-package jalview.gui;\r
-\r
-import jalview.jbgui.*;\r
-import jalview.schemes.*;\r
-import jalview.io.*;\r
-\r
-import jalview.bin.Cache;\r
-import javax.swing.*;\r
-import java.awt.event.ActionEvent;\r
-import java.awt.*;\r
-\r
-\r
-public class Preferences extends GPreferences\r
-{\r
- static boolean preferencesLoaded=false;\r
-\r
- public static boolean showFullscreen=false;\r
- public static boolean showFullId=true;\r
- public static boolean showAnnotation=true;\r
- public static boolean showConservation=true;\r
- public static boolean showQuality=true;\r
- public static boolean showIdentity=true;\r
- public static String fontName="SansSerif";\r
- public static String fontSize="10";\r
- public static String fontStyle=Font.PLAIN+"";\r
- public static char gapSymbol='-';\r
- public static String defaultColour=null;\r
- public static boolean showStartupFile=true;\r
- public static String startupFile = "http://www.jalview.org/examples/exampleFile.jar";\r
-\r
- JInternalFrame frame;\r
-\r
- public static void initPreferences()\r
- {\r
- String string = Cache.getProperty("SHOW_FULL_ID");\r
- if(string!=null)\r
- showFullId = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("SHOW_FULLSCREEN");\r
- if(string!=null)\r
- showFullscreen = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("SHOW_ANNOTATIONS");\r
- if(string!=null)\r
- showAnnotation = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("SHOW_CONSERVATION");\r
- if(string!=null)\r
- showConservation = Boolean.valueOf(string).booleanValue();\r
- string = Cache.getProperty("SHOW_QUALITY");\r
- if(string!=null)\r
- showQuality = Boolean.valueOf(string).booleanValue();\r
- string = Cache.getProperty("SHOW_IDENTITY");\r
- if(string!=null)\r
- showIdentity = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("GAP_SYMBOL");\r
- if(string!=null)\r
- gapSymbol = string.charAt(0);\r
-\r
- string = Cache.getProperty("SHOW_FULL_ID");\r
- if(string!=null)\r
- showFullId = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("FONT_NAME");\r
- if (string != null)\r
- fontName = string;\r
-\r
- string = Cache.getProperty("FONT_STYLE");\r
- if (string != null)\r
- fontStyle = string;\r
-\r
- string = Cache.getProperty("FONT_SIZE");\r
- if (string != null)\r
- fontSize = string;\r
-\r
-\r
- string = Cache.getProperty("DEFAULT_COLOUR");\r
- if(string!=null)\r
- defaultColour = string;\r
-\r
- string = Cache.getProperty("STARTUP_FILE");\r
- if(string!=null)\r
- startupFile = string;\r
-\r
- string = Cache.getProperty("SHOW_STARTUP_FILE");\r
- if(string!=null)\r
- showStartupFile = Boolean.valueOf(string).booleanValue();\r
-\r
- preferencesLoaded = true;\r
- }\r
-\r
- public Preferences()\r
- {\r
- initPreferences();\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Preferences", 480,390 );\r
-\r
- fullID.setSelected(showFullId);\r
- String string = Cache.getProperty("SHOW_FULLSCREEN");\r
- boolean value = false;\r
- if(string!=null)\r
- value = Boolean.valueOf(string).booleanValue();\r
-\r
- fullScreen.setSelected(value);\r
- annotations.setSelected(showAnnotation);\r
-\r
- conservation.setEnabled(showAnnotation);\r
- quality.setEnabled(showAnnotation);\r
- identity.setEnabled(showAnnotation);\r
-\r
- conservation.setSelected(showConservation);\r
- quality.setSelected(showQuality);\r
- identity.setSelected(showIdentity);\r
-\r
- for(int i=0; i<12; i++)\r
- colour.addItem( ColourSchemeProperty.getColourName(i) );\r
-\r
- string = Cache.getProperty("DEFAULT_COLOUR");\r
- if(string!=null)\r
- colour.setSelectedItem( string );\r
- else\r
- colour.setSelectedIndex( 11 );\r
-\r
- String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
- for(int i=0; i<fonts.length; i++)\r
- fontNameCB.addItem(fonts[i]);\r
-\r
- for(int i=1; i<31; i++)\r
- fontSizeCB.addItem(i+"");\r
-\r
- fontStyleCB.addItem("plain");\r
- fontStyleCB.addItem("bold");\r
- fontStyleCB.addItem("italic");\r
-\r
- fontNameCB.setSelectedItem(fontName);\r
- fontSizeCB.setSelectedItem(fontSize);\r
- fontStyleCB.setSelectedItem(fontStyle);\r
-\r
- gapSymbolCB.addItem("-");\r
- gapSymbolCB.addItem(".");\r
-\r
- gapSymbolCB.setSelectedItem( gapSymbol+"" );\r
-\r
- startupCheckbox.setSelected(showStartupFile);\r
- startupFileTextfield.setText(startupFile);\r
-\r
- }\r
-\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
- showFullId = fullID.isSelected() ;\r
- showFullscreen = fullScreen.isSelected();\r
- showAnnotation = annotations.isSelected();\r
- showConservation = conservation.isSelected();\r
- showQuality = quality.isSelected();\r
- showIdentity = identity.isSelected();\r
