URL", + sequenceUrlLinks.getDefaultUrlId()); + Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected())); @@ -589,6 +733,8 @@ public class Preferences extends GPreferences Boolean.toString(pirjv.isSelected())); Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected())); + Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON", + Boolean.toString(embbedBioJSON.isSelected())); jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected(); Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", @@ -641,27 +787,30 @@ public class Preferences extends GPreferences return validateChimeraPath(); } + /** * 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")); + 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()); + FileFormatI format = chooser.getSelectedFormat(); + if (format != null) + { + Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT", + format.toString()); + } startupFileTextfield.setText(chooser.getSelectedFile() .getAbsolutePath()); } @@ -673,6 +822,7 @@ public class Preferences extends GPreferences * @param e * DOCUMENT ME! */ + @Override public void cancel_actionPerformed(ActionEvent e) { try @@ -691,6 +841,7 @@ public class Preferences extends GPreferences * @param e * DOCUMENT ME! */ + @Override public void annotations_actionPerformed(ActionEvent e) { conservation.setEnabled(annotations.isSelected()); @@ -704,23 +855,31 @@ 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.desktop, link, MessageManager.getString("label.new_sequence_url_link"), - JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { - nameLinks.addElement(link.getName()); - urlLinks.addElement(link.getURL()); - updateLinkData(); - valid = true; + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isUniqueName(link.getName())) + { + ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow( + link.getName(), link.getURL()); + valid = true; + } + else + { + link.notifyDuplicate(); + continue; + } } } else @@ -730,40 +889,45 @@ 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()); + link.setName(linkUrlTable.getValueAt(index, 0).toString()); + link.setURL(linkUrlTable.getValueAt(index, 1).toString()); boolean valid = false; while (!valid) { - - if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link, - MessageManager.getString("label.new_sequence_url_link"), - JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION) + if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + MessageManager.getString("label.edit_sequence_url_link"), + JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { - nameLinks.setElementAt(link.getName(), index); - urlLinks.setElementAt(link.getURL(), index); - updateLinkData(); - valid = true; + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isUniqueName(link.getName())) + { + linkUrlTable.setValueAt(link.getName(), index, 0); + linkUrlTable.setValueAt(link.getURL(), index, 1); + valid = true; + } + else + { + link.notifyDuplicate(); + continue; + } } } - else { break; @@ -771,32 +935,33 @@ 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")); + chooser.setDialogTitle(MessageManager + .getString("label.select_default_browser")); int value = chooser.showOpenDialog(this); @@ -814,13 +979,14 @@ 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() + public static List getGroupURLLinks() { return groupURLLinks; } @@ -829,7 +995,8 @@ public class Preferences extends GPreferences public void minColour_actionPerformed(JPanel panel) { Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground()); + MessageManager.getString("label.select_colour_minimum_value"), + minColour.getBackground()); if (col != null) { panel.setBackground(col); @@ -841,7 +1008,8 @@ public class Preferences extends GPreferences public void maxColour_actionPerformed(JPanel panel) { Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground()); + MessageManager.getString("label.select_colour_maximum_value"), + maxColour.getBackground()); if (col != null) { panel.setBackground(col); @@ -866,12 +1034,10 @@ 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); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .getString("warn.user_defined_width_requirements"), + MessageManager.getString("label.invalid_id_column_width"), + JvOptionPane.WARNING_MESSAGE); userIdWidth.setText(""); } } @@ -894,10 +1060,10 @@ public class Preferences extends GPreferences File f = new File(chimeraPath.getText()); if (!f.canExecute()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.invalid_chimera_path"), MessageManager.getString("label.invalid_name"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); return false; } } @@ -932,15 +1098,14 @@ public class Preferences extends GPreferences } if (!found) { - String[] options = - { "OK", "Help" }; - int showHelp = JOptionPane.showInternalOptionDialog( + String[] options = { "OK", "Help" }; + int showHelp = JvOptionPane.showInternalOptionDialog( Desktop.desktop, JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.chimera_missing")), - "", JOptionPane.YES_NO_OPTION, - JOptionPane.WARNING_MESSAGE, null, options, options[0]); - if (showHelp == JOptionPane.NO_OPTION) + "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, + null, options, options[0]); + if (showHelp == JvOptionPane.NO_OPTION) { try { @@ -953,4 +1118,99 @@ public class Preferences extends GPreferences } } + public class OptionsParam + { + private String name; + + private String code; + + public OptionsParam(String name, String code) + { + this.name = name; + this.code = code; + } + + public String getName() + { + return name; + } + + public void setName(String name) + { + this.name = name; + } + + public String getCode() + { + return code; + } + + public void setCode(String code) + { + this.code = code; + } + + @Override + public String toString() + { + return name; + } + + @Override + public boolean equals(Object that) + { + if (!(that instanceof OptionsParam)) + { + return false; + } + return this.code.equalsIgnoreCase(((OptionsParam) that).code); + } + + @Override + public int hashCode() + { + return name.hashCode() + code.hashCode(); + } + } + + private class UrlListSelectionHandler implements ListSelectionListener + { + + @Override + public void valueChanged(ListSelectionEvent e) + { + ListSelectionModel lsm = (ListSelectionModel) e.getSource(); + + int index = lsm.getMinSelectionIndex(); + if (index == -1) + { + // no selection, so disable delete/edit buttons + editLink.setEnabled(false); + deleteLink.setEnabled(false); + return; + } + int modelIndex = linkUrlTable.convertRowIndexToModel(index); + + // enable/disable edit and delete link buttons + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isRowDeletable(modelIndex)) + { + deleteLink.setEnabled(true); + } + else + { + deleteLink.setEnabled(false); + } + + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isRowEditable(modelIndex)) + { + editLink.setEnabled(true); + } + else + { + editLink.setEnabled(false); + } + } +} }