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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.Container; |
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import java.awt.Dimension; |
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import java.awt.FontMetrics; |
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import java.awt.Graphics; |
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import java.awt.Graphics2D; |
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import java.awt.GridLayout; |
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import java.awt.Point; |
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import java.awt.Rectangle; |
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import java.awt.Toolkit; |
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import java.awt.Window; |
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import java.awt.datatransfer.Clipboard; |
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import java.awt.datatransfer.ClipboardOwner; |
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import java.awt.datatransfer.DataFlavor; |
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import java.awt.datatransfer.Transferable; |
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import java.awt.dnd.DnDConstants; |
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import java.awt.dnd.DropTargetDragEvent; |
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import java.awt.dnd.DropTargetDropEvent; |
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import java.awt.dnd.DropTargetEvent; |
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import java.awt.dnd.DropTargetListener; |
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import java.awt.event.ActionEvent; |
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import java.awt.event.ActionListener; |
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import java.awt.event.InputEvent; |
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import java.awt.event.KeyEvent; |
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import java.awt.event.MouseAdapter; |
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import java.awt.event.MouseEvent; |
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import java.awt.event.WindowAdapter; |
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import java.awt.event.WindowEvent; |
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import java.awt.geom.AffineTransform; |
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import java.beans.PropertyChangeEvent; |
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import java.beans.PropertyChangeListener; |
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import java.beans.PropertyVetoException; |
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import java.io.File; |
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import java.io.FileNotFoundException; |
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import java.io.FileWriter; |
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import java.io.IOException; |
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import java.lang.reflect.Field; |
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import java.net.URL; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.HashMap; |
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import java.util.Hashtable; |
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import java.util.List; |
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import java.util.ListIterator; |
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import java.util.Locale; |
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import java.util.Map; |
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import java.util.Vector; |
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import java.util.concurrent.ExecutorService; |
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import java.util.concurrent.Executors; |
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import java.util.concurrent.Semaphore; |
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import javax.swing.AbstractAction; |
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import javax.swing.Action; |
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import javax.swing.ActionMap; |
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import javax.swing.Box; |
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import javax.swing.BoxLayout; |
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import javax.swing.DefaultDesktopManager; |
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import javax.swing.DesktopManager; |
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import javax.swing.InputMap; |
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import javax.swing.JButton; |
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import javax.swing.JCheckBox; |
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import javax.swing.JComboBox; |
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import javax.swing.JComponent; |
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import javax.swing.JDesktopPane; |
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import javax.swing.JFrame; |
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import javax.swing.JInternalFrame; |
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import javax.swing.JLabel; |
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import javax.swing.JMenuItem; |
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import javax.swing.JOptionPane; |
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import javax.swing.JPanel; |
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import javax.swing.JPopupMenu; |
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import javax.swing.JProgressBar; |
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import javax.swing.JScrollPane; |
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import javax.swing.JTextArea; |
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import javax.swing.JTextField; |
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import javax.swing.JTextPane; |
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import javax.swing.KeyStroke; |
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import javax.swing.SwingUtilities; |
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import javax.swing.WindowConstants; |
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import javax.swing.event.HyperlinkEvent; |
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import javax.swing.event.HyperlinkEvent.EventType; |
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import javax.swing.event.InternalFrameAdapter; |
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import javax.swing.event.InternalFrameEvent; |
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import javax.swing.text.JTextComponent; |
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import org.stackoverflowusers.file.WindowsShortcut; |
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import jalview.api.AlignViewportI; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.structures.JalviewStructureDisplayI; |
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import jalview.bin.Cache; |
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import jalview.bin.Jalview; |
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import jalview.bin.Jalview.ExitCode; |
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import jalview.bin.argparser.Arg; |
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import jalview.bin.groovy.JalviewObject; |
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import jalview.bin.groovy.JalviewObjectI; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.ImageExporter.ImageWriterI; |
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import jalview.gui.QuitHandler.QResponse; |
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import jalview.io.AppletFormatAdapter; |
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import jalview.io.BackupFiles; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileFormat; |
