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package jalview.gui; |
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import java.awt.BorderLayout; |
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import java.awt.Color; |
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import java.awt.Component; |
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import java.awt.Dimension; |
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import java.awt.Font; |
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import java.awt.event.ActionEvent; |
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import java.awt.event.ActionListener; |
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import java.io.File; |
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import java.util.ArrayList; |
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import java.util.List; |
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import java.util.concurrent.CompletableFuture; |
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import javax.help.HelpSetException; |
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import javax.swing.JComboBox; |
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import javax.swing.JInternalFrame; |
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import javax.swing.JPanel; |
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import javax.swing.ListSelectionModel; |
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import javax.swing.RowFilter; |
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import javax.swing.RowSorter; |
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import javax.swing.SortOrder; |
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import javax.swing.event.DocumentEvent; |
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import javax.swing.event.DocumentListener; |
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import javax.swing.event.ListSelectionEvent; |
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import javax.swing.event.ListSelectionListener; |
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import javax.swing.table.TableCellRenderer; |
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import javax.swing.table.TableColumn; |
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import javax.swing.table.TableModel; |
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import javax.swing.table.TableRowSorter; |
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import ext.edu.ucsf.rbvi.strucviz2.StructureManager; |
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import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; |
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import jalview.bin.Cache; |
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import jalview.bin.Console; |
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import jalview.bin.MemorySetting; |
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import jalview.ext.pymol.PymolManager; |
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import jalview.gui.Help.HelpId; |
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import jalview.gui.StructureViewer.ViewerType; |
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import jalview.io.BackupFiles; |
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import jalview.io.BackupFilesPresetEntry; |
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import jalview.io.FileFormatI; |
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import jalview.io.JalviewFileChooser; |
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import jalview.io.JalviewFileView; |
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import jalview.jbgui.GPreferences; |
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import jalview.jbgui.GSequenceLink; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.schemes.ColourSchemes; |
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import jalview.schemes.ResidueColourScheme; |
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import jalview.urls.UrlLinkTableModel; |
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import jalview.urls.api.UrlProviderFactoryI; |
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import jalview.urls.api.UrlProviderI; |
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import jalview.urls.desktop.DesktopUrlProviderFactory; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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import jalview.util.UrlConstants; |
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import jalview.ws.sifts.SiftsSettings; |
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@author |
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@version |
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| 2% |
Uncovered Elements: 691 (705) |
Complexity: 127 |
Complexity Density: 0.23 |
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public class Preferences extends GPreferences |
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{ |
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public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME"; |
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public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA"; |
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public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR"; |
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public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT"; |
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public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC"; |
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public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN"; |
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public static final String ADD_SS_ANN = "ADD_SS_ANN"; |
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public static final String USE_RNAVIEW = "USE_RNAVIEW"; |
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public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB"; |
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public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY"; |
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public static final String CHIMERA_PATH = "CHIMERA_PATH"; |
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public static final String CHIMERAX_PATH = "CHIMERAX_PATH"; |
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public static final String PYMOL_PATH = "PYMOL_PATH"; |
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public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; |
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public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE"; |
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public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY"; |
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public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START"; |
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public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP"; |
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public static final String GAP_COLOUR = "GAP_COLOUR"; |
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public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR"; |
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private static final int MIN_FONT_SIZE = 1; |
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private static final int MAX_FONT_SIZE = 30; |
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public static final String SHOW_STRUC_PROVIDER = "SHOW_STRUCTURE_PROVIDER"; |
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private String previousProxyType; |
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private static Preferences INSTANCE = null; |
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public static UrlProviderI sequenceUrlLinks; |
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public static UrlLinkTableModel dataModel; |
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public static List<String> groupURLLinks; |
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| 100% |
Uncovered Elements: 0 (13) |
Complexity: 3 |
Complexity Density: 0.27 |
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static... |
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{ |
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Cache.disableSessionProperties(); |
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String inMenuString = Cache.getDefault("SEQUENCE_LINKS", ""); |
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String notInMenuString = Cache.getDefault("STORED_LINKS", ""); |