- defaultColour = colour.getSelectedItem().toString();\r
- gapSymbol = gapSymbolCB.getSelectedItem().toString().charAt(0);\r
- fontName = fontNameCB.getSelectedItem().toString();\r
- fontSize = fontSizeCB.getSelectedItem().toString();\r
- fontStyle = fontStyleCB.getSelectedItem().toString();\r
- startupFile = startupFileTextfield.getText();\r
- showStartupFile = startupCheckbox.isSelected();\r
-\r
- Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));\r
- Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString( showFullscreen ) );\r
-\r
- Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString( showAnnotation ));\r
- Cache.setProperty("SHOW_CONSERVATION", Boolean.toString( showConservation ));\r
- Cache.setProperty("SHOW_QUALITY", Boolean.toString( showQuality ));\r
- Cache.setProperty("SHOW_IDENTITY", Boolean.toString( showIdentity ));\r
-\r
- Cache.setProperty("DEFAULT_COLOUR", defaultColour);\r
- Cache.setProperty("GAP_SYMBOL", gapSymbol+"");\r
-\r
- Cache.setProperty("FONT_NAME", fontName);\r
- Cache.setProperty("FONT_STYLE", fontStyle);\r
- Cache.setProperty("FONT_SIZE", fontSize);\r
-\r
- Cache.setProperty("STARTUP_FILE", startupFile);\r
- Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));\r
-\r
-\r
-\r
- try {\r
- frame.setClosed(true);\r
- } catch (Exception ex) {}\r
-\r
- }\r
-\r
- public void startupFileTextfield_mouseClicked()\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},\r
- new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}\r
- ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Select startup file");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());\r
- startupFileTextfield.setText( chooser.getSelectedFile().getAbsolutePath() );\r
- }\r
- }\r
-\r
-\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- frame.setClosed(true);\r
- }catch(Exception ex){}\r
- }\r
-\r
- public void annotations_actionPerformed(ActionEvent e)\r
- {\r
- conservation.setEnabled(annotations.isSelected());\r
- quality.setEnabled(annotations.isSelected());\r
- identity.setEnabled(annotations.isSelected());\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
+import jalview.urls.UrlLinkTableModel;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.UrlConstants;
+import jalview.ws.sifts.SiftsSettings;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+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.ArrayList;
+import java.util.List;
+
+import javax.help.HelpSetException;
+import javax.swing.JColorChooser;
+import javax.swing.JFileChooser;
+import javax.swing.JInternalFrame;
+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;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Preferences extends GPreferences
+{
+ public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+
+ public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
+ public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+ public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+ public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+
+ public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+ 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 SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+ public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+
+ private static final int MIN_FONT_SIZE = 1;
+
+ private static final int MAX_FONT_SIZE = 30;
+
+ /**
+ * Holds name and link separated with | character. Sequence ID must be
+ * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
+ */
+ public static UrlProviderI sequenceUrlLinks;
+
+ public static UrlLinkTableModel dataModel;
+
+ /**
+ * Holds name and link separated with | character. Sequence IDS and Sequences
+ * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
+ * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
+ * for first and second token specified after a pipe character at end |,|.
+ * (TODO: proper escape for using | to separate ids or sequences
+ */
+
+ public static List<String> groupURLLinks;
+ static
+ {
+ // 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())
+ {
+ 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>();
+ }
+
+ JInternalFrame frame;
+
+ DasSourceBrowser dasSource;
+
+ private WsPreferences wsPrefs;
+
+ private OptionsParam promptEachTimeOpt = new OptionsParam(
+ MessageManager.getString("label.prompt_each_time"),
+ "Prompt each time");
+
+ private OptionsParam lineArtOpt = new OptionsParam(
+ MessageManager.getString("label.lineart"), "Lineart");
+
+ private OptionsParam textOpt = new OptionsParam(
+ MessageManager.getString("action.text"), "Text");
+
+ /**
+ * Creates a new Preferences object.