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import jalview.io.FileFormatException; |
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import jalview.io.FileFormatI; |
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import jalview.io.FileFormats; |
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import jalview.io.FileLoader; |
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import jalview.io.FormatAdapter; |
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import jalview.io.IdentifyFile; |
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import jalview.io.JalviewFileChooser; |
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import jalview.io.JalviewFileView; |
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import jalview.io.NewickFile; |
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import jalview.io.exceptions.ImageOutputException; |
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import jalview.jbgui.GSplitFrame; |
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import jalview.jbgui.GStructureViewer; |
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import jalview.project.Jalview2XML; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.urls.IdOrgSettings; |
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import jalview.util.ArgParserUtils; |
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import jalview.util.ArgParserUtils.BaseInfo; |
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import jalview.util.BrowserLauncher; |
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import jalview.util.ChannelProperties; |
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import jalview.util.FileUtils; |
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import jalview.util.ImageMaker.TYPE; |
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import jalview.util.LaunchUtils; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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import jalview.util.ShortcutKeyMaskExWrapper; |
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import jalview.util.UrlConstants; |
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import jalview.viewmodel.AlignmentViewport; |
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import jalview.ws.params.ParamManager; |
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import jalview.ws.utils.UrlDownloadClient; |
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@author |
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@version |
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| 44% |
Uncovered Elements: 983 (1,756) |
Complexity: 470 |
Complexity Density: 0.42 |
|
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public class Desktop extends jalview.jbgui.GDesktop |
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implements DropTargetListener, ClipboardOwner, IProgressIndicator, |
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jalview.api.StructureSelectionManagerProvider, JalviewObjectI |
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{ |
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private static final String CITATION; |
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| 83.3% |
Uncovered Elements: 3 (18) |
Complexity: 4 |
Complexity Density: 0.33 |
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static... |
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{ |
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URL bg_logo_url = ChannelProperties.getImageURL( |
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"bg_logo." + String.valueOf(SplashScreen.logoSize)); |
177 |
54 |
URL uod_logo_url = ChannelProperties.getImageURL( |
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"uod_banner." + String.valueOf(SplashScreen.logoSize)); |
179 |
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boolean logo = (bg_logo_url != null || uod_logo_url != null); |
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StringBuilder sb = new StringBuilder(); |
181 |
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sb.append( |
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"<br><br>Jalview is free software released under GPLv3.<br><br>Development is managed by The Barton Group, University of Dundee, Scotland, UK."); |
183 |
54 |
if (logo) |
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{ |
185 |
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sb.append("<br>"); |
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} |
187 |
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sb.append(bg_logo_url == null ? "" |
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: "<img alt=\"Barton Group logo\" src=\"" |
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+ bg_logo_url.toString() + "\">"); |
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sb.append(uod_logo_url == null ? "" |
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: " <img alt=\"University of Dundee shield\" src=\"" |
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+ uod_logo_url.toString() + "\">"); |
193 |
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sb.append( |
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"<br><br>For help, see <a href=\"https://www.jalview.org/help/faq\">www.jalview.org/faq</a> and join <a href=\"https://discourse.jalview.org\">discourse.jalview.org</a>"); |
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sb.append("<br><br>If you use Jalview, please cite:" |
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+ "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" |
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+ "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench" |
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+ "<br>Bioinformatics <a href=\"https://doi.org/10.1093/bioinformatics/btp033\">doi: 10.1093/bioinformatics/btp033</a>"); |
199 |
54 |
CITATION = sb.toString(); |
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} |
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private static final String DEFAULT_AUTHORS = "The Jalview Authors (See AUTHORS file for current list)"; |
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204 |
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private static int DEFAULT_MIN_WIDTH = 300; |
205 |
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private static int DEFAULT_MIN_HEIGHT = 250; |
207 |
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208 |
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private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600; |
209 |
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private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70; |
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private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; |
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public static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT"; |
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public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>(); |
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218 |
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private static int DRAG_MODE = JDesktopPane.OUTLINE_DRAG_MODE; |
219 |
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| 85.7% |
Uncovered Elements: 1 (7) |
Complexity: 3 |
Complexity Density: 1 |
|
220 |
150 |
public static void setLiveDragMode(boolean b)... |
221 |
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{ |
222 |
150 |
DRAG_MODE = b ? JDesktopPane.LIVE_DRAG_MODE |
223 |
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: JDesktopPane.OUTLINE_DRAG_MODE; |
224 |
150 |
if (desktop != null) |
225 |
130 |
desktop.setDragMode(DRAG_MODE); |
226 |
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} |
227 |
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228 |
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private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); |
229 |
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230 |
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public static boolean nosplash = false; |
231 |
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232 |