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String defaultUrl = Cache.getDefault("DEFAULT_URL", |
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UrlConstants.DEFAULT_LABEL); |
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if (inMenuString.isEmpty() && notInMenuString.isEmpty()) |
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{ |
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inMenuString = UrlConstants.DEFAULT_STRING; |
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} |
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UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl, |
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inMenuString, notInMenuString); |
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sequenceUrlLinks = factory.createUrlProvider(); |
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dataModel = new UrlLinkTableModel(sequenceUrlLinks); |
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groupURLLinks = new ArrayList<>(); |
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Cache.enableSessionProperties(); |
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} |
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JInternalFrame frame; |
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private WsPreferences wsPrefs; |
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private OptionsParam promptEachTimeOpt = new OptionsParam( |
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MessageManager.getString("label.prompt_each_time"), |
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LineartOptions.PROMPT_EACH_TIME); |
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private OptionsParam lineArtOpt = new OptionsParam( |
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MessageManager.getString("label.lineart"), "Lineart"); |
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private OptionsParam textOpt = new OptionsParam( |
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MessageManager.getString("action.text"), "Text"); |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 4 |
Complexity Density: 1.33 |
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public static Preferences getInstance()... |
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{ |
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if (INSTANCE == null || INSTANCE.frame == null |
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|| INSTANCE.frame.isClosed()) |
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{ |
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INSTANCE = new Preferences(); |
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} |
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return INSTANCE; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public static void openPreferences()... |
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{ |
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openPreferences(null, null); |
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} |
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
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public static void openPreferences(TabRef selectTab, String message)... |
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{ |
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Preferences p = getInstance(); |
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if (selectTab != null) |
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p.selectTab(selectTab, message); |
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p.frame.show(); |
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p.frame.moveToFront(); |
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p.frame.grabFocus(); |
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} |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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public void selectTab(TabRef selectTab, String message)... |
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{ |
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this.selectTab(selectTab); |
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if (message != null) |
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this.setMessage(message); |
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this.frame.show(); |
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} |
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| 0% |
Uncovered Elements: 221 (221) |
Complexity: 21 |
Complexity Density: 0.11 |
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private Preferences()... |
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{ |
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super(); |
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260 |
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Cache.disableSessionProperties(); |
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frame = new JInternalFrame(); |
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frame.setFrameIcon(null); |
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frame.setContentPane(this); |
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if (!Platform.isJS()) |
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{ |
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wsPrefs = new WsPreferences(); |
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wsTab.add(wsPrefs, BorderLayout.CENTER); |
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} |
275 |
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int width = 500, height = 450; |
276 |
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if (Platform.isAMacAndNotJS()) |
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{ |
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width = 570; |
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height = 480; |
280 |
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} |
281 |
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282 |
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Desktop.addInternalFrame(frame, |
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MessageManager.getString("label.preferences"), width, height); |
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frame.setMinimumSize(new Dimension(width, height)); |
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seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true)); |
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rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false)); |
291 |
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fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false)); |
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annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true)); |
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conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true)); |
295 |
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quality.setSelected(Cache.getDefault("SHOW_QUALITY", true)); |
296 |
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identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true)); |
297 |
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ssConsensus.setSelected(Cache.getDefault("SHOW_SS_CONSENSUS", false)); |
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openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false)); |
299 |
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showUnconserved |
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.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false)); |
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showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false)); |
302 |
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showGroupConsensus |
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.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false)); |
304 |
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showGroupConservation.setSelected( |
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Cache.getDefault("SHOW_GROUP_CONSERVATION", false)); |
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showConsensHistogram.setSelected( |
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Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true)); |
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showConsensLogo |
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.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false)); |
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showNpTooltip |
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.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); |