+ */
+ public Preferences()
+ {
+ super();
+ 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())
+ {
+ width = 570;
+ height = 480;
+ }
+
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.preferences"), width, height);
+ frame.setMinimumSize(new Dimension(width, height));
+
+ /*
+ * 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));
+ showUnconserved
+ .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();
+ for (int i = 0; i < fonts.length; i++)
+ {
+ fontNameCB.addItem(fonts[i]);
+ }
+
+ for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
+ {
+ fontSizeCB.addItem(i + "");
+ }
+
+ fontStyleCB.addItem("plain");
+ 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
+ + ""));
+
+ smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+ scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
+ false));
+
+ idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
+
+ wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+
+ gapSymbolCB.addItem("-");
+ gapSymbolCB.addItem(".");
+
+ 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"));
+
+ sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
+ SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ sortAnnBy.setSelectedItem(savedSort.toString());
+
+ sortAutocalc.addItem("Autocalculated first");
+ sortAutocalc.addItem("Autocalculated last");
+ final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
+ sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
+ : sortAutocalc.getItemAt(1));
+ startupCheckbox
+ .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+ startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+ + "/examples/exampleFile_2_3.jar"));
+
+ /*
+ * Set Colours tab defaults
+ */
+ protColour.addItem(ResidueColourScheme.NONE);
+ nucColour.addItem(ResidueColourScheme.NONE);
+ for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
+ {
+ String name = cs.getSchemeName();
+ protColour.addItem(name);
+ nucColour.addItem(name);
+ }
+ 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));
+
+ /*
+ * Set Structure tab defaults.
+ */
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ structFromPdb.setSelected(structSelected);
+ useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
+ useRnaView.setEnabled(structSelected);
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setEnabled(structSelected);
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setEnabled(structSelected);
+ structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
+ ViewerType.JMOL.name()));
+ chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
+ chimeraPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateChimeraPath();
+ }
+ });
+
+ 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
+ */
+
+ // 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);
+ sorter.sort();
+
+ // set up filtering
+ ActionListener onReset;
+ onReset = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterTB.setText("");
+ sorter.setRowFilter(RowFilter.regexFilter(""));
+ }
+
+ };
+ 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));
+ useProxy_actionPerformed(); // make sure useProxy is correctly initialised
+ proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
+ proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
+
+ defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
+
+ usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
+ // note antisense here: default is true
+ questionnaire
+ .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));
+ 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));
+ clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
+ fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
+ msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
+ pfamjv.setSelected(Cache.getDefault("PFAM_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));
+
+ /*
+ * 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));
+
+ annotations_actionPerformed(null); // update the display of the annotation
+ // settings
+ }
+
+ /**
+ * Save user selections on the Preferences tabs to the Cache and write out to
+ * file.
+ *
+ * @param e
+ */
+ @Override
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ if (!validateSettings())
+ {
+ return;
+ }
+
+ /*
+ * Save Visual settings
+ */
+ Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
+ Boolean.toString(seqLimit.isSelected()));
+ Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
+ Boolean.toString(rightAlign.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
+ Boolean.toString(fullScreen.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
+ Boolean.toString(openoverv.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Boolean.toString(annotations.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.toString(conservation.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Boolean.toString(quality.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.toString(identity.isSelected()));
+
+ Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
+ .getSelectedItem().toString());
+
+ Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
+ .getSelectedItem().toString());
+
+ Cache.applicationProperties.setProperty("ID_ITALICS",
+ Boolean.toString(idItalics.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
+ Boolean.toString(showUnconserved.isSelected()));
+ Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
+ Boolean.toString(showOccupancy.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+ Boolean.toString(showGroupConsensus.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
+ Boolean.toString(showGroupConservation.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