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233 |
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234 |
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235 |
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private BlogReader jvnews = null; |
236 |
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237 |
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private File projectFile; |
238 |
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239 |
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240 |
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@param |
241 |
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@see |
242 |
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|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
243 |
0 |
public void addJalviewPropertyChangeListener(... |
244 |
|
PropertyChangeListener listener) |
245 |
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{ |
246 |
0 |
changeSupport.addJalviewPropertyChangeListener(listener); |
247 |
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} |
248 |
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|
249 |
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|
250 |
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@param |
251 |
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@param |
252 |
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@see |
253 |
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|
254 |
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|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
255 |
397 |
public void addJalviewPropertyChangeListener(String propertyName,... |
256 |
|
PropertyChangeListener listener) |
257 |
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{ |
258 |
397 |
changeSupport.addJalviewPropertyChangeListener(propertyName, listener); |
259 |
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} |
260 |
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|
261 |
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|
262 |
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@param |
263 |
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@param |
264 |
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@see |
265 |
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|
266 |
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|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
267 |
260 |
public void removeJalviewPropertyChangeListener(String propertyName,... |
268 |
|
PropertyChangeListener listener) |
269 |
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{ |
270 |
260 |
changeSupport.removeJalviewPropertyChangeListener(propertyName, |
271 |
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listener); |
272 |
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} |
273 |
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|
274 |
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|
275 |
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public static Desktop instance; |
276 |
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|
277 |
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public static MyDesktopPane desktop; |
278 |
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|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
279 |
2904 |
public static MyDesktopPane getDesktop()... |
280 |
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{ |
281 |
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|
282 |
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|
283 |
2904 |
return desktop; |
284 |
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} |
285 |
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286 |
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static int openFrameCount = 0; |
287 |
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|
288 |
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static final int xOffset = 30; |
289 |
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290 |
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static final int yOffset = 30; |
291 |
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|
292 |
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public static jalview.ws.jws1.Discoverer discoverer; |
293 |
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294 |
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public static Object[] jalviewClipboard; |
295 |
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|
296 |
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public static boolean internalCopy = false; |
297 |
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|
298 |
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static int fileLoadingCount = 0; |
299 |
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|
|
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| 20% |
Uncovered Elements: 36 (45) |
Complexity: 19 |
Complexity Density: 0.76 |
|
300 |
|
class MyDesktopManager implements DesktopManager |
301 |
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{ |
302 |
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|
303 |
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private DesktopManager delegate; |
304 |
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|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
305 |
75 |
public MyDesktopManager(DesktopManager delegate)... |
306 |
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{ |
307 |
75 |
this.delegate = delegate; |
308 |
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} |
309 |
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|
|
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| 50% |
Uncovered Elements: 2 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
310 |
743 |
@Override... |
311 |
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public void activateFrame(JInternalFrame f) |
312 |
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{ |
313 |
743 |
try |
314 |
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{ |
315 |
743 |
delegate.activateFrame(f); |
316 |
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} catch (NullPointerException npe) |
317 |
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{ |
318 |
0 |
Point p = getMousePosition(); |
319 |
0 |
instance.showPasteMenu(p.x, p.y); |
320 |
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} |
321 |
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} |
322 |
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|
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
323 |
0 |
@Override... |
324 |
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public void beginDraggingFrame(JComponent f) |
325 |
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{ |
326 |
0 |
delegate.beginDraggingFrame(f); |
327 |
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} |
328 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
329 |
0 |
@Override... |
330 |
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public void beginResizingFrame(JComponent f, int direction) |
331 |
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{ |
332 |
0 |
delegate.beginResizingFrame(f, direction); |
333 |
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} |
334 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
335 |
431 |
@Override... |
336 |
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public void closeFrame(JInternalFrame f) |
337 |
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{ |
338 |
431 |
delegate.closeFrame(f); |
339 |
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} |
340 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
341 |
722 |
@Override... |
342 |
|
public void deactivateFrame(JInternalFrame f) |
343 |
|
{ |
344 |
722 |
delegate.deactivateFrame(f); |
345 |
|
} |
346 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
347 |
0 |
@Override... |
348 |
|
public void deiconifyFrame(JInternalFrame f) |
349 |
|
{ |
350 |
0 |
delegate.deiconifyFrame(f); |
351 |
|
} |
352 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
353 |
0 |
@Override... |
354 |
|
public void dragFrame(JComponent f, int newX, int newY) |
355 |
|
{ |
356 |
0 |
if (newY < 0) |
357 |
|
{ |
358 |
0 |
newY = 0; |
359 |
|
} |
360 |
0 |
delegate.dragFrame(f, newX, newY); |