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showDbRefTooltip |
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.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); |
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String[] fonts = java.awt.GraphicsEnvironment |
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.getLocalGraphicsEnvironment().getAvailableFontFamilyNames(); |
317 |
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for (int i = 0; i < fonts.length; i++) |
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{ |
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fontNameCB.addItem(fonts[i]); |
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} |
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for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++) |
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{ |
324 |
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fontSizeCB.addItem(i + ""); |
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} |
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327 |
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fontStyleCB.addItem("plain"); |
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fontStyleCB.addItem("bold"); |
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fontStyleCB.addItem("italic"); |
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fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif")); |
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fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10")); |
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fontStyleCB.setSelectedItem( |
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Cache.getDefault("FONT_STYLE", Font.PLAIN + "")); |
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336 |
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smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true)); |
337 |
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scaleProteinToCdna |
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.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false)); |
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340 |
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idItalics.setSelected(Cache.getDefault("ID_ITALICS", true)); |
341 |
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342 |
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wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false)); |
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344 |
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gapSymbolCB.addItem("-"); |
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gapSymbolCB.addItem("."); |
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gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-")); |
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sortby.addItem("No sort"); |
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sortby.addItem("Id"); |
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sortby.addItem("Pairwise Identity"); |
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sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort")); |
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sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString()); |
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sortAnnBy |
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.addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString()); |
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sortAnnBy |
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.addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString()); |
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SequenceAnnotationOrder savedSort = SequenceAnnotationOrder |
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.valueOf(Cache.getDefault(SORT_ANNOTATIONS, |
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SequenceAnnotationOrder.NONE.name())); |
362 |
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sortAnnBy.setSelectedItem(savedSort.toString()); |
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364 |
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sortAutocalc.addItem("Autocalculated first"); |
365 |
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sortAutocalc.addItem("Autocalculated last"); |
366 |
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final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true); |
367 |
0 |
sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0) |
368 |
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: sortAutocalc.getItemAt(1)); |
369 |
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startupCheckbox |
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.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true)); |
371 |
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startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE", |
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Cache.getDefault("www.jalview.org", "https://www.jalview.org") |
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+ "/examples/exampleFile_2_7.jvp")); |
374 |
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375 |
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376 |
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377 |
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378 |
0 |
protColour.addItem(ResidueColourScheme.NONE); |
379 |
0 |
nucColour.addItem(ResidueColourScheme.NONE); |
380 |
0 |
for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes()) |
381 |
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{ |
382 |
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String name = cs.getSchemeName(); |
383 |
0 |
protColour.addItem(name); |
384 |
0 |
nucColour.addItem(name); |
385 |
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} |
386 |
0 |
String oldProp = Cache.getDefault(DEFAULT_COLOUR, |
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ResidueColourScheme.NONE); |
388 |
0 |
String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null); |
389 |
0 |
protColour.setSelectedItem(newProp != null ? newProp : oldProp); |
390 |
0 |
newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null); |
391 |
0 |
nucColour.setSelectedItem(newProp != null ? newProp : oldProp); |
392 |
0 |
minColour.setBackground( |
393 |
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Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); |
394 |
0 |
maxColour.setBackground( |
395 |
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Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); |
396 |
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397 |
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398 |
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399 |
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400 |
0 |
gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR, |
401 |
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OverviewCanvas.OVERVIEW_DEFAULT_GAP)); |
402 |
0 |
hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR, |
403 |
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OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN)); |
404 |
0 |
useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false)); |
405 |
0 |
gapLabel.setEnabled(!useLegacyGap.isSelected()); |
406 |
0 |
gapColour.setEnabled(!useLegacyGap.isSelected()); |
407 |
0 |
showHiddenAtStart |
408 |
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.setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false)); |
409 |
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|
410 |
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411 |
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412 |
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413 |
0 |
final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true); |
414 |
0 |
structFromPdb.setSelected(structSelected); |
415 |
0 |
addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true)); |
416 |
0 |
addSecondaryStructure.setEnabled(structSelected); |
417 |
0 |
addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true)); |
418 |
0 |
addTempFactor.setEnabled(structSelected); |
419 |
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420 |
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421 |
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422 |
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423 |
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424 |
0 |
String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, |
425 |
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ViewerType.JMOL.name()); |
426 |
0 |
structViewer.setSelectedItem(viewerType); |