+ Boolean.toString(showConsensHistogram.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+ Boolean.toString(showConsensLogo.isSelected()));
+ Cache.applicationProperties.setProperty("ANTI_ALIAS",
+ Boolean.toString(smoothFont.isSelected()));
+ Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+ Boolean.toString(scaleProteinToCdna.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+ Boolean.toString(showNpTooltip.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+ Boolean.toString(showDbRefTooltip.isSelected()));
+
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
+ Boolean.toString(wrap.isSelected()));
+
+ Cache.applicationProperties.setProperty("STARTUP_FILE",
+ startupFileTextfield.getText());
+ Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
+ Boolean.toString(startupCheckbox.isSelected()));
+
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
+ .getSelectedItem().toString());
+
+ // 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());
+ }
+
+ final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
+ .valueOf(showAutocalcFirst).toString());
+
+ /*
+ * Save Colours settings
+ */
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
+ .getSelectedItem().toString());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ minColour.getBackground());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ maxColour.getBackground());
+
+ /*
+ * Save Structure settings
+ */
+ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+ Boolean.toString(addTempFactor.isSelected()));
+ Cache.applicationProperties.setProperty(ADD_SS_ANN,
+ Boolean.toString(addSecondaryStructure.isSelected()));
+ Cache.applicationProperties.setProperty(USE_RNAVIEW,
+ Boolean.toString(useRnaView.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+ Boolean.toString(structFromPdb.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
+ .getSelectedItem().toString());
+ Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+ Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
+ Boolean.toString(siftsMapping.isSelected()));
+ SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
+
+ /*
+ * Save Output settings
+ */
+ Cache.applicationProperties.setProperty("EPS_RENDERING",
+ ((OptionsParam) epsRendering.getSelectedItem()).getCode());
+
+ /*
+ * Save Connections settings
+ */
+ Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+
+ jalview.util.BrowserLauncher.resetBrowser();
+
+ // save user-defined and selected links
+ String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
+ if (menuLinks.isEmpty())
+ {
+ Cache.applicationProperties.remove("SEQUENCE_LINKS");
+ }
+ else
+ {
+ Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+ menuLinks.toString());
+ }
+
+ String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
+ if (nonMenuLinks.isEmpty())
+ {
+ Cache.applicationProperties.remove("STORED_LINKS");
+ }
+ else
+ {
+ Cache.applicationProperties.setProperty("STORED_LINKS",
+ nonMenuLinks.toString());
+ }
+
+ Cache.applicationProperties.setProperty("DEFAULT_URL",
+ sequenceUrlLinks.getPrimaryUrlId());
+
+ Cache.applicationProperties.setProperty("USE_PROXY",
+ Boolean.toString(useProxy.isSelected()));
+
+ Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
+
+ Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
+
+ if (useProxy.isSelected())
+ {
+ System.setProperty("http.proxyHost", proxyServerTB.getText());
+ System.setProperty("http.proxyPort", proxyPortTB.getText());
+ }
+ else
+ {
+ System.setProperty("http.proxyHost", "");
+ System.setProperty("http.proxyPort", "");
+ }
+ Cache.setProperty("VERSION_CHECK",
+ Boolean.toString(versioncheck.isSelected()));
+ if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
+ {
+ // default is false - we only set this if the user has actively agreed
+ Cache.setProperty("USAGESTATS",
+ Boolean.toString(usagestats.isSelected()));
+ }
+ if (!questionnaire.isSelected())
+ {
+ 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");
+ }
+
+ /*
+ * Save Output settings
+ */
+ Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
+ Boolean.toString(blcjv.isSelected()));
+ Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
+ Boolean.toString(clustaljv.isSelected()));
+ Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
+ Boolean.toString(fastajv.isSelected()));
+ Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
+ Boolean.toString(msfjv.isSelected()));
+ Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
+ Boolean.toString(pfamjv.isSelected()));
+ Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
+ Boolean.toString(pileupjv.isSelected()));
+ Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
+ 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",
+ Boolean.toString(autoIdWidth.isSelected()));
+ userIdWidth_actionPerformed();
+ Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+ userIdWidth.getText());
+
+ /*
+ * Save Editing settings
+ */
+ Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+ Boolean.toString(autoCalculateConsCheck.isSelected()));
+ Cache.applicationProperties.setProperty("SORT_BY_TREE",
+ Boolean.toString(sortByTree.isSelected()));
+ Cache.applicationProperties.setProperty("PAD_GAPS",
+ Boolean.toString(padGaps.isSelected()));
+
+ dasSource.saveProperties(Cache.applicationProperties);
+ wsPrefs.updateAndRefreshWsMenuConfig(false);
+ Cache.saveProperties();
+ Desktop.instance.doConfigureStructurePrefs();
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * Do any necessary validation before saving settings. Return focus to the
+ * first tab which fails validation.