361 |
|
} |
362 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
363 |
0 |
@Override... |
364 |
|
public void endDraggingFrame(JComponent f) |
365 |
|
{ |
366 |
0 |
delegate.endDraggingFrame(f); |
367 |
0 |
desktop.repaint(); |
368 |
|
} |
369 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
370 |
0 |
@Override... |
371 |
|
public void endResizingFrame(JComponent f) |
372 |
|
{ |
373 |
0 |
delegate.endResizingFrame(f); |
374 |
0 |
desktop.repaint(); |
375 |
|
} |
376 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
377 |
0 |
@Override... |
378 |
|
public void iconifyFrame(JInternalFrame f) |
379 |
|
{ |
380 |
0 |
delegate.iconifyFrame(f); |
381 |
|
} |
382 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
383 |
0 |
@Override... |
384 |
|
public void maximizeFrame(JInternalFrame f) |
385 |
|
{ |
386 |
0 |
delegate.maximizeFrame(f); |
387 |
|
} |
388 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
389 |
0 |
@Override... |
390 |
|
public void minimizeFrame(JInternalFrame f) |
391 |
|
{ |
392 |
0 |
delegate.minimizeFrame(f); |
393 |
|
} |
394 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
395 |
0 |
@Override... |
396 |
|
public void openFrame(JInternalFrame f) |
397 |
|
{ |
398 |
0 |
delegate.openFrame(f); |
399 |
|
} |
400 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
401 |
0 |
@Override... |
402 |
|
public void resizeFrame(JComponent f, int newX, int newY, int newWidth, |
403 |
|
int newHeight) |
404 |
|
{ |
405 |
0 |
if (newY < 0) |
406 |
|
{ |
407 |
0 |
newY = 0; |
408 |
|
} |
409 |
0 |
delegate.resizeFrame(f, newX, newY, newWidth, newHeight); |
410 |
|
} |
411 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
412 |
0 |
@Override... |
413 |
|
public void setBoundsForFrame(JComponent f, int newX, int newY, |
414 |
|
int newWidth, int newHeight) |
415 |
|
{ |
416 |
0 |
delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight); |
417 |
|
} |
418 |
|
|
419 |
|
|
420 |
|
|
421 |
|
} |
422 |
|
|
423 |
|
|
424 |
|
|
425 |
|
|
|
|
| 84.7% |
Uncovered Elements: 13 (85) |
Complexity: 13 |
Complexity Density: 0.21 |
|
426 |
75 |
public Desktop()... |
427 |
|
{ |
428 |
75 |
super(); |
429 |
|
|
430 |
|
|
431 |
|
|
432 |
|
|
433 |
|
|
434 |
75 |
instance = this; |
435 |
|
|
436 |
75 |
doConfigureStructurePrefs(); |
437 |
75 |
setTitle(ChannelProperties.getProperty("app_name") + " " |
438 |
|
+ Cache.getProperty("VERSION")); |
439 |
|
|
440 |
|
|
441 |
|
|
442 |
|
|
443 |
|
|
444 |
|
|
445 |
|
|
446 |
|
|
447 |
|
|
448 |
|
|
449 |
|
|
450 |
|
|
451 |
|
|
452 |
|
|
453 |
75 |
if (Platform.isLinux()) |
454 |
|
{ |
455 |
75 |
if (LaunchUtils.getJavaVersion() >= 11) |
456 |
|
{ |
457 |
|
|
458 |
|
|
459 |
|
|
460 |
|
|
461 |
75 |
jalview.bin.Console.errPrintln( |
462 |
|
"Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that."); |
463 |
|
} |
464 |
75 |
final String awtAppClassName = "awtAppClassName"; |
465 |
75 |
try |
466 |
|
{ |
467 |
75 |
Toolkit xToolkit = Toolkit.getDefaultToolkit(); |
468 |
75 |
Field[] declaredFields = xToolkit.getClass().getDeclaredFields(); |
469 |
75 |
Field awtAppClassNameField = null; |
470 |
|
|
471 |
75 |
if (Arrays.stream(declaredFields) |
472 |
|
.anyMatch(f -> f.getName().equals(awtAppClassName))) |
473 |
|
{ |
474 |
75 |
awtAppClassNameField = xToolkit.getClass() |
475 |
|
.getDeclaredField(awtAppClassName); |
476 |
|
} |
477 |
|
|
478 |
75 |
String title = ChannelProperties.getProperty("app_name"); |
479 |
75 |
if (awtAppClassNameField != null) |
480 |
|
{ |
481 |
75 |
awtAppClassNameField.setAccessible(true); |
482 |
75 |
awtAppClassNameField.set(xToolkit, title); |
483 |
|
} |
484 |
|
else |
485 |
|
{ |
486 |
0 |
jalview.bin.Console |
487 |
|
.debug("XToolkit: " + awtAppClassName + " not found"); |
488 |
|
} |
489 |
|
} catch (Exception e) |
490 |
|
{ |
491 |
0 |
jalview.bin.Console.debug("Error setting " + awtAppClassName); |
492 |
0 |
jalview.bin.Console.trace(Cache.getStackTraceString(e)); |
493 |
|
} |
494 |
|
} |
495 |
|
|
496 |
75 |
setIconImages(ChannelProperties.getIconList()); |
497 |
|
|
498 |
|
|
499 |
75 |
this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); |
500 |
75 |
addWindowListener(new WindowAdapter() |
501 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
502 |
0 |
@Override... |
503 |
|
public void windowClosing(WindowEvent ev) |
504 |
|
{ |
505 |
0 |
QuitHandler.QResponse ret = desktopQuit(true, true); |
506 |
|
} |
507 |
|
}); |
508 |
|
|
509 |
75 |
boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false); |
510 |
|
|
511 |
75 |
boolean showjconsole = Cache.getArgCacheDefault(Arg.JAVACONSOLE, |
512 |
|
"SHOW_JAVA_CONSOLE", false); |
513 |
|
|
514 |
|
|
515 |
75 |
startDialogQueue(); |
516 |
|
|
517 |
75 |
if (!Platform.isJS()) |
518 |
|
|
519 |
|
|
520 |
|
|
521 |
|
|
522 |
|
|
523 |
|
{ |
524 |
75 |
Desktop.instance.acquireDialogQueue(); |
525 |
|
|
526 |
75 |
jconsole = new Console(this); |
527 |
75 |
jconsole.setHeader(Cache.getVersionDetailsForConsole()); |
528 |
75 |
showConsole(showjconsole); |
529 |
|
|
530 |
75 |
Desktop.instance.releaseDialogQueue(); |
531 |
|
} |
532 |
|
|
533 |
75 |
desktop = new MyDesktopPane(selmemusage); |
534 |
|
|
535 |
75 |
showMemusage.setSelected(selmemusage); |
536 |
75 |
desktop.setBackground(Color.white); |
537 |
|
|
538 |
75 |
getContentPane().setLayout(new BorderLayout()); |
539 |
|
|
540 |
|
|
541 |
|
|
542 |
|
|
543 |
|
|
544 |
|
|
545 |
75 |
if (Platform.isJS()) |
546 |
|
{ |
547 |
0 |
getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); |
548 |
|
} |
549 |
|
|
550 |
75 |
getContentPane().add(desktop, BorderLayout.CENTER); |
551 |
75 |
desktop.setDragMode(DRAG_MODE); |
552 |
|
|
553 |
|
|
554 |
|
|
555 |
75 |
desktop.setDesktopManager(new MyDesktopManager( |
556 |
75 |
Platform.isJS() ? desktop.getDesktopManager() |
557 |
|
: new DefaultDesktopManager())); |
558 |
|
|
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
|
|
564 |
|
|
565 |
|
|
566 |
75 |
Rectangle dims = getLastKnownDimensions(""); |
567 |
75 |
if (dims != null) |
568 |
|
{ |
569 |
59 |
setBounds(dims); |
570 |
|
} |
571 |
|
else |
572 |
|
{ |
573 |
16 |
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); |
574 |
16 |
int xPos = Math.max(5, (screenSize.width - 900) / 2); |
575 |
16 |
int yPos = Math.max(5, (screenSize.height - 650) / 2); |
576 |
16 |
setBounds(xPos, yPos, 900, 650); |
577 |
|
} |
578 |
|
|
579 |
75 |
if (!Platform.isJS()) |
580 |
|
|
581 |
|
|
582 |
|
|
583 |
|
|
584 |
|
|
585 |
|
{ |
586 |
75 |
showNews.setVisible(false); |
587 |
|
|
588 |
75 |
experimentalFeatures.setSelected(showExperimental()); |
589 |
|
|
590 |
75 |
getIdentifiersOrgData(); |
591 |
|
|
592 |
75 |
checkURLLinks(); |
593 |
|
|
594 |
|
|
595 |
75 |
if (!nosplash) |
596 |
|
{ |
597 |
50 |
SwingUtilities.invokeLater(new Runnable() |
598 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
599 |
50 |
@Override... |
600 |
|
public void run() |
601 |
|
{ |
602 |
50 |
new SplashScreen(true); |
603 |
|
} |
604 |
|
}); |
605 |
|
} |
606 |
|
|
607 |
|
|
608 |
|
|
609 |
75 |
new Thread(new Runnable() |
610 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
611 |
75 |
@Override... |
612 |
|
public void run() |
613 |
|
{ |
614 |
75 |
jalview.bin.Console.debug("Filechooser init thread started."); |
615 |
|
|
616 |
75 |
JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), |
617 |
|
null); |
618 |
75 |
jalview.bin.Console.debug("Filechooser init thread finished."); |
619 |
|
} |
620 |
|
}).start(); |
621 |
|
|
622 |
75 |
changeSupport.addJalviewPropertyChangeListener("services", |
623 |
|
new PropertyChangeListener() |
624 |
|
{ |
625 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
626 |
1341 |
@Override... |
627 |
|
public void propertyChange(PropertyChangeEvent evt) |
628 |
|
{ |
629 |
1341 |
jalview.bin.Console |
630 |
|
.debug("Firing service changed event for " |
631 |
|
+ evt.getNewValue()); |
632 |
1341 |
JalviewServicesChanged(evt); |
633 |
|
} |
634 |
|
}); |
635 |
|
} |
636 |
|
|
637 |
75 |
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); |
638 |
|
|
639 |
75 |
MouseAdapter ma; |
640 |
75 |
this.addMouseListener(ma = new MouseAdapter() |
641 |
|
{ |
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
642 |
0 |
@Override... |
643 |
|
public void mousePressed(MouseEvent evt) |