427 |
0 |
String viewerPath = ""; |
428 |
0 |
ViewerType type = null; |
429 |
0 |
try |
430 |
|
{ |
431 |
0 |
type = ViewerType.valueOf(viewerType); |
432 |
0 |
switch (type) |
433 |
|
{ |
434 |
0 |
case JMOL: |
435 |
0 |
break; |
436 |
0 |
case CHIMERA: |
437 |
0 |
viewerPath = Cache.getDefault(CHIMERA_PATH, ""); |
438 |
0 |
break; |
439 |
0 |
case CHIMERAX: |
440 |
0 |
viewerPath = Cache.getDefault(CHIMERAX_PATH, ""); |
441 |
0 |
break; |
442 |
0 |
case PYMOL: |
443 |
0 |
viewerPath = Cache.getDefault(PYMOL_PATH, ""); |
444 |
0 |
break; |
445 |
|
} |
446 |
|
} catch (IllegalArgumentException e) |
447 |
|
{ |
448 |
0 |
Console.error("Unknown structure viewer type: " + viewerType |
449 |
|
+ ", defaulting to Jmol"); |
450 |
0 |
type = ViewerType.JMOL; |
451 |
|
} |
452 |
0 |
structureViewerPath.setText(viewerPath); |
453 |
|
|
454 |
0 |
structureViewerPath.addActionListener(new ActionListener() |
455 |
|
{ |
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 7 |
Complexity Density: 0.41 |
|
456 |
0 |
@Override... |
457 |
|
public void actionPerformed(ActionEvent e) |
458 |
|
{ |
459 |
0 |
if (validateViewerPath()) |
460 |
|
{ |
461 |
0 |
String path = structureViewerPath.getText(); |
462 |
0 |
try |
463 |
|
{ |
464 |
0 |
ViewerType type = ViewerType.valueOf(viewerType); |
465 |
0 |
switch (type) |
466 |
|
{ |
467 |
0 |
case JMOL: |
468 |
0 |
break; |
469 |
0 |
case CHIMERA: |
470 |
0 |
Cache.setProperty(CHIMERA_PATH, path); |
471 |
0 |
break; |
472 |
0 |
case CHIMERAX: |
473 |
0 |
Cache.setProperty(CHIMERAX_PATH, path); |
474 |
0 |
break; |
475 |
0 |
case PYMOL: |
476 |
0 |
Cache.setProperty(PYMOL_PATH, path); |
477 |
0 |
break; |
478 |
|
} |
479 |
|
} catch (IllegalArgumentException x) |
480 |
|
{ |
481 |
0 |
Console.error("Failed to set path - unknown viewer type", x); |
482 |
|
} |
483 |
|
} |
484 |
|
} |
485 |
|
}); |
486 |
|
|
487 |
0 |
if (Cache.getDefault("MAP_WITH_SIFTS", false)) |
488 |
|
{ |
489 |
0 |
siftsMapping.setSelected(true); |
490 |
|
} |
491 |
|
else |
492 |
|
{ |
493 |
0 |
nwMapping.setSelected(true); |
494 |
|
} |
495 |
|
|
496 |
0 |
SiftsSettings |
497 |
|
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); |
498 |
|
|
499 |
|
|
500 |
|
|
501 |
|
|
502 |
|
|
503 |
|
|
504 |
0 |
linkUrlTable.setModel(dataModel); |
505 |
0 |
final TableRowSorter<TableModel> sorter = new TableRowSorter<>( |
506 |
|
linkUrlTable.getModel()); |
507 |
0 |
linkUrlTable.setRowSorter(sorter); |
508 |
0 |
List<RowSorter.SortKey> sortKeys = new ArrayList<>(); |
509 |
|
|
510 |
0 |
UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel(); |
511 |
0 |
sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(), |
512 |
|
SortOrder.DESCENDING)); |
513 |
0 |
sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(), |
514 |
|
SortOrder.DESCENDING)); |
515 |
0 |
sortKeys.add( |
516 |
|
new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING)); |
517 |
|
|
518 |
0 |
sorter.setSortKeys(sortKeys); |
519 |
|
|
520 |
|
|
521 |
|
|
522 |
|
|
523 |
0 |
ActionListener onReset; |
524 |
0 |
onReset = new ActionListener() |
525 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
526 |
0 |
@Override... |
527 |
|
public void actionPerformed(ActionEvent e) |
528 |
|
{ |
529 |
0 |
filterTB.setText(""); |
530 |
0 |
sorter.setRowFilter(RowFilter.regexFilter("")); |
531 |
|
} |
532 |
|
|
533 |
|
}; |
534 |
0 |
doReset.addActionListener(onReset); |
535 |
|
|
536 |
|
|
537 |
0 |
final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>() |
538 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
539 |
0 |
@Override... |
540 |
|
public boolean include( |
541 |
|
Entry<? extends TableModel, ? extends Object> entry) |
542 |
|
{ |
543 |
0 |
return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry); |
544 |
|
} |
545 |
|
}; |
546 |
|
|
547 |
0 |
final TableRowSorter<TableModel> customSorter = new TableRowSorter<>( |
548 |
|
linkUrlTable.getModel()); |
549 |
0 |
customSorter.setRowFilter(customUrlFilter); |
550 |
|
|
551 |
0 |
ActionListener onCustomOnly; |
552 |
0 |
onCustomOnly = new ActionListener() |
553 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
554 |
0 |
@Override... |
555 |
|
public void actionPerformed(ActionEvent e) |
556 |
|
{ |
557 |
0 |
filterTB.setText(""); |
558 |
0 |
sorter.setRowFilter(customUrlFilter); |
559 |
|
} |
560 |
|
}; |
561 |
0 |
userOnly.addActionListener(onCustomOnly); |
562 |
|
|
563 |
0 |
filterTB.getDocument().addDocumentListener(new DocumentListener() |
564 |
|
{ |
565 |
|
String caseInsensitiveFlag = "(?i)"; |
566 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
567 |
0 |
@Override... |
568 |
|
public void changedUpdate(DocumentEvent e) |
569 |
|
{ |
570 |
0 |
sorter.setRowFilter(RowFilter |
571 |
|
.regexFilter(caseInsensitiveFlag + filterTB.getText())); |
572 |
|
} |
573 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
574 |
0 |
@Override... |
575 |
|
public void removeUpdate(DocumentEvent e) |
576 |
|
{ |
577 |
0 |
sorter.setRowFilter(RowFilter |
578 |
|
.regexFilter(caseInsensitiveFlag + filterTB.getText())); |
579 |
|
} |
580 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
581 |
0 |
@Override... |
582 |
|
public void insertUpdate(DocumentEvent e) |
583 |
|
{ |
584 |
0 |
sorter.setRowFilter(RowFilter |
585 |
|
.regexFilter(caseInsensitiveFlag + filterTB.getText())); |
586 |
|
} |
587 |
|
}); |
588 |
|
|
589 |
|
|
590 |
0 |
linkUrlTable.getSelectionModel() |
591 |
|
.addListSelectionListener(new UrlListSelectionHandler()); |
592 |
|
|
593 |
|
|
594 |
0 |
int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel()) |
595 |
|
.getPrimaryColumn(); |
596 |
0 |
String onClickName = linkUrlTable.getColumnName(onClickCol); |
597 |
0 |
linkUrlTable.getColumn(onClickName) |
598 |
|
.setCellRenderer(new RadioButtonRenderer()); |
599 |
0 |
linkUrlTable.getColumn(onClickName) |
600 |
|
.setCellEditor(new RadioButtonEditor()); |
601 |
|
|
602 |
|
|
603 |
0 |
for (int column = 0; column < linkUrlTable.getColumnCount(); column++) |
604 |
|
{ |
605 |
0 |
if (linkUrlTable.getModel().getColumnClass(column) |
606 |
|
.equals(Boolean.class)) |
607 |
|
{ |
608 |
0 |
TableColumn tableColumn = linkUrlTable.getColumnModel() |
609 |
|
.getColumn(column); |
610 |
0 |
int preferredWidth = tableColumn.getMinWidth(); |
611 |
|
|
612 |
0 |
TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0, |
613 |
|
column); |
614 |
0 |
Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column); |
615 |
0 |
int cwidth = c.getPreferredSize().width |
616 |
|
+ linkUrlTable.getIntercellSpacing().width; |
617 |
0 |
preferredWidth = Math.max(preferredWidth, cwidth); |
618 |
|
|
619 |
0 |
tableColumn.setPreferredWidth(preferredWidth); |
620 |
|
} |
621 |
|
} |
622 |
|
|
623 |
0 |
String proxyTypeString = Cache.getDefault("USE_PROXY", "false"); |
624 |
0 |
previousProxyType = proxyTypeString; |
625 |
0 |
switch (proxyTypeString) |
626 |
|
{ |
627 |
0 |
case Cache.PROXYTYPE_NONE: |
628 |
0 |
proxyType.setSelected(noProxy.getModel(), true); |
629 |
0 |
break; |
630 |
0 |
case Cache.PROXYTYPE_SYSTEM: |
631 |
0 |
proxyType.setSelected(systemProxy.getModel(), true); |
632 |
0 |
break; |
633 |
0 |
case Cache.PROXYTYPE_CUSTOM: |
634 |
0 |
proxyType.setSelected(customProxy.getModel(), true); |
635 |
0 |
break; |
636 |
0 |
default: |
637 |
0 |
Console.warn( |
638 |
|
"Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): " |
639 |
|
+ proxyTypeString); |
640 |
|
} |
641 |
0 |
proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", "")); |
642 |
0 |
proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", "")); |
643 |
0 |
proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", "")); |
644 |
0 |
proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", "")); |
645 |
0 |
proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false)); |
646 |
0 |
proxyAuthUsernameTB |
647 |
|
.setText(Cache.getDefault("PROXY_AUTH_USERNAME", "")); |
648 |
|
|
649 |
0 |
proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? "" |
650 |
|
: new String(Cache.proxyAuthPassword)); |
651 |
0 |
setCustomProxyEnabled(); |
652 |
0 |
applyProxyButtonEnabled(false); |
653 |
|
|
654 |
0 |
usagestats.setSelected(Cache.getDefault("USAGESTATS", false)); |
655 |
|
|
656 |
0 |
questionnaire |
657 |
|
.setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); |
658 |
0 |
versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); |
659 |
|
|
660 |
|
|
661 |
|
|
662 |
|
|
663 |
0 |
setupOutputCombo(epsRendering, "EPS_RENDERING"); |
664 |
0 |
setupOutputCombo(htmlRendering, "HTML_RENDERING"); |
665 |
0 |
setupOutputCombo(svgRendering, "SVG_RENDERING"); |
666 |
0 |
autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); |
667 |
0 |
userIdWidth.setEnabled(!autoIdWidth.isSelected()); |
668 |
0 |
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); |