+ *
+ * @return
+ */
+ private boolean validateSettings()
+ {
+ if (!validateStructure())
+ {
+ structureTab.requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ protected boolean validateStructure()
+ {
+ return validateChimeraPath();
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ @Override
+ public void startupFileTextfield_mouseClicked()
+ {
+ 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"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ FileFormatI format = chooser.getSelectedFormat();
+ if (format != null)
+ {
+ Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+ format.getName());
+ }
+ startupFileTextfield.setText(chooser.getSelectedFile()
+ .getAbsolutePath());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @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()
+ && (identity.isSelected() || showGroupConsensus.isSelected()));
+ showConsensLogo.setEnabled(annotations.isSelected()
+ && (identity.isSelected() || showGroupConsensus.isSelected()));
+ }
+
+ @Override
+ public void newLink_actionPerformed(ActionEvent e)
+ {
+ GSequenceLink link = new GSequenceLink();
+ boolean valid = false;
+ while (!valid)
+ {
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ MessageManager.getString("label.new_sequence_url_link"),
+ JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
+ {
+ if (link.checkValid())
+ {
+ if (((UrlLinkTableModel) linkUrlTable.getModel())
+ .isUniqueName(link.getName()))
+ {
+ ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
+ link.getName(), link.getURL());
+ valid = true;
+ }
+ else
+ {
+ link.notifyDuplicate();
+ continue;
+ }
+ }
+ }
+ else
+ {
+ break;
+ }
+ }
+ }
+
+ @Override
+ public void editLink_actionPerformed(ActionEvent e)
+ {
+ GSequenceLink link = new GSequenceLink();
+
+ int index = linkUrlTable.getSelectedRow();
+ if (index == -1)
+ {
+ // button no longer enabled if row is not selected
+ Cache.log.debug("Edit with no row selected in linkUrlTable");
+ return;
+ }
+
+ 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 (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ MessageManager.getString("label.edit_sequence_url_link"),
+ JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
+ {
+ if (link.checkValid())
+ {
+ 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 = linkUrlTable.getSelectedRow();
+ int modelIndex = -1;
+ if (index == -1)
+ {
+ // button no longer enabled if row is not selected
+ Cache.log.debug("Delete with no row selected in linkUrlTable");
+ return;
+ }
+ else
+ {
+ modelIndex = linkUrlTable.convertRowIndexToModel(index);
+ }
+
+ // 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"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+ }
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * 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 List<String> getGroupURLLinks()
+ {
+ return groupURLLinks;
+ }
+
+ @Override
+ public void minColour_actionPerformed(JPanel panel)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_colour_minimum_value"),
+ minColour.getBackground());
+ if (col != null)
+ {
+ panel.setBackground(col);
+ }
+ panel.repaint();
+ }
+
+ @Override
+ public void maxColour_actionPerformed(JPanel panel)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_colour_maximum_value"),
+ maxColour.getBackground());
+ if (col != null)
+ {
+ panel.setBackground(col);
+ }
+ panel.repaint();
+ }
+
+ @Override
+ protected void userIdWidth_actionPerformed()
+ {
+ try
+ {
+ String val = userIdWidth.getText().trim();
+ if (val.length() > 0)
+ {
+ Integer iw = Integer.parseInt(val);
+ if (iw.intValue() < 12)
+ {
+ throw new NumberFormatException();
+ }
+ userIdWidth.setText(iw.toString());
+ }
+ } catch (NumberFormatException x)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("warn.user_defined_width_requirements"),
+ MessageManager.getString("label.invalid_id_column_width"),
+ JvOptionPane.WARNING_MESSAGE);
+ userIdWidth.setText("");
+ }
+ }
+
+ @Override
+ protected void autoIdWidth_actionPerformed()
+ {
+ userIdWidth.setEnabled(!autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+ }
+
+ /**
+ * Returns true if chimera path is to a valid executable, else show an error
+ * dialog.
+ */
+ private boolean validateChimeraPath()
+ {
+ if (chimeraPath.getText().trim().length() > 0)
+ {
+ File f = new File(chimeraPath.getText());
+ if (!f.canExecute())
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.invalid_chimera_path"),
+ MessageManager.getString("label.invalid_name"),
+ JvOptionPane.ERROR_MESSAGE);
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * If Chimera is selected, check it can be found on default or user-specified
+ * path, if not show a warning/help dialog.
+ */
+ @Override
+ protected void structureViewer_actionPerformed(String selectedItem)
+ {
+ if (!selectedItem.equals(ViewerType.CHIMERA.name()))
+ {
+ return;
+ }
+ boolean found = false;
+
+ /*
+ * Try user-specified and standard paths for Chimera executable.
+ */
+ List<String> paths = StructureManager.getChimeraPaths();
+ paths.add(0, chimeraPath.getText());
+ for (String path : paths)
+ {
+ if (new File(path.trim()).canExecute())
+ {
+ found = true;
+ break;
+ }
+ }
+ if (!found)
+ {
+ String[] options = { "OK", "Help" };
+ int showHelp = JvOptionPane.showInternalOptionDialog(
+ Desktop.desktop,
+ JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_missing")),
+ "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
+ if (showHelp == JvOptionPane.NO_OPTION)
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.StructureViewer);
+ } catch (HelpSetException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+ 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);
+ }
+ }
+}
+}