644 |
|
{ |
645 |
0 |
if (evt.isPopupTrigger()) |
646 |
|
{ |
647 |
0 |
showPasteMenu(evt.getX(), evt.getY()); |
648 |
|
} |
649 |
|
} |
650 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
651 |
0 |
@Override... |
652 |
|
public void mouseReleased(MouseEvent evt) |
653 |
|
{ |
654 |
0 |
if (evt.isPopupTrigger()) |
655 |
|
{ |
656 |
0 |
showPasteMenu(evt.getX(), evt.getY()); |
657 |
|
} |
658 |
|
} |
659 |
|
}); |
660 |
75 |
desktop.addMouseListener(ma); |
661 |
|
|
662 |
|
|
663 |
|
|
664 |
75 |
jalview.bin.Console.info((Platform.isJS() ? "JALVIEWJS" : "JALVIEW") |
665 |
|
+ ": CREATED DESKTOP"); |
666 |
|
|
667 |
|
} |
668 |
|
|
669 |
|
|
670 |
|
|
671 |
|
|
672 |
|
|
673 |
|
@return |
674 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
675 |
75 |
public boolean showExperimental()... |
676 |
|
{ |
677 |
75 |
String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, |
678 |
|
Boolean.FALSE.toString()); |
679 |
75 |
return Boolean.valueOf(experimental).booleanValue(); |
680 |
|
} |
681 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
682 |
75 |
public void doConfigureStructurePrefs()... |
683 |
|
{ |
684 |
|
|
685 |
75 |
StructureSelectionManager ssm = StructureSelectionManager |
686 |
|
.getStructureSelectionManager(this); |
687 |
75 |
StructureSelectionManager.doConfigureStructurePrefs(ssm); |
688 |
|
} |
689 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
690 |
42 |
public void checkForNews()... |
691 |
|
{ |
692 |
42 |
final Desktop me = this; |
693 |
|
|
694 |
42 |
new Thread(new Runnable() |
695 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
696 |
42 |
@Override... |
697 |
|
public void run() |
698 |
|
{ |
699 |
42 |
jalview.bin.Console.debug("Starting news thread."); |
700 |
42 |
jvnews = new BlogReader(me); |
701 |
42 |
showNews.setVisible(true); |
702 |
42 |
jalview.bin.Console.debug("Completed news thread."); |
703 |
|
} |
704 |
|
}).start(); |
705 |
|
} |
706 |
|
|
|
|
| 80% |
Uncovered Elements: 1 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
707 |
75 |
public void getIdentifiersOrgData()... |
708 |
|
{ |
709 |
75 |
if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) |
710 |
|
{ |
711 |
75 |
new Thread(new Runnable() |
712 |
|
{ |
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
713 |
75 |
@Override... |
714 |
|
public void run() |
715 |
|
{ |
716 |
75 |
jalview.bin.Console |
717 |
|
.debug("Downloading data from identifiers.org"); |
718 |
75 |
try |
719 |
|
{ |
720 |
75 |
UrlDownloadClient.download(IdOrgSettings.getUrl(), |
721 |
|
IdOrgSettings.getDownloadLocation()); |
722 |
|
} catch (IOException e) |
723 |
|
{ |
724 |
0 |
jalview.bin.Console |
725 |
|
.debug("Exception downloading identifiers.org data" |
726 |
|
+ e.getMessage()); |
727 |
|
} |
728 |
|
} |
729 |
|
}).start(); |
730 |
75 |
; |
731 |
|
} |
732 |
|
} |
733 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
734 |
0 |
@Override... |
735 |
|
protected void showNews_actionPerformed(ActionEvent e) |
736 |
|
{ |
737 |
0 |
showNews(showNews.isSelected()); |
738 |
|
} |
739 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 4 |
Complexity Density: 1 |
|
740 |
0 |
void showNews(boolean visible)... |
741 |
|
{ |
742 |
0 |
jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news."); |
743 |
0 |
showNews.setSelected(visible); |
744 |
0 |
if (visible && !jvnews.isVisible()) |
745 |
|
{ |
746 |
0 |
new Thread(new Runnable() |
747 |
|
{ |
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
748 |
0 |
@Override... |
749 |
|
public void run() |
750 |
|
{ |
751 |
0 |
long now = System.currentTimeMillis(); |
752 |
0 |
Desktop.instance.setProgressBar( |
753 |
|
MessageManager.getString("status.refreshing_news"), now); |
754 |
0 |
jvnews.refreshNews(); |
755 |
0 |
Desktop.instance.setProgressBar(null, now); |
756 |
0 |
jvnews.showNews(); |
757 |
|
} |
758 |
|
}).start(); |
759 |
|
} |
760 |
|
} |
761 |
|
|
762 |
|
|
763 |
|
|
764 |
|
|
765 |
|
@param |
766 |
|
|
767 |
|
@return |
768 |
|
|
769 |
|
|
|
|
| 77.4% |
Uncovered Elements: 7 (31) |
Complexity: 8 |
Complexity Density: 0.35 |
|
770 |
150 |
Rectangle getLastKnownDimensions(String windowName)... |
771 |
|
{ |
772 |
|
|
773 |
150 |
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); |
774 |
150 |
String x = Cache.getProperty(windowName + "SCREEN_X"); |
775 |
150 |
String y = Cache.getProperty(windowName + "SCREEN_Y"); |
776 |
150 |
String width = Cache.getProperty(windowName + "SCREEN_WIDTH"); |
777 |
150 |
String height = Cache.getProperty(windowName + "SCREEN_HEIGHT"); |
778 |
150 |
if ((x != null) && (y != null) && (width != null) && (height != null)) |
779 |
|
{ |
780 |
118 |
int ix = Integer.parseInt(x), iy = Integer.parseInt(y), |
781 |
|
iw = Integer.parseInt(width), ih = Integer.parseInt(height); |
782 |
118 |
if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null) |
783 |
|
{ |
784 |
|
|
785 |
|
|
786 |
|
|
787 |
118 |
double sw = ((1f * screenSize.width) / (1f * Integer |
788 |
|
.parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH")))); |
789 |
118 |
double sh = ((1f * screenSize.height) / (1f * Integer |
790 |
|
.parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT")))); |
791 |
|
|
792 |
118 |
ix = (int) (ix * sw); |
793 |
118 |
iw = (int) (iw * sw); |
794 |
118 |
iy = (int) (iy * sh); |
795 |
118 |
ih = (int) (ih * sh); |
796 |
118 |
if (ix >= screenSize.width) |
797 |
|
{ |
798 |
0 |
jalview.bin.Console.debug( |
799 |
|
"Window geometry location recall error: shifting horizontal to within screenbounds."); |
800 |
0 |
ix = ix % screenSize.width; |
801 |
|
} |
802 |
118 |
if (iy >= screenSize.height) |
803 |
|
{ |
804 |
0 |
jalview.bin.Console.debug( |
805 |
|
"Window geometry location recall error: shifting vertical to within screenbounds."); |
806 |
0 |
iy = iy % screenSize.height; |
807 |
|
} |
808 |
118 |
jalview.bin.Console.debug( |
809 |
|
"Got last known dimensions for " + windowName + ": x:" + ix |
810 |
|
+ " y:" + iy + " width:" + iw + " height:" + ih); |
811 |
|
} |
812 |
|
|
813 |
118 |
return new Rectangle(ix, iy, iw, ih); |
814 |
|
} |
815 |
32 |
return null; |
816 |
|
} |
817 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
818 |
0 |
void showPasteMenu(int x, int y)... |
819 |
|
{ |
820 |
0 |
JPopupMenu popup = new JPopupMenu(); |
821 |
0 |
JMenuItem item = new JMenuItem( |
822 |
|
MessageManager.getString("label.paste_new_window")); |
823 |
0 |
item.addActionListener(new ActionListener() |
824 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
825 |
0 |
@Override... |
826 |
|
public void actionPerformed(ActionEvent evt) |
827 |
|
{ |
828 |
0 |
paste(); |
829 |
|
} |
830 |
|
}); |
831 |
|
|
832 |
0 |
popup.add(item); |
833 |
0 |
popup.show(this, x, y); |
834 |
|
} |
835 |
|
|
|
|
| 51.7% |
Uncovered Elements: 14 (29) |
Complexity: 6 |
Complexity Density: 0.29 |
|
836 |
1 |
public void paste()... |
837 |
|
{ |
838 |
|
|
839 |
|
|
840 |
|
|
841 |
|
|
842 |
|
|
843 |
|
|
844 |
1 |
if (Desktop.jalviewClipboard != null) |
845 |
|
{ |
846 |
|
|
847 |
|
|
848 |
|
|
849 |
1 |
SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; |
850 |
|
|
851 |
1 |
SequenceI[] sequences = new SequenceI[newseq.length]; |
852 |
16 |
for (int i = 0; i < newseq.length; i++) |
853 |
|
{ |
854 |
15 |
sequences[i] = new Sequence(newseq[i]); |
855 |
|
} |
856 |
1 |
Alignment alignment = new Alignment(sequences); |
857 |
|
|
858 |
1 |
alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); |
859 |
1 |
AlignFrame af = new AlignFrame(alignment, AlignFrame.DEFAULT_WIDTH, |
860 |
|
AlignFrame.DEFAULT_HEIGHT); |
861 |
1 |
String newtitle = new String("Copied sequences"); |
862 |
|
|
863 |
1 |
if (Desktop.jalviewClipboard[2] != null) |
864 |
|
{ |
865 |
0 |
HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; |
866 |
0 |
af.viewport.setHiddenColumns(hc); |
867 |
|
} |
868 |
|
|
869 |
1 |
Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH, |
870 |
|
AlignFrame.DEFAULT_HEIGHT); |
871 |
|
|
872 |
|
} |
873 |
|
else |
874 |
|
{ |
875 |
0 |
try |
876 |
|
{ |
877 |
0 |
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); |
878 |
0 |
Transferable contents = c.getContents(this); |
879 |
|
|
880 |
0 |
if (contents != null) |
881 |
|
{ |
882 |
0 |
String file = (String) contents |
883 |
|
.getTransferData(DataFlavor.stringFlavor); |