669 |
0 |
Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"); |
670 |
0 |
userIdWidth.setText(wi == null ? "" : wi.toString()); |
671 |
|
|
672 |
|
|
673 |
0 |
blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true)); |
674 |
0 |
clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true)); |
675 |
0 |
fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true)); |
676 |
0 |
msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true)); |
677 |
0 |
pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true)); |
678 |
0 |
pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true)); |
679 |
0 |
pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true)); |
680 |
0 |
modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false)); |
681 |
0 |
embbedBioJSON |
682 |
|
.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true)); |
683 |
|
|
684 |
|
|
685 |
|
|
686 |
|
|
687 |
0 |
autoCalculateConsCheck |
688 |
|
.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true)); |
689 |
0 |
padGaps.setSelected(Cache.getDefault("PAD_GAPS", false)); |
690 |
0 |
sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false)); |
691 |
|
|
692 |
0 |
annotations_actionPerformed(null); |
693 |
|
|
694 |
|
|
695 |
|
|
696 |
|
|
697 |
|
|
698 |
0 |
loadLastSavedBackupsOptions(); |
699 |
|
|
700 |
|
|
701 |
|
|
702 |
|
|
703 |
|
|
704 |
|
|
705 |
0 |
Cache.enableSessionProperties(); |
706 |
|
} |
707 |
|
|
708 |
|
|
709 |
|
|
710 |
|
|
711 |
|
|
712 |
|
@param |
713 |
|
@param |
714 |
|
|
|
|
| 0% |
Uncovered Elements: 17 (17) |
Complexity: 4 |
Complexity Density: 0.36 |
|
715 |
0 |
protected void setupOutputCombo(JComboBox<Object> comboBox,... |
716 |
|
String propertyKey) |
717 |
|
{ |
718 |
0 |
Cache.disableSessionProperties(); |
719 |
|
|
720 |
0 |
comboBox.addItem(promptEachTimeOpt); |
721 |
0 |
comboBox.addItem(lineArtOpt); |
722 |
0 |
comboBox.addItem(textOpt); |
723 |
|
|
724 |
|
|
725 |
|
|
726 |
|
|
727 |
0 |
String defaultOption = Platform.isJS() ? "Text" |
728 |
|
: Cache.getDefault(propertyKey, "Prompt each time"); |
729 |
0 |
if (defaultOption.equalsIgnoreCase("Text")) |
730 |
|
{ |
731 |
0 |
comboBox.setSelectedItem(textOpt); |
732 |
|
} |
733 |
0 |
else if (defaultOption.equalsIgnoreCase("Lineart")) |
734 |
|
{ |
735 |
0 |
comboBox.setSelectedItem(lineArtOpt); |
736 |
|
} |
737 |
|
else |
738 |
|
{ |
739 |
0 |
comboBox.setSelectedItem(promptEachTimeOpt); |
740 |
|
} |
741 |
|
|
742 |
0 |
Cache.enableSessionProperties(); |
743 |
|
} |
744 |
|
|
745 |
|
|
746 |
|
|
747 |
|
|
748 |
|
|
749 |
|
@param |
750 |
|
|
|
|
| 0% |
Uncovered Elements: 134 (134) |
Complexity: 14 |
Complexity Density: 0.12 |
|
751 |
0 |
@Override... |
752 |
|
public void ok_actionPerformed(ActionEvent e) |
753 |
|
{ |
754 |
0 |
Cache.disableSessionProperties(); |
755 |
|
|
756 |
0 |
if (!validateSettings()) |
757 |
|
{ |
758 |
0 |
return; |
759 |
|
} |
760 |
|
|
761 |
|
|
762 |
|
|
763 |
|
|
764 |
0 |
saveProxySettings(); |
765 |
|
|
766 |
|
|
767 |
|
|
768 |
|
|
769 |
|
|
770 |
0 |
Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", |
771 |
|
Boolean.toString(seqLimit.isSelected())); |
772 |
0 |
Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", |
773 |
|
Boolean.toString(rightAlign.isSelected())); |
774 |
0 |
Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", |
775 |
|
Boolean.toString(fullScreen.isSelected())); |
776 |
0 |
Cache.applicationProperties.setProperty("SHOW_OVERVIEW", |
777 |
|
Boolean.toString(openoverv.isSelected())); |
778 |
0 |
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", |
779 |
|
Boolean.toString(annotations.isSelected())); |
780 |
0 |
Cache.applicationProperties.setProperty("SHOW_CONSERVATION", |
781 |
|
Boolean.toString(conservation.isSelected())); |
782 |
0 |
Cache.applicationProperties.setProperty("SHOW_QUALITY", |
783 |
|
Boolean.toString(quality.isSelected())); |
784 |
0 |
Cache.applicationProperties.setProperty("SHOW_IDENTITY", |
785 |
|
Boolean.toString(identity.isSelected())); |
786 |
|
|
787 |
0 |
Cache.applicationProperties.setProperty("SHOW_SS_CONSENSUS", |
788 |
|
Boolean.toString(ssConsensus.isSelected())); |
789 |
|
|
790 |
0 |
Cache.applicationProperties.setProperty("GAP_SYMBOL", |
791 |
|
gapSymbolCB.getSelectedItem().toString()); |
792 |
|
|
793 |
0 |
Cache.applicationProperties.setProperty("FONT_NAME", |
794 |
|
fontNameCB.getSelectedItem().toString()); |
795 |
0 |
Cache.applicationProperties.setProperty("FONT_STYLE", |
796 |
|
fontStyleCB.getSelectedItem().toString()); |
797 |
0 |
Cache.applicationProperties.setProperty("FONT_SIZE", |
798 |
|
fontSizeCB.getSelectedItem().toString()); |
799 |
|
|
800 |
0 |
Cache.applicationProperties.setProperty("ID_ITALICS", |
801 |
|
Boolean.toString(idItalics.isSelected())); |
802 |
0 |
Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", |
803 |
|
Boolean.toString(showUnconserved.isSelected())); |
804 |
0 |
Cache.applicationProperties.setProperty(SHOW_OCCUPANCY, |
805 |
|
Boolean.toString(showOccupancy.isSelected())); |
806 |
0 |
Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", |
807 |
|
Boolean.toString(showGroupConsensus.isSelected())); |
808 |
0 |
Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION", |
809 |
|
Boolean.toString(showGroupConservation.isSelected())); |
810 |
0 |
Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM", |
811 |
|
Boolean.toString(showConsensHistogram.isSelected())); |
812 |
0 |
Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", |
813 |
|
Boolean.toString(showConsensLogo.isSelected())); |
814 |
0 |
Cache.applicationProperties.setProperty("ANTI_ALIAS", |
815 |
|
Boolean.toString(smoothFont.isSelected())); |
816 |
0 |
Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA, |
817 |
|
Boolean.toString(scaleProteinToCdna.isSelected())); |
818 |
0 |
Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", |
819 |
|
Boolean.toString(showNpTooltip.isSelected())); |
820 |
0 |
Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", |
821 |
|
Boolean.toString(showDbRefTooltip.isSelected())); |
822 |
|
|
823 |
0 |
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", |
824 |
|
Boolean.toString(wrap.isSelected())); |
825 |
|
|
826 |
0 |
Cache.applicationProperties.setProperty("STARTUP_FILE", |
827 |
|
startupFileTextfield.getText()); |
828 |
0 |
Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", |
829 |
|
Boolean.toString(startupCheckbox.isSelected())); |
830 |
|
|
831 |
0 |
Cache.applicationProperties.setProperty("SORT_ALIGNMENT", |
832 |
|
sortby.getSelectedItem().toString()); |
833 |
|
|
834 |
|
|
835 |
0 |
SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder |
836 |
|
.forDescription(sortAnnBy.getSelectedItem().toString()); |
837 |
0 |
if (annSortOrder != null) |
838 |
|
{ |
839 |
0 |
Cache.applicationProperties.setProperty(SORT_ANNOTATIONS, |
840 |
|
annSortOrder.name()); |
841 |
|
} |
842 |
|
|
843 |
0 |
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0; |
844 |
0 |
Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, |
845 |
|
Boolean.valueOf(showAutocalcFirst).toString()); |
846 |
|
|
847 |
|
|
848 |
|
|
849 |
|
|
850 |
0 |
Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, |
851 |
|
protColour.getSelectedItem().toString()); |
852 |
0 |
Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, |
853 |
|
nucColour.getSelectedItem().toString()); |
854 |
0 |
Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", |
855 |
|
minColour.getBackground()); |
856 |
0 |
Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", |
857 |
|
maxColour.getBackground()); |
858 |
|
|
859 |
|
|
860 |
|
|
861 |
|
|
862 |
0 |
Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground()); |
863 |
0 |
Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground()); |
864 |
0 |
Cache.applicationProperties.setProperty(USE_LEGACY_GAP, |
865 |
|
Boolean.toString(useLegacyGap.isSelected())); |
866 |
0 |
Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START, |
867 |
|
Boolean.toString(showHiddenAtStart.isSelected())); |
868 |
|
|
869 |
|
|
870 |
|
|
871 |
|
|
872 |
0 |
Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN, |
873 |
|
Boolean.toString(addTempFactor.isSelected())); |
874 |
0 |
Cache.applicationProperties.setProperty(ADD_SS_ANN, |
875 |
|
Boolean.toString(addSecondaryStructure.isSelected())); |
876 |
0 |
Cache.applicationProperties.setProperty(STRUCT_FROM_PDB, |
877 |
|
Boolean.toString(structFromPdb.isSelected())); |
878 |
0 |
String viewer = structViewer.getSelectedItem().toString(); |
879 |
0 |
String viewerPath = structureViewerPath.getText(); |
880 |
0 |
Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer); |
881 |
0 |
if (viewer.equals(ViewerType.CHIMERA.name())) |
882 |
|
{ |
883 |
0 |
Cache.setOrRemove(CHIMERA_PATH, viewerPath); |
884 |
|
} |
885 |
0 |
else if (viewer.equals(ViewerType.CHIMERAX.name())) |
886 |
|
{ |
887 |
0 |
Cache.setOrRemove(CHIMERAX_PATH, viewerPath); |
888 |
|
} |
889 |
0 |
else if (viewer.equals(ViewerType.PYMOL.name())) |
890 |
|
{ |
891 |
0 |
Cache.setOrRemove(PYMOL_PATH, viewerPath); |
892 |
|
} |
893 |
0 |
Cache.applicationProperties.setProperty("MAP_WITH_SIFTS", |
894 |
|
Boolean.toString(siftsMapping.isSelected())); |
895 |
0 |
SiftsSettings.setMapWithSifts(siftsMapping.isSelected()); |
896 |
|
|
897 |
|
|
898 |
|
|
899 |
|
|
900 |
0 |
Cache.applicationProperties.setProperty("EPS_RENDERING", |
901 |
|
((OptionsParam) epsRendering.getSelectedItem()).getCode()); |
902 |
0 |
Cache.applicationProperties.setProperty("HTML_RENDERING", |
903 |
|
((OptionsParam) htmlRendering.getSelectedItem()).getCode()); |
904 |
0 |
Cache.applicationProperties.setProperty("SVG_RENDERING", |
905 |
|
((OptionsParam) svgRendering.getSelectedItem()).getCode()); |
906 |
|
|
907 |
|
|
908 |
|
|
909 |
|
|
910 |
|
|
911 |
|
|
912 |
|
|
913 |
0 |
String menuLinks = sequenceUrlLinks.writeUrlsAsString(true); |
914 |
0 |
if (menuLinks.isEmpty()) |
915 |
|
{ |
916 |
0 |
Cache.applicationProperties.remove("SEQUENCE_LINKS"); |
917 |
|
} |
918 |
|
else |
919 |
|
{ |
920 |
0 |
Cache.applicationProperties.setProperty("SEQUENCE_LINKS", |
921 |
|
menuLinks.toString()); |
922 |
|
} |
923 |
|
|
924 |
0 |
String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false); |
925 |
0 |
if (nonMenuLinks.isEmpty()) |
926 |
|
{ |
927 |
0 |
Cache.applicationProperties.remove("STORED_LINKS"); |
928 |
|
} |
929 |
|
else |
930 |
|
{ |
931 |
0 |
Cache.applicationProperties.setProperty("STORED_LINKS", |
932 |
|
nonMenuLinks.toString()); |
933 |
|
} |
934 |
|
|
935 |
0 |
Cache.applicationProperties.setProperty("DEFAULT_URL", |
936 |
|
sequenceUrlLinks.getPrimaryUrlId()); |
937 |
|
|
938 |
0 |
Cache.setProperty("VERSION_CHECK", |
939 |
|
Boolean.toString(versioncheck.isSelected())); |
940 |
0 |
if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected()) |
941 |
|
{ |
942 |
|
|
943 |
0 |
Cache.setProperty("USAGESTATS", |
944 |
|
Boolean.toString(usagestats.isSelected())); |
945 |
|
} |
946 |
0 |
if (!questionnaire.isSelected()) |
947 |
|
{ |
948 |
0 |
Cache.setProperty("NOQUESTIONNAIRES", "true"); |
949 |
|
} |
950 |
|
else |
951 |
|
{ |
952 |
|
|
953 |
|
|
954 |
0 |
Cache.removeProperty("NOQUESTIONNAIRES"); |
955 |
|
} |
956 |
|
|
957 |
|
|
958 |
|
|
959 |
|
|
960 |
0 |
Cache.applicationProperties.setProperty("BLC_JVSUFFIX", |
961 |
|
Boolean.toString(blcjv.isSelected())); |
962 |
0 |
Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", |
963 |
|
Boolean.toString(clustaljv.isSelected())); |
964 |
0 |
Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", |
965 |
|
Boolean.toString(fastajv.isSelected())); |
966 |
0 |
Cache.applicationProperties.setProperty("MSF_JVSUFFIX", |
967 |
|
Boolean.toString(msfjv.isSelected())); |
968 |
0 |
Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", |
969 |
|
Boolean.toString(pfamjv.isSelected())); |
970 |
0 |
Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", |
971 |
|
Boolean.toString(pileupjv.isSelected())); |
972 |
0 |
Cache.applicationProperties.setProperty("PIR_JVSUFFIX", |
973 |
|
Boolean.toString(pirjv.isSelected())); |
974 |
0 |
Cache.applicationProperties.setProperty("PIR_MODELLER", |
975 |
|
Boolean.toString(modellerOutput.isSelected())); |
976 |
0 |
Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON", |
977 |
|
Boolean.toString(embbedBioJSON.isSelected())); |
978 |
0 |
jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected(); |
979 |
|
|
980 |
0 |
Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH", |
981 |
|
Boolean.toString(autoIdWidth.isSelected())); |
982 |
0 |
userIdWidth_actionPerformed(); |
983 |
0 |
Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH", |
984 |
|
userIdWidth.getText()); |
985 |
|
|
986 |
|
|
987 |
|
|
988 |
|
|
989 |
0 |
Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", |
990 |
|
Boolean.toString(autoCalculateConsCheck.isSelected())); |
991 |
0 |
Cache.applicationProperties.setProperty("SORT_BY_TREE", |
992 |
|
Boolean.toString(sortByTree.isSelected())); |
993 |
0 |
Cache.applicationProperties.setProperty("PAD_GAPS", |
994 |
|
Boolean.toString(padGaps.isSelected())); |
995 |
|
|
996 |
0 |
if (!Platform.isJS()) |
997 |
|
{ |
998 |
0 |
wsPrefs.updateAndRefreshWsMenuConfig(false); |
999 |
|
} |
1000 |
|
|
1001 |
|
|
1002 |
|
|
1003 |
|
|
1004 |
0 |
Cache.applicationProperties.setProperty(BackupFiles.ENABLED, |
1005 |
|
Boolean.toString(enableBackupFiles.isSelected())); |
1006 |
0 |
int preset = getComboIntStringKey(backupfilesPresetsCombo); |
1007 |
0 |
Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", |
1008 |
|
Integer.toString(preset)); |
1009 |
|
|
1010 |
0 |
if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM) |
1011 |
|
{ |
1012 |
0 |
BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry(); |
1013 |
0 |
BackupFilesPresetEntry.backupfilesPresetEntriesValues.put( |
1014 |
|
BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE); |
1015 |
0 |
Cache.applicationProperties.setProperty( |
1016 |
|
BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString()); |
1017 |
|
} |
1018 |
|
|
1019 |
0 |
BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues |
1020 |
|
.get(preset); |
1021 |
0 |
Cache.applicationProperties.setProperty( |
1022 |
|
BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString()); |
1023 |
|
|
1024 |
|
|
1025 |
|
|
1026 |
|
|
1027 |
0 |
Cache.applicationProperties.setProperty( |
1028 |
|
MemorySetting.CUSTOMISED_SETTINGS, |
1029 |
|
Boolean.toString(customiseMemorySetting.isSelected())); |
1030 |
0 |
Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC, |
1031 |
|
Integer.toString(jvmMemoryPercentSlider.getValue())); |
1032 |
0 |
Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX, |
1033 |
|
jvmMemoryMaxTextField.getText()); |
1034 |
|
|
1035 |
|
|
1036 |
|
|
1037 |
|
|
1038 |
|
|
1039 |
0 |
Cache.saveProperties(); |
1040 |
0 |
Desktop.instance.doConfigureStructurePrefs(); |
1041 |
0 |
try |
1042 |
|
{ |
1043 |
0 |
frame.setClosed(true); |
1044 |
|
} catch (Exception ex) |
1045 |
|
{ |
1046 |
|
} |
1047 |
|
|
1048 |
0 |
Cache.enableSessionProperties(); |
1049 |
|
} |
1050 |
|
|
|
|
| 0% |
Uncovered Elements: 21 (21) |
Complexity: 5 |
Complexity Density: 0.33 |
|
1051 |
0 |
@Override... |
1052 |
|
public void saveProxySettings() |
1053 |
|
{ |
1054 |
0 |
Cache.disableSessionProperties(); |
1055 |
|
|
1056 |
0 |
String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM |
1057 |
0 |
: noProxy.isSelected() ? Cache.PROXYTYPE_NONE |
1058 |
|
: Cache.PROXYTYPE_SYSTEM; |
1059 |
0 |
Cache.applicationProperties.setProperty("USE_PROXY", newProxyType); |
1060 |
0 |
Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText()); |
1061 |
0 |
Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText()); |
1062 |
0 |
Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText()); |
1063 |
0 |
Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText()); |
1064 |
0 |
Cache.setOrRemove("PROXY_AUTH", |
1065 |
|
Boolean.toString(proxyAuth.isSelected())); |
1066 |
0 |
Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText()); |
1067 |
0 |
Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword(); |
1068 |
0 |
Cache.setProxyPropertiesFromPreferences(previousProxyType); |
1069 |
0 |
if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM) |
1070 |
|
|| !newProxyType.equals(previousProxyType)) |
1071 |
|
{ |
1072 |
|
|
1073 |
0 |
wsPrefs.update++; |
1074 |
|
} |
1075 |
0 |
previousProxyType = newProxyType; |
1076 |
|
|
1077 |
0 |
Cache.enableSessionProperties(); |
1078 |
|
} |
1079 |
|
|
1080 |
|
|
1081 |
|
|
1082 |
|
|
1083 |
|
|
1084 |
|
@return |
1085 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1086 |
0 |
private boolean validateSettings()... |
1087 |
|
{ |
1088 |
0 |
if (!validateStructure()) |
1089 |
|
{ |
1090 |
0 |
structureTab.requestFocusInWindow(); |
1091 |
0 |
return false; |
1092 |
|
} |
1093 |
0 |
return true; |
1094 |
|
} |
1095 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1096 |
0 |
@Override... |
1097 |
|
protected boolean validateStructure() |
1098 |
|
{ |
1099 |
0 |
return validateViewerPath(); |
1100 |
|
|
1101 |
|
} |
1102 |
|
|
1103 |
|
|
1104 |
|
|
1105 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
1106 |
0 |
@Override... |
1107 |
|
public void startupFileTextfield_mouseClicked() |
1108 |
|
{ |
1109 |
0 |
Cache.disableSessionProperties(); |
1110 |
|
|
1111 |
|
|
1112 |
|
|
1113 |
0 |
JalviewFileChooser chooser = JalviewFileChooser |
1114 |
|
.forRead(Cache.getProperty("LAST_DIRECTORY"), null); |
1115 |
0 |
chooser.setFileView(new JalviewFileView()); |
1116 |
0 |
chooser.setDialogTitle( |