884 |
|
|
885 |
0 |
FileFormatI format = new IdentifyFile().identify(file, |
886 |
|
DataSourceType.PASTE); |
887 |
|
|
888 |
0 |
new FileLoader().LoadFile(file, DataSourceType.PASTE, format); |
889 |
|
|
890 |
|
} |
891 |
|
} catch (Exception ex) |
892 |
|
{ |
893 |
0 |
jalview.bin.Console.outPrintln( |
894 |
|
"Unable to paste alignment from system clipboard:\n" + ex); |
895 |
|
} |
896 |
|
} |
897 |
|
} |
898 |
|
|
899 |
|
|
900 |
|
|
901 |
|
|
902 |
|
@param |
903 |
|
|
904 |
|
@param |
905 |
|
|
906 |
|
@param |
907 |
|
|
908 |
|
@param |
909 |
|
|
910 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
911 |
430 |
public static synchronized void addInternalFrame(... |
912 |
|
final JInternalFrame frame, String title, int w, int h) |
913 |
|
{ |
914 |
430 |
addInternalFrame(frame, title, true, w, h, true, false); |
915 |
|
} |
916 |
|
|
917 |
|
|
918 |
|
|
919 |
|
|
920 |
|
@param |
921 |
|
|
922 |
|
@param |
923 |
|
|
924 |
|
@param |
925 |
|
|
926 |
|
|
927 |
|
@param |
928 |
|
|
929 |
|
@param |
930 |
|
|
931 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
932 |
0 |
public static synchronized void addInternalFrame(... |
933 |
|
final JInternalFrame frame, String title, boolean makeVisible, |
934 |
|
int w, int h) |
935 |
|
{ |
936 |
0 |
addInternalFrame(frame, title, makeVisible, w, h, true, false); |
937 |
|
} |
938 |
|
|
939 |
|
|
940 |
|
|
941 |
|
|
942 |
|
@param |
943 |
|
|
944 |
|
@param |
945 |
|
|
946 |
|
@param |
947 |
|
|
948 |
|
@param |
949 |
|
|
950 |
|
@param |
951 |
|
|
952 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
953 |
17 |
public static synchronized void addInternalFrame(... |
954 |
|
final JInternalFrame frame, String title, int w, int h, |
955 |
|
boolean resizable) |
956 |
|
{ |
957 |
17 |
addInternalFrame(frame, title, true, w, h, resizable, false); |
958 |
|
} |
959 |
|
|
960 |
|
|
961 |
|
|
962 |
|
|
963 |
|
@param |
964 |
|
|
965 |
|
@param |
966 |
|
|
967 |
|
@param |
968 |
|
|
969 |
|
|
970 |
|
@param |
971 |
|
|
972 |
|
@param |
973 |
|
|
974 |
|
@param |
975 |
|
|
976 |
|
@param |
977 |
|
|
978 |
|
|
|
|
| 82.5% |
Uncovered Elements: 10 (57) |
Complexity: 17 |
Complexity Density: 0.4 |
|
979 |
506 |
public static synchronized void addInternalFrame(... |
980 |
|
final JInternalFrame frame, String title, boolean makeVisible, |
981 |
|
int w, int h, boolean resizable, boolean ignoreMinSize) |
982 |
|
{ |
983 |
|
|
984 |
|
|
985 |
|
|
986 |
|
|
987 |
|
|
988 |
|
|
989 |
506 |
frame.setTitle(title); |
990 |
506 |
if (frame.getWidth() < 1 || frame.getHeight() < 1) |
991 |
|
{ |
992 |
136 |
frame.setSize(w, h); |
993 |
|
} |
994 |
|
|
995 |
|
|
996 |
|
|
997 |
|
|
998 |
506 |
if (instance == null || (System.getProperty("java.awt.headless") != null |
999 |
|
&& System.getProperty("java.awt.headless").equals("true"))) |
1000 |
|
{ |
1001 |
52 |
return; |
1002 |
|
} |
1003 |
|
|
1004 |
454 |
openFrameCount++; |
1005 |
|
|
1006 |
454 |
if (!ignoreMinSize) |
1007 |
|
{ |
1008 |
395 |
frame.setMinimumSize( |
1009 |
|
new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT)); |
1010 |
|
|
1011 |
|
|
1012 |
|
|
1013 |
|
|
1014 |
|
|
1015 |
395 |
if (frame instanceof AlignFrame) |
1016 |
|
{ |
1017 |
295 |
frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, |
1018 |
|
ALIGN_FRAME_DEFAULT_MIN_HEIGHT)); |
1019 |
|
} |
1020 |
|
} |
1021 |
|
|
1022 |
454 |
frame.setVisible(makeVisible); |
1023 |
454 |
frame.setClosable(true); |
1024 |
454 |
frame.setResizable(resizable); |
1025 |
454 |
frame.setMaximizable(resizable); |
1026 |
454 |
frame.setIconifiable(resizable); |
1027 |
454 |
frame.setOpaque(Platform.isJS()); |
1028 |
|
|
1029 |
454 |
if (frame.getX() < 1 && frame.getY() < 1) |
1030 |
|
{ |
1031 |
344 |
frame.setLocation(xOffset * openFrameCount, |
1032 |
|
yOffset * ((openFrameCount - 1) % 10) + yOffset); |
1033 |
|
} |
1034 |
|
|
1035 |
|
|
1036 |
|
|
1037 |
|
|
1038 |
|
|
1039 |
454 |
final JMenuItem menuItem = new JMenuItem(title); |
1040 |
454 |
frame.addInternalFrameListener(new InternalFrameAdapter() |
1041 |
|
{ |
|
|
| 88.9% |
Uncovered Elements: 1 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
1042 |
637 |
@Override... |
1043 |
|
public void internalFrameActivated(InternalFrameEvent evt) |
1044 |
|
{ |
1045 |
637 |
JInternalFrame itf = desktop.getSelectedFrame(); |
1046 |
637 |
if (itf != null) |
1047 |
|
{ |
1048 |
637 |
if (itf instanceof AlignFrame) |
1049 |
|
{ |
1050 |
437 |
Jalview.getInstance().setCurrentAlignFrame((AlignFrame) itf); |
1051 |
|
} |
1052 |
637 |
itf.requestFocus(); |
1053 |
|
} |
1054 |
|
} |
1055 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
1056 |
401 |
@Override... |
1057 |
|
public void internalFrameClosed(InternalFrameEvent evt) |
1058 |
|
{ |
1059 |
401 |
PaintRefresher.RemoveComponent(frame); |
1060 |
|
|
1061 |
|
|
1062 |
|
|
1063 |
|
|
1064 |
401 |
if (openFrameCount > 0) |
1065 |
|
{ |
1066 |
388 |
openFrameCount--; |
1067 |
|
} |
1068 |
|
|
1069 |
|
|
1070 |
|
|
1071 |
|
|
1072 |
401 |
if (menuItem.getActionListeners().length > 0) |
1073 |
|
{ |
1074 |
380 |
menuItem.removeActionListener(menuItem.getActionListeners()[0]); |
1075 |
|
} |
1076 |
401 |
windowMenu.remove(menuItem); |
1077 |
|
} |
1078 |
|
}); |
1079 |
|
|
1080 |
454 |
menuItem.addActionListener(new ActionListener() |
1081 |
|
{ |
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1082 |
0 |
@Override... |
1083 |
|
public void actionPerformed(ActionEvent e) |
1084 |
|
{ |
1085 |
0 |
try |
1086 |
|
{ |
1087 |
0 |
frame.setSelected(true); |
1088 |
0 |
frame.setIcon(false); |
1089 |
|
} catch (java.beans.PropertyVetoException ex) |
1090 |
|
{ |
1091 |
|
|
1092 |
|
} |
1093 |
|
} |
1094 |
|
}); |
1095 |
|
|
1096 |
454 |
setKeyBindings(frame); |
1097 |
|
|
1098 |
|
|
1099 |
|
|
1100 |
454 |
int tries = 3; |
1101 |
454 |
boolean shown = false; |
1102 |
454 |
Exception last = null; |
1103 |
454 |
do |
1104 |
|
{ |
1105 |
454 |
try |
1106 |
|
{ |
1107 |
454 |
desktop.add(frame); |
1108 |
454 |
shown = true; |
1109 |
|
} catch (IllegalArgumentException iaex) |
1110 |
|
{ |
1111 |
0 |
last = iaex; |
1112 |
0 |
tries--; |
1113 |
0 |
jalview.bin.Console.info("Squashed IllegalArgument Exception (" |
1114 |
|
+ tries + " left) for " + frame.getTitle(), iaex); |
1115 |
0 |
try |
1116 |
|
{ |
1117 |
0 |
Thread.sleep(5); |
1118 |
|
} catch (InterruptedException iex) |
1119 |
|
{ |
1120 |
|
} |
1121 |
0 |
; |
1122 |
|
} |
1123 |
454 |
} while (!shown && tries > 0); |
1124 |
454 |
if (!shown) |
1125 |
|
{ |
1126 |
0 |
jalview.bin.Console.error( |
1127 |
|
"Serious Problem whilst showing window " + frame.getTitle(), |
1128 |
|
last); |
1129 |
|
} |
1130 |
|
|
1131 |
454 |
windowMenu.add(menuItem); |
1132 |
|
|
1133 |
454 |
frame.toFront(); |
1134 |
454 |
try |
1135 |
|
{ |
1136 |
454 |
frame.setSelected(true); |
1137 |
454 |
frame.requestFocus(); |
1138 |
|
} catch (java.beans.PropertyVetoException ve) |
1139 |
|
{ |
1140 |
|
} catch (java.lang.ClassCastException cex) |
1141 |
|
{ |
1142 |
0 |
jalview.bin.Console.warn( |
1143 |
|
"Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869", |
1144 |
|
cex); |
1145 |
|
} |
1146 |
|
} |
1147 |
|
|
1148 |
|
|
1149 |
|
|
1150 |
|
|
1151 |
|
|
1152 |
|
@param |
1153 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
|
1154 |
454 |
private static void setKeyBindings(JInternalFrame frame)... |
1155 |
|
{ |
1156 |
454 |
@SuppressWarnings("serial") |
1157 |
|
final Action closeAction = new AbstractAction() |
1158 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1159 |
0 |
@Override... |
1160 |
|
public void actionPerformed(ActionEvent e) |
1161 |
|
{ |
1162 |
0 |
frame.dispose(); |
1163 |
|
} |
1164 |
|
}; |
1165 |
|
|
1166 |
|
|
1167 |
|
|
1168 |
|
|
1169 |
454 |
KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, |
1170 |
|
InputEvent.CTRL_DOWN_MASK); |
1171 |
454 |
KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, |
1172 |
|
ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()); |
1173 |
|
|
1174 |
454 |
InputMap inputMap = frame |
1175 |
|
.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); |
1176 |
454 |
String ctrlW = ctrlWKey.toString(); |
1177 |
454 |
inputMap.put(ctrlWKey, ctrlW); |
1178 |
454 |
inputMap.put(cmdWKey, ctrlW); |
1179 |
|
|
1180 |
454 |
ActionMap actionMap = frame.getActionMap(); |
1181 |