1117 |
|
MessageManager.getString("label.select_startup_file")); |
1118 |
|
|
1119 |
0 |
int value = chooser.showOpenDialog(this); |
1120 |
|
|
1121 |
0 |
if (value == JalviewFileChooser.APPROVE_OPTION) |
1122 |
|
{ |
1123 |
0 |
FileFormatI format = chooser.getSelectedFormat(); |
1124 |
0 |
if (format != null) |
1125 |
|
{ |
1126 |
0 |
Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT", |
1127 |
|
format.getName()); |
1128 |
|
} |
1129 |
0 |
startupFileTextfield |
1130 |
|
.setText(chooser.getSelectedFile().getAbsolutePath()); |
1131 |
|
} |
1132 |
|
|
1133 |
0 |
Cache.enableSessionProperties(); |
1134 |
|
} |
1135 |
|
|
1136 |
|
|
1137 |
|
|
1138 |
|
|
1139 |
|
@param |
1140 |
|
|
1141 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 3 |
Complexity Density: 0.6 |
|
1142 |
0 |
@Override... |
1143 |
|
public void cancel_actionPerformed(ActionEvent e) |
1144 |
|
{ |
1145 |
0 |
try |
1146 |
|
{ |
1147 |
0 |
if (!Platform.isJS()) |
1148 |
|
{ |
1149 |
0 |
wsPrefs.updateWsMenuConfig(true); |
1150 |
0 |
wsPrefs.refreshWs_actionPerformed(e); |
1151 |
|
} |
1152 |
0 |
frame.setClosed(true); |
1153 |
|
} catch (Exception ex) |
1154 |
|
{ |
1155 |
|
} |
1156 |
|
} |
1157 |
|
|
1158 |
|
|
1159 |
|
|
1160 |
|
|
1161 |
|
@param |
1162 |
|
|
1163 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
|
1164 |
0 |
@Override... |
1165 |
|
public void annotations_actionPerformed(ActionEvent e) |
1166 |
|
{ |
1167 |
0 |
conservation.setEnabled(annotations.isSelected()); |
1168 |
0 |
quality.setEnabled(annotations.isSelected()); |
1169 |
0 |
identity.setEnabled(annotations.isSelected()); |
1170 |
0 |
ssConsensus.setEnabled(annotations.isSelected()); |
1171 |
0 |
showOccupancy.setEnabled(annotations.isSelected()); |
1172 |
0 |
showGroupConsensus.setEnabled(annotations.isSelected()); |
1173 |
0 |
showGroupConservation.setEnabled(annotations.isSelected()); |
1174 |
0 |
showConsensHistogram.setEnabled(annotations.isSelected() |
1175 |
|
&& (identity.isSelected() || showGroupConsensus.isSelected())); |
1176 |
0 |
showConsensLogo.setEnabled(annotations.isSelected() |
1177 |
|
&& (identity.isSelected() || showGroupConsensus.isSelected())); |
1178 |
|
} |
1179 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 5 |
Complexity Density: 0.45 |
|
1180 |
0 |
@Override... |
1181 |
|
public void newLink_actionPerformed(ActionEvent e) |
1182 |
|
{ |
1183 |
0 |
GSequenceLink link = new GSequenceLink(); |
1184 |
0 |
boolean valid = false; |
1185 |
0 |
while (!valid) |
1186 |
|
{ |
1187 |
0 |
if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, |
1188 |
|
MessageManager.getString("label.new_sequence_url_link"), |
1189 |
|
JvOptionPane.OK_CANCEL_OPTION, -1, |
1190 |
|
null) == JvOptionPane.OK_OPTION) |
1191 |
|
{ |
1192 |
0 |
if (link.checkValid()) |
1193 |
|
{ |
1194 |
0 |
if (((UrlLinkTableModel) linkUrlTable.getModel()) |
1195 |
|
.isUniqueName(link.getName())) |
1196 |
|
{ |
1197 |
0 |
((UrlLinkTableModel) linkUrlTable.getModel()) |
1198 |
|
.insertRow(link.getName(), link.getURL()); |
1199 |
0 |
valid = true; |
1200 |
|
} |
1201 |
|
else |
1202 |
|
{ |
1203 |
0 |
link.notifyDuplicate(); |
1204 |
0 |
continue; |
1205 |
|
} |
1206 |
|
} |
1207 |
|
} |
1208 |
|
else |
1209 |
|
{ |
1210 |
0 |
break; |
1211 |
|
} |
1212 |
|
} |
1213 |
|
} |
1214 |
|
|
|
|
| 0% |
Uncovered Elements: 31 (31) |
Complexity: 7 |
Complexity Density: 0.33 |
|
1215 |
0 |
@Override... |
1216 |
|
public void editLink_actionPerformed(ActionEvent e) |
1217 |
|
{ |
1218 |
0 |
GSequenceLink link = new GSequenceLink(); |
1219 |
|
|
1220 |
0 |
int index = linkUrlTable.getSelectedRow(); |
1221 |
0 |
if (index == -1) |
1222 |
|
{ |
1223 |
|
|
1224 |
0 |
Console.debug("Edit with no row selected in linkUrlTable"); |
1225 |
0 |
return; |
1226 |
|
} |
1227 |
|
|
1228 |
0 |
int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel()) |
1229 |
|
.getNameColumn(); |
1230 |
0 |
int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel()) |
1231 |
|
.getUrlColumn(); |
1232 |
0 |
String oldName = linkUrlTable.getValueAt(index, nameCol).toString(); |
1233 |
0 |
link.setName(oldName); |
1234 |
0 |
link.setURL(linkUrlTable.getValueAt(index, urlCol).toString()); |
1235 |
|
|
1236 |
0 |
boolean valid = false; |
1237 |
0 |
while (!valid) |
1238 |
|
{ |
1239 |
0 |
if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, |
1240 |
|
MessageManager.getString("label.edit_sequence_url_link"), |
1241 |
|
JvOptionPane.OK_CANCEL_OPTION, -1, |
1242 |
|
null) == JvOptionPane.OK_OPTION) |
1243 |
|
{ |
1244 |
0 |
if (link.checkValid()) |
1245 |
|
{ |
1246 |
0 |
if ((oldName.equals(link.getName())) |
1247 |
|
|| (((UrlLinkTableModel) linkUrlTable.getModel()) |
1248 |
|
.isUniqueName(link.getName()))) |
1249 |
|
{ |
1250 |
0 |
linkUrlTable.setValueAt(link.getName(), index, nameCol); |
1251 |
0 |
linkUrlTable.setValueAt(link.getURL(), index, urlCol); |
1252 |
0 |
valid = true; |
1253 |
|
} |
1254 |
|
else |
1255 |
|
{ |
1256 |
0 |
link.notifyDuplicate(); |
1257 |
0 |
continue; |
1258 |
|
} |
1259 |
|
} |
1260 |
|
} |
1261 |
|
else |
1262 |
|
{ |
1263 |
0 |
break; |
1264 |
|
} |
1265 |
|
} |
1266 |
|
} |
1267 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
1268 |
0 |
@Override... |
1269 |
|
public void deleteLink_actionPerformed(ActionEvent e) |
1270 |
|
{ |
1271 |
0 |
int index = linkUrlTable.getSelectedRow(); |
1272 |
0 |
int modelIndex = -1; |
1273 |
0 |
if (index == -1) |
1274 |
|
{ |
1275 |
|
|
1276 |
0 |
Console.debug("Delete with no row selected in linkUrlTable"); |
1277 |
0 |
return; |
1278 |
|
} |
1279 |
|
else |
1280 |
|
{ |
1281 |
0 |
modelIndex = linkUrlTable.convertRowIndexToModel(index); |
1282 |
|
} |
1283 |
|
|
1284 |
|
|
1285 |
0 |
((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex); |
1286 |
|
} |
1287 |
|
|
1288 |
|
|
1289 |
|
|
1290 |
|
|
1291 |
|
@see |
1292 |
|
|
1293 |
|
|
1294 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1295 |
0 |
@Override... |
1296 |
|
protected void showunconserved_actionPerformed(ActionEvent e) |
1297 |
|
{ |
1298 |
|
|
1299 |
0 |
super.showunconserved_actionPerformed(e); |
1300 |
|
} |
1301 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1302 |
0 |
public static List<String> getGroupURLLinks()... |
1303 |
|
{ |
1304 |
0 |
return groupURLLinks; |
1305 |
|
} |
1306 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1307 |
0 |
@Override... |
1308 |
|
public void minColour_actionPerformed(JPanel panel) |
1309 |
|
{ |
1310 |
0 |
JalviewColourChooser.showColourChooser(this, |
1311 |
|
MessageManager.getString("label.select_colour_minimum_value"), |
1312 |
|
panel); |
1313 |
|
} |
1314 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1315 |
0 |
@Override... |
1316 |
|
public void maxColour_actionPerformed(JPanel panel) |
1317 |
|
{ |
1318 |
0 |
JalviewColourChooser.showColourChooser(this, |
1319 |
|
MessageManager.getString("label.select_colour_maximum_value"), |
1320 |
|
panel); |
1321 |
|
} |
1322 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1323 |
0 |
@Override... |
1324 |
|
public void gapColour_actionPerformed(JPanel gap) |
1325 |
|
{ |
1326 |
0 |
if (!useLegacyGap.isSelected()) |
1327 |
|
{ |
1328 |
0 |
JalviewColourChooser.showColourChooser(this, |
1329 |
|
MessageManager.getString("label.select_gap_colour"), gap); |
1330 |
|
} |
1331 |
|
} |
1332 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1333 |
0 |
@Override... |
1334 |
|
public void hiddenColour_actionPerformed(JPanel hidden) |
1335 |
|
{ |
1336 |
0 |
JalviewColourChooser.showColourChooser(this, |
1337 |
|
MessageManager.getString("label.select_hidden_colour"), hidden); |
1338 |
|
} |
1339 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
1340 |
0 |
@Override... |
1341 |
|
protected void useLegacyGaps_actionPerformed(ActionEvent e) |
1342 |
|
{ |
1343 |
0 |
boolean enabled = useLegacyGap.isSelected(); |
1344 |
0 |
if (enabled) |
1345 |
|
{ |
1346 |
0 |
gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP); |
1347 |
|
} |
1348 |
|
else |
1349 |
|
{ |
1350 |
0 |
gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP); |
1351 |
|
} |
1352 |
0 |
gapColour.setEnabled(!enabled); |
1353 |
0 |
gapLabel.setEnabled(!enabled); |
1354 |
|
} |
1355 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
1356 |
0 |
@Override... |
1357 |
|
protected void resetOvDefaults_actionPerformed(ActionEvent e) |
1358 |
|
{ |
1359 |
0 |
useLegacyGap.setSelected(false); |
1360 |
0 |
useLegacyGaps_actionPerformed(null); |
1361 |
0 |
showHiddenAtStart.setSelected(false); |
1362 |
0 |
hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN); |
1363 |
|
} |
1364 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 4 |
Complexity Density: 0.44 |
|
1365 |
0 |
@Override... |
1366 |
|
protected void userIdWidth_actionPerformed() |
1367 |
|
{ |
1368 |
0 |