454 |
actionMap.put(ctrlW, closeAction); |
1182 |
|
} |
1183 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1184 |
0 |
@Override... |
1185 |
|
public void lostOwnership(Clipboard clipboard, Transferable contents) |
1186 |
|
{ |
1187 |
0 |
if (!internalCopy) |
1188 |
|
{ |
1189 |
0 |
Desktop.jalviewClipboard = null; |
1190 |
|
} |
1191 |
|
|
1192 |
0 |
internalCopy = false; |
1193 |
|
} |
1194 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1195 |
0 |
@Override... |
1196 |
|
public void dragEnter(DropTargetDragEvent evt) |
1197 |
|
{ |
1198 |
|
} |
1199 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1200 |
0 |
@Override... |
1201 |
|
public void dragExit(DropTargetEvent evt) |
1202 |
|
{ |
1203 |
|
} |
1204 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1205 |
0 |
@Override... |
1206 |
|
public void dragOver(DropTargetDragEvent evt) |
1207 |
|
{ |
1208 |
|
} |
1209 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1210 |
0 |
@Override... |
1211 |
|
public void dropActionChanged(DropTargetDragEvent evt) |
1212 |
|
{ |
1213 |
|
} |
1214 |
|
|
1215 |
|
|
1216 |
|
|
1217 |
|
|
1218 |
|
@return |
1219 |
|
|
|
|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 6 |
Complexity Density: 0.38 |
|
1220 |
0 |
public boolean loadDroppedFiles(List<Object> files,... |
1221 |
|
List<DataSourceType> protocols, List<Object> failed, |
1222 |
|
List<Exception> failed_exceptions) |
1223 |
|
{ |
1224 |
0 |
for (int i = 0; i < files.size(); i++) |
1225 |
|
{ |
1226 |
0 |
Object file = files.get(i); |
1227 |
0 |
try |
1228 |
|
{ |
1229 |
|
|
1230 |
0 |
String fileName = file.toString(); |
1231 |
0 |
DataSourceType protocol = (protocols == null) ? DataSourceType.FILE |
1232 |
|
: protocols.get(i); |
1233 |
0 |
FileFormatI format = null; |
1234 |
|
|
1235 |
0 |
if (fileName.endsWith(".jar")) |
1236 |
|
{ |
1237 |
0 |
format = FileFormat.Jalview; |
1238 |
|
} |
1239 |
|
else |
1240 |
|
{ |
1241 |
0 |
format = new IdentifyFile().identify(file, protocol); |
1242 |
|
} |
1243 |
0 |
if (file instanceof File) |
1244 |
|
{ |
1245 |
0 |
Platform.cacheFileData((File) file); |
1246 |
|
} |
1247 |
0 |
new FileLoader().LoadFile(null, file, protocol, format); |
1248 |
|
} catch (Exception x) |
1249 |
|
{ |
1250 |
0 |
failed.add(file); |
1251 |
0 |
failed_exceptions.add(x); |
1252 |
0 |
jalview.bin.Console.warn( |
1253 |
|
"Unexpected Exception when handling " + file.toString(), x); |
1254 |
|
} |
1255 |
|
} |
1256 |
0 |
return failed.size() == 0; |
1257 |
|
} |
1258 |
|
|
1259 |
|
|
1260 |
|
|
1261 |
|
|
1262 |
|
|
1263 |
|
@return |
1264 |
|
|
|
|
| 0% |
Uncovered Elements: 96 (96) |
Complexity: 24 |
Complexity Density: 0.38 |
|
1265 |
0 |
public boolean processAndLoadDroppedFiles(List<Object> files,... |
1266 |
|
List<DataSourceType> protocols, List<Object> failed, |
1267 |
|
List<Exception> failed_exceptions) |
1268 |
|
{ |
1269 |
|
|
1270 |
0 |
List<String> filenames = new ArrayList<>(); |
1271 |
0 |
for (int i = 0; i < files.size(); i++) |
1272 |
|
{ |
1273 |
0 |
filenames.add(files.get(i).toString()); |
1274 |
|
} |
1275 |
|
|
1276 |
|
|
1277 |
|
|
1278 |
0 |
Map<String, BaseInfo> baseInfoMap = ArgParserUtils |
1279 |
|
.processFilenames(filenames, false, files); |
1280 |
|
|
1281 |
0 |
Object file = null; |
1282 |
0 |
try |
1283 |
|
{ |
1284 |
|
|
1285 |
0 |
for (int i = 0; i < files.size(); i++) |
1286 |
|
{ |
1287 |
|
|
1288 |
0 |
file = files.get(i); |
1289 |
0 |
String fileName = file.toString(); |
1290 |
0 |
DataSourceType protocol = (protocols == null) ? DataSourceType.FILE |
1291 |
|
: protocols.get(i); |
1292 |
0 |
FileFormatI format = null; |
1293 |
|
|
1294 |
0 |
if (fileName.toLowerCase(Locale.ROOT).endsWith(".jar")) |
1295 |
|
{ |
1296 |
0 |
format = FileFormat.Jalview; |
1297 |
|
} |
1298 |
|
else |
1299 |
|
{ |
1300 |
0 |
format = new IdentifyFile().identify(file, protocol); |
1301 |
|
} |
1302 |
|
|
1303 |
|
|
1304 |
0 |
String ext = FileUtils.getExtension(fileName); |
1305 |
0 |
boolean isFeatures = ArgParserUtils.featuresExtensions |
1306 |
|
.contains(ext); |
1307 |
0 |
boolean isAnnotations = ArgParserUtils.annotationsExtensions |
1308 |
|
.contains(ext); |
1309 |
0 |
boolean isTree = ArgParserUtils.treeExtensions.contains(ext); |
1310 |
0 |
if (isFeatures || isAnnotations || isTree) |
1311 |
|
{ |
1312 |
0 |
String base = FileUtils.getBase(fileName); |
1313 |
0 |
AlignFrame matchingAf = null; |
1314 |
0 |
AlignFrame[] afs = Desktop.instance.getAlignFrames(); |
1315 |
0 |
boolean dontSkip = false; |
1316 |
0 |
for (AlignFrame af : afs) |
1317 |
|
{ |
1318 |
0 |
String afFilename = af.fileName; |
1319 |
0 |
String afTitle = af.getTitle(); |
1320 |
|
|
1321 |
|
|
1322 |
|
|
1323 |
|
|
1324 |
|
|
1325 |
|
|
1326 |
|
|
1327 |
|
|
1328 |
|
|
1329 |
|
|
1330 |
|
|
1331 |
|
|
1332 |
|
|
1333 |
0 |
if (base.equals(FileUtils.getBase(afFilename)) |
1334 |
|
|| base.equals(FileUtils.getBase(afTitle))) |
1335 |
|
{ |
1336 |
0 |
matchingAf = af; |
1337 |
0 |
break; |
1338 |
|
} |
1339 |
|
} |
1340 |
0 |
if (matchingAf != null) |
1341 |
|
{ |
1342 |
0 |
if (isFeatures) |
1343 |
|
{ |
1344 |
0 |
matchingAf.parseFeaturesFile(fileName, |
1345 |
|
AppletFormatAdapter.checkProtocol(fileName)); |
1346 |
|
} |
1347 |
0 |
else if (isAnnotations) |
1348 |
|
{ |
1349 |
0 |
matchingAf.loadJalviewDataFile(fileName, null, null, null); |
1350 |
|
} |
1351 |
0 |
else if (isTree) |
1352 |
|
{ |
1353 |
0 |
try |
1354 |
|
{ |
1355 |
0 |
NewickFile nf = new NewickFile(fileName, |
1356 |
|
AppletFormatAdapter.checkProtocol(fileName)); |
1357 |
0 |
matchingAf.getViewport().setCurrentTree( |
1358 |
|
matchingAf.showNewickTree(nf, fileName).getTree()); |
1359 |
|
} catch (IOException e) |
1360 |
|
{ |
1361 |
0 |
jalview.bin.Console.warn( |
1362 |
|
"Couldn't add potential tree '" + fileName + "'"); |
1363 |
0 |
dontSkip = true; |
1364 |
|
} |
1365 |
|
} |
1366 |
0 |
if (!dontSkip) |
1367 |
|
{ |
1368 |
|
|
1369 |
0 |
continue; |
1370 |
|
} |
1371 |
|
} |
1372 |
|
} |
1373 |
|
|
1374 |
0 |
if (file instanceof File) |
1375 |
|
{ |
1376 |
0 |
Platform.cacheFileData((File) file); |
1377 |
|
} |
1378 |
|
|
1379 |
0 |
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fileName, |
1380 |
|
protocol, format); |
1381 |
|
|
1382 |
0 |
if (baseInfoMap.containsKey(fileName) && baseInfoMap.get(fileName) |
1383 |
|
.getAssociatedFilesMap() != null) |
1384 |
|
{ |
1385 |
0 |
BaseInfo bi = baseInfoMap.get(fileName); |
1386 |
0 |
if (bi.getAssociatedFilesMap().containsKey(Arg.FEATURES)) |
1387 |
|
{ |
1388 |
0 |
String featuresfile = bi.getAssociatedFilesMap() |
1389 |
|
.get(Arg.FEATURES); |
1390 |
0 |
af.parseFeaturesFile(featuresfile, |
1391 |
|
AppletFormatAdapter.checkProtocol(featuresfile)); |
1392 |
|
} |
1393 |
0 |
if (bi.getAssociatedFilesMap().containsKey(Arg.ANNOTATIONS)) |
1394 |
|
{ |
1395 |
0 |
String annotationsfile = bi.getAssociatedFilesMap() |
1396 |
|
.get(Arg.ANNOTATIONS); |
1397 |
0 |
af.loadJalviewDataFile(annotationsfile, null, null, null); |
1398 |
|
} |
1399 |
0 |
if (bi.getAssociatedFilesMap().containsKey(Arg.TREE)) |
1400 |
|
{ |
1401 |
0 |
String treefile = bi.getAssociatedFilesMap().get(Arg.TREE); |
1402 |
0 |
try |
1403 |
|
{ |
1404 |
0 |
NewickFile nf = new NewickFile(treefile, |
1405 |
|
AppletFormatAdapter.checkProtocol(treefile)); |
1406 |
0 |
af.getViewport().setCurrentTree( |
1407 |
|
af.showNewickTree(nf, treefile).getTree()); |
1408 |
|
} catch (IOException e) |
1409 |
|
{ |
1410 |
0 |
jalview.bin.Console.warn( |
1411 |
|
"Couldn't add potential tree '" + treefile + "'"); |
1412 |
|
} |
1413 |
|
|
1414 |
|
} |
1415 |
|
|
1416 |
|
} |
1417 |
|
|
1418 |
|
} |
1419 |
|
} catch (Exception ex) |
1420 |
|
{ |
1421 |
|
|
1422 |
0 |
jalview.bin.Console.warn( |
1423 |
|
"Unexpected exception whilst handling drop to Desktop.", ex); |
1424 |
0 |
failed.add(file); |
1425 |
0 |
failed_exceptions.add(ex); |
1426 |
0 |
return false; |
1427 |
|
} |
1428 |
0 |
return failed.size() == 0; |
1429 |
|
} |
1430 |
|
|
|
|
| 0% |
Uncovered Elements: 23 (23) |
Complexity: 5 |
Complexity Density: 0.26 |
|
1431 |
0 |
@Override... |
1432 |
|
public void drop(DropTargetDropEvent evt) |
1433 |
|
{ |
1434 |
0 |
boolean success = true; |
1435 |
|
|
1436 |
|
|
1437 |
0 |
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); |
1438 |
0 |