try |
1369 |
|
{ |
1370 |
0 |
String val = userIdWidth.getText().trim(); |
1371 |
0 |
if (val.length() > 0) |
1372 |
|
{ |
1373 |
0 |
Integer iw = Integer.parseInt(val); |
1374 |
0 |
if (iw.intValue() < 12) |
1375 |
|
{ |
1376 |
0 |
throw new NumberFormatException(); |
1377 |
|
} |
1378 |
0 |
userIdWidth.setText(iw.toString()); |
1379 |
|
} |
1380 |
|
} catch (NumberFormatException x) |
1381 |
|
{ |
1382 |
0 |
userIdWidth.setText(""); |
1383 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
1384 |
|
MessageManager |
1385 |
|
.getString("warn.user_defined_width_requirements"), |
1386 |
|
MessageManager.getString("label.invalid_id_column_width"), |
1387 |
|
JvOptionPane.WARNING_MESSAGE); |
1388 |
|
} |
1389 |
|
} |
1390 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1391 |
0 |
@Override... |
1392 |
|
protected void autoIdWidth_actionPerformed() |
1393 |
|
{ |
1394 |
0 |
userIdWidth.setEnabled(!autoIdWidth.isSelected()); |
1395 |
0 |
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); |
1396 |
|
} |
1397 |
|
|
1398 |
|
|
1399 |
|
|
1400 |
|
|
1401 |
|
|
1402 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
1403 |
0 |
private boolean validateViewerPath()... |
1404 |
|
{ |
1405 |
0 |
if (structureViewerPath.getText().trim().length() > 0) |
1406 |
|
{ |
1407 |
0 |
File f = new File(structureViewerPath.getText()); |
1408 |
0 |
if (!f.canExecute()) |
1409 |
|
{ |
1410 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
1411 |
|
MessageManager.getString("label.invalid_viewer_path"), |
1412 |
|
MessageManager.getString("label.invalid_viewer_path"), |
1413 |
|
JvOptionPane.ERROR_MESSAGE); |
1414 |
0 |
return false; |
1415 |
|
} |
1416 |
|
} |
1417 |
0 |
return true; |
1418 |
|
} |
1419 |
|
|
1420 |
|
|
1421 |
|
|
1422 |
|
|
1423 |
|
|
|
|
| 0% |
Uncovered Elements: 73 (73) |
Complexity: 16 |
Complexity Density: 0.28 |
|
1424 |
0 |
@Override... |
1425 |
|
protected void structureViewer_actionPerformed(String selectedItem) |
1426 |
|
{ |
1427 |
0 |
if (selectedItem.equals(ViewerType.JMOL.name())) |
1428 |
|
{ |
1429 |
0 |
structureViewerPath.setEnabled(false); |
1430 |
0 |
structureViewerPathLabel.setEnabled(false); |
1431 |
0 |
return; |
1432 |
|
} |
1433 |
0 |
boolean found = false; |
1434 |
0 |
structureViewerPath.setEnabled(true); |
1435 |
0 |
structureViewerPathLabel.setEnabled(true); |
1436 |
0 |
structureViewerPathLabel.setText(MessageManager |
1437 |
|
.formatMessage("label.viewer_path", selectedItem)); |
1438 |
|
|
1439 |
|
|
1440 |
|
|
1441 |
|
|
1442 |
0 |
String viewerPath = ""; |
1443 |
0 |
List<String> paths = null; |
1444 |
0 |
Cache.disableSessionProperties(); |
1445 |
0 |
try |
1446 |
|
{ |
1447 |
0 |
ViewerType viewerType = ViewerType.valueOf(selectedItem); |
1448 |
0 |
switch (viewerType) |
1449 |
|
{ |
1450 |
0 |
case JMOL: |
1451 |
|
|
1452 |
0 |
break; |
1453 |
0 |
case CHIMERA: |
1454 |
0 |
viewerPath = Cache.getDefault(CHIMERA_PATH, ""); |
1455 |
0 |
paths = StructureManager.getChimeraPaths(false); |
1456 |
0 |
break; |
1457 |
0 |
case CHIMERAX: |
1458 |
0 |
viewerPath = Cache.getDefault(CHIMERAX_PATH, ""); |
1459 |
0 |
paths = StructureManager.getChimeraPaths(true); |
1460 |
0 |
break; |
1461 |
0 |
case PYMOL: |
1462 |
0 |
viewerPath = Cache.getDefault(PYMOL_PATH, ""); |
1463 |
0 |
paths = PymolManager.getPymolPaths(); |
1464 |
0 |
break; |
1465 |
|
} |
1466 |
|
} catch (IllegalArgumentException e) |
1467 |
|
{ |
1468 |
|
|
1469 |
|
} |
1470 |
0 |
Cache.enableSessionProperties(); |
1471 |
0 |
structureViewerPath.setText(viewerPath); |
1472 |
|
|
1473 |
0 |
jalview.bin.Console |
1474 |
0 |
.debug("Found " + (paths == null ? null : paths.size()) |
1475 |
|
+ " paths to look for " + selectedItem.toString()); |
1476 |
0 |
if (paths == null) |
1477 |
|
{ |
1478 |
0 |
paths = new ArrayList<>(); |
1479 |
|
} |
1480 |
0 |
paths.add(0, structureViewerPath.getText()); |
1481 |
0 |
for (String path : paths) |
1482 |
|
{ |
1483 |
0 |
jalview.bin.Console.debug("Looking for " + selectedItem.toString() |
1484 |
|
+ " in " + path.trim()); |
1485 |
0 |
if (new File(path.trim()).canExecute()) |
1486 |
|
{ |
1487 |
0 |
jalview.bin.Console.debug( |
1488 |
|
"Found " + selectedItem.toString() + " in " + path.trim()); |
1489 |
0 |
found = true; |
1490 |
0 |
break; |
1491 |
|
} |
1492 |
|
} |
1493 |
|
|
1494 |
0 |
if (!found) |
1495 |
|
{ |
1496 |
0 |
String[] options = { "OK", "Help" }; |
1497 |
0 |
int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop, |
1498 |
|
JvSwingUtils.wrapTooltip(true, |
1499 |
|
MessageManager.getString("label.viewer_missing")), |
1500 |
|
"", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, |
1501 |
|
null, options, options[0]); |
1502 |
|
|
1503 |
0 |
if (showHelp == JvOptionPane.NO_OPTION) |
1504 |
|
{ |
1505 |
0 |
this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null); |
1506 |
0 |
try |
1507 |
|
{ |
1508 |
0 |
Help.showHelpWindow(HelpId.StructureViewer); |
1509 |
|
} catch (HelpSetException e) |
1510 |
|
{ |
1511 |
0 |
e.printStackTrace(); |
1512 |
|
} |
1513 |
|
} |
1514 |
0 |
else if (showHelp == JvOptionPane.OK_OPTION) |
1515 |
|
{ |
1516 |
0 |
this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null); |
1517 |
0 |
CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> { |
1518 |
0 |
try |
1519 |
|
{ |
1520 |
0 |
for (int i = 0; i < 3; i++) |
1521 |
|
{ |
1522 |
0 |
structureViewerPath.setBackground(Color.PINK); |
1523 |
0 |
Thread.sleep(500); |
1524 |
0 |
structureViewerPath.setBackground(Color.WHITE); |
1525 |
0 |
Thread.sleep(500); |
1526 |
|
} |
1527 |
|
} catch (InterruptedException e) |
1528 |
|
{ |
1529 |
|
} |
1530 |
|
}); |
1531 |
|
} |
1532 |
|
} |
1533 |
|
} |
1534 |
|
|
|
|
| 0% |
Uncovered Elements: 21 (21) |
Complexity: 9 |
Complexity Density: 0.82 |
|
1535 |
|
public class OptionsParam |
1536 |
|
{ |
1537 |
|
private String name; |
1538 |
|
|
1539 |
|
private String code; |
1540 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1541 |
0 |
public OptionsParam(String name, String code)... |
1542 |
|
{ |
1543 |
0 |
this.name = name; |
1544 |
0 |
this.code = code; |
1545 |
|
} |
1546 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1547 |
0 |
public String getName()... |
1548 |
|
{ |
1549 |
0 |
return name; |
1550 |
|
} |
1551 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1552 |
0 |
public void setName(String name)... |
1553 |
|
{ |
1554 |
0 |
this.name = name; |
1555 |
|
} |
1556 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1557 |
0 |
public String getCode()... |
1558 |
|
{ |
1559 |
0 |
return code; |
1560 |
|
} |
1561 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1562 |
0 |
public void setCode(String code)... |
1563 |
|
{ |
1564 |
0 |
this.code = code; |
1565 |
|
} |
1566 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1567 |
0 |
@Override... |
1568 |
|
public String toString() |
1569 |
|
{ |
1570 |
0 |
return name; |
1571 |
|
} |
1572 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1573 |
0 |
@Override... |
1574 |
|
public boolean equals(Object that) |
1575 |
|
{ |
1576 |
0 |
if (!(that instanceof OptionsParam)) |
1577 |
|
{ |
1578 |
0 |
return false; |
1579 |
|
} |
1580 |
0 |
return this.code.equalsIgnoreCase(((OptionsParam) that).code); |
1581 |
|
} |
1582 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1583 |
0 |
@Override... |
1584 |
|
public int hashCode() |
1585 |
|
{ |
1586 |
0 |
return name.hashCode() + code.hashCode(); |
1587 |
|
} |
1588 |
|
} |
1589 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 4 |
Complexity Density: 0.31 |
|
1590 |
|
private class UrlListSelectionHandler implements ListSelectionListener |
1591 |
|
{ |
1592 |
|
|
|
|
| 0% |
Uncovered Elements: 19 (19) |
Complexity: 4 |
Complexity Density: 0.31 |
|
1593 |
0 |
@Override... |
1594 |
|
public void valueChanged(ListSelectionEvent e) |
1595 |
|
{ |
1596 |
0 |
ListSelectionModel lsm = (ListSelectionModel) e.getSource(); |
1597 |
|
|
1598 |
0 |
int index = lsm.getMinSelectionIndex(); |
1599 |
0 |
if (index == -1) |
1600 |
|
{ |
1601 |
|
|
1602 |
0 |
editLink.setEnabled(false); |
1603 |
0 |
deleteLink.setEnabled(false); |
1604 |
0 |
return; |
1605 |
|
} |
1606 |
0 |
int modelIndex = linkUrlTable.convertRowIndexToModel(index); |
1607 |
|
|
1608 |
|
|
1609 |
0 |
if (((UrlLinkTableModel) linkUrlTable.getModel()) |
1610 |
|
.isRowDeletable(modelIndex)) |
1611 |
|
{ |
1612 |
0 |
deleteLink.setEnabled(true); |
1613 |
|
} |
1614 |
|
else |
1615 |
|
{ |
1616 |
0 |
deleteLink.setEnabled(false); |
1617 |
|
} |
1618 |
|
|
1619 |
0 |
if (((UrlLinkTableModel) linkUrlTable.getModel()) |
1620 |
|
.isRowEditable(modelIndex)) |
1621 |
|
{ |
1622 |
0 |
editLink.setEnabled(true); |
1623 |
|
} |
1624 |
|
else |
1625 |
|
{ |
1626 |
0 |
editLink.setEnabled(false); |
1627 |
|
} |
1628 |
|
} |
1629 |
|
} |
1630 |
|
} |