Transferable t = evt.getTransferable(); |
1439 |
0 |
List<Object> files = new ArrayList<>(); |
1440 |
0 |
List<DataSourceType> protocols = new ArrayList<>(); |
1441 |
|
|
1442 |
0 |
try |
1443 |
|
{ |
1444 |
0 |
Desktop.transferFromDropTarget(files, protocols, evt, t); |
1445 |
|
} catch (Exception e) |
1446 |
|
{ |
1447 |
0 |
e.printStackTrace(); |
1448 |
0 |
success = false; |
1449 |
|
} |
1450 |
0 |
try |
1451 |
|
{ |
1452 |
0 |
if (files != null) |
1453 |
|
{ |
1454 |
0 |
List<Object> failed = new ArrayList<Object>(); |
1455 |
0 |
List<Exception> failed_exceptions = new ArrayList<Exception>(); |
1456 |
0 |
if (!showExperimental()) |
1457 |
|
{ |
1458 |
0 |
success = loadDroppedFiles(files, protocols, failed, |
1459 |
|
failed_exceptions); |
1460 |
|
} |
1461 |
|
else |
1462 |
|
{ |
1463 |
0 |
success = processAndLoadDroppedFiles(files, protocols, failed, |
1464 |
|
failed_exceptions); |
1465 |
|
} |
1466 |
|
} |
1467 |
|
} catch (Throwable ex) |
1468 |
|
{ |
1469 |
0 |
jalview.bin.Console.warn( |
1470 |
|
"Unexpected exception whilst handling drop to Desktop.", ex); |
1471 |
0 |
success = false; |
1472 |
|
} |
1473 |
0 |
evt.dropComplete(success); |
1474 |
|
|
1475 |
|
} |
1476 |
|
|
1477 |
|
|
1478 |
|
|
1479 |
|
|
1480 |
|
@param |
1481 |
|
|
1482 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 3 |
Complexity Density: 0.23 |
|
1483 |
0 |
@Override... |
1484 |
|
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) |
1485 |
|
{ |
1486 |
|
|
1487 |
0 |
JalviewFileChooser chooser = JalviewFileChooser.forRead( |
1488 |
|
Cache.getProperty("LAST_DIRECTORY"), null, |
1489 |
|
BackupFiles.getEnabled()); |
1490 |
|
|
1491 |
0 |
chooser.setFileView(new JalviewFileView()); |
1492 |
0 |
chooser.setDialogTitle( |
1493 |
|
MessageManager.getString("label.open_local_file")); |
1494 |
0 |
chooser.setToolTipText(MessageManager.getString("action.open")); |
1495 |
|
|
1496 |
0 |
chooser.setResponseHandler(0, () -> { |
1497 |
0 |
File selectedFile = chooser.getSelectedFile(); |
1498 |
0 |
Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); |
1499 |
|
|
1500 |
0 |
FileFormatI format = chooser.getSelectedFormat(); |
1501 |
|
|
1502 |
|
|
1503 |
|
|
1504 |
|
|
1505 |
|
|
1506 |
|
|
1507 |
0 |
if (FileFormats.getInstance().isIdentifiable(format)) |
1508 |
|
{ |
1509 |
0 |
try |
1510 |
|
{ |
1511 |
0 |
format = new IdentifyFile().identify(selectedFile, |
1512 |
|
DataSourceType.FILE); |
1513 |
|
} catch (FileFormatException e) |
1514 |
|
{ |
1515 |
|
|
1516 |
|
} |
1517 |
|
} |
1518 |
|
|
1519 |
0 |
new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, |
1520 |
|
format); |
1521 |
|
}); |
1522 |
0 |
chooser.showOpenDialog(this); |
1523 |
|
} |
1524 |
|
|
1525 |
|
|
1526 |
|
|
1527 |
|
|
1528 |
|
@param |
1529 |
|
|
|
|
| 0% |
Uncovered Elements: 52 (52) |
Complexity: 10 |
Complexity Density: 0.26 |
|
1530 |
0 |
@Override... |
1531 |
|
public void inputURLMenuItem_actionPerformed(AlignViewport viewport) |
1532 |
|
{ |
1533 |
|
|
1534 |
|
|
1535 |
0 |
JLabel label = new JLabel( |
1536 |
|
MessageManager.getString("label.input_file_url")); |
1537 |
|
|
1538 |
0 |
JPanel panel = new JPanel(new GridLayout(2, 1)); |
1539 |
0 |
panel.add(label); |
1540 |
|
|
1541 |
|
|
1542 |
|
|
1543 |
|
|
1544 |
|
|
1545 |
0 |
JComponent history; |
1546 |
0 |
String urlBase = "https://www."; |
1547 |
0 |
if (Platform.isJS()) |
1548 |
|
{ |
1549 |
0 |
history = new JTextField(urlBase, 35); |
1550 |
|
} |
1551 |
|
else |
1552 |
|
|
1553 |
|
|
1554 |
|
|
1555 |
|
|
1556 |
|
|
1557 |
|
{ |
1558 |
0 |
JComboBox<String> asCombo = new JComboBox<>(); |
1559 |
0 |
asCombo.setPreferredSize(new Dimension(400, 20)); |
1560 |
0 |
asCombo.setEditable(true); |
1561 |
0 |
asCombo.addItem(urlBase); |
1562 |
0 |
String historyItems = Cache.getProperty("RECENT_URL"); |
1563 |
0 |
if (historyItems != null) |
1564 |
|
{ |
1565 |
0 |
for (String token : historyItems.split("\\t")) |
1566 |
|
{ |
1567 |
0 |
asCombo.addItem(token); |
1568 |
|
} |
1569 |
|
} |
1570 |
0 |
history = asCombo; |
1571 |
|
} |
1572 |
0 |
panel.add(history); |
1573 |
|
|
1574 |
0 |
Object[] options = new Object[] { MessageManager.getString("action.ok"), |
1575 |
|
MessageManager.getString("action.cancel") }; |
1576 |
0 |
Runnable action = () -> { |
1577 |
0 |
@SuppressWarnings("unchecked") |
1578 |
0 |
String url = (history instanceof JTextField |
1579 |
|
? ((JTextField) history).getText() |
1580 |
|
: ((JComboBox<String>) history).getEditor().getItem() |
1581 |
|
.toString().trim()); |
1582 |
|
|
1583 |
0 |
if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) |
1584 |
|
{ |
1585 |
0 |
if (viewport != null) |
1586 |
|
{ |
1587 |
0 |
new FileLoader().LoadFile(viewport, url, DataSourceType.URL, |
1588 |
|
FileFormat.Jalview); |
1589 |
|
} |
1590 |
|
else |
1591 |
|
{ |
1592 |
0 |
new FileLoader().LoadFile(url, DataSourceType.URL, |
1593 |
|
FileFormat.Jalview); |
1594 |
|
} |
1595 |
|
} |
1596 |
|
else |
1597 |
|
{ |
1598 |
0 |
FileFormatI format = null; |
1599 |
0 |
try |
1600 |
|
{ |
1601 |
0 |
format = new IdentifyFile().identify(url, DataSourceType.URL); |
1602 |
|
} catch (FileNotFoundException e) |
1603 |
|
{ |
1604 |
0 |
jalview.bin.Console.error("URL '" + url + "' not found", e); |
1605 |
|
} catch (FileFormatException e) |
1606 |
|
{ |
1607 |
0 |
jalview.bin.Console.error( |
1608 |
|
"File at URL '" + url + "' format not recognised", e); |
1609 |
|
} |
1610 |
|
|
1611 |
0 |
if (format == null) |
1612 |
|
{ |
1613 |
0 |
String msg = MessageManager.formatMessage("label.couldnt_locate", |
1614 |
|
url); |
1615 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, |
1616 |
|
MessageManager.getString("label.url_not_found"), |
1617 |
|
JvOptionPane.WARNING_MESSAGE); |
1618 |
0 |
return; |
1619 |
|
} |
1620 |
|
|
1621 |
0 |
if (viewport != null) |
1622 |
|
{ |
1623 |
0 |
new FileLoader().LoadFile(viewport, url, DataSourceType.URL, |
1624 |
|
format); |
1625 |
|
} |
1626 |
|
else |
1627 |
|
{ |
1628 |
0 |
new FileLoader().LoadFile(url, DataSourceType.URL, format); |
1629 |
|
} |
1630 |
|
} |
1631 |
|
}; |
1632 |
0 |
String dialogOption = MessageManager |
1633 |
|
.getString("label.input_alignment_from_url"); |
1634 |
0 |
JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action) |
1635 |
|
.showInternalDialog(panel, dialogOption, |
1636 |
|
JvOptionPane.YES_NO_CANCEL_OPTION, |
1637 |
|
JvOptionPane.PLAIN_MESSAGE, null, options, |
1638 |
|
MessageManager.getString("action.ok")); |
1639 |
|
} |
1640 |
|
|
1641 |
|
|
1642 |
|
|
1643 |
|
|
1644 |
|
@param |
1645 |
|
|
1646 |
|
|
1647 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1648 |
0 |
@Override... |
1649 |
|
public void inputTextboxMenuItem_actionPerformed( |
1650 |
|
AlignmentViewPanel viewPanel) |
1651 |
|
{ |
1652 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
1653 |
0 |
cap.setForInput(viewPanel); |
1654 |
0 |
Desktop.addInternalFrame(cap, |
1655 |
|
MessageManager.getString("label.cut_paste_alignmen_file"), true, |
1656 |
|
600, 500); |
1657 |
|
} |
1658 |
|
|
1659 |
|
|
1660 |
|
|
1661 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1662 |
0 |
public void desktopQuit()... |
1663 |
|
{ |
1664 |
0 |
desktopQuit(true, false); |
1665 |
|
} |
1666 |
|
|
1667 |
|
|
1668 |
|
|
1669 |
|
|
1670 |
|
|
1671 |
|
@param |
1672 |
|
|
1673 |
|
@param |
1674 |
|
|
1675 |
|
|
|
|
| 64.9% |
Uncovered Elements: 13 (37) |
Complexity: 9 |
Complexity Density: 0.39 |
|
1676 |
81 |
public void quitTheDesktop(boolean dispose, boolean terminateJvm)... |
1677 |
|
{ |
1678 |
81 |
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); |
1679 |
81 |
Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); |
1680 |
81 |
Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); |
1681 |
81 |
storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, |
1682 |
|
getWidth(), getHeight())); |
1683 |
|
|
1684 |
81 |
if (jconsole != null) |
1685 |
|
{ |
1686 |
81 |
storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); |
1687 |
81 |
jconsole.stopConsole(); |
1688 |
|
} |
1689 |
|
|
1690 |
81 |
if (jvnews != null) |
1691 |
|
{ |
1692 |
63 |
storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); |
1693 |
|
} |
1694 |
|
|
1695 |
|
|
1696 |
|
|
1697 |
81 |
closeAll_actionPerformed(null); |
1698 |
|
|
1699 |
81 |
if (dialogExecutor != null) |
1700 |
|
{ |
1701 |
40 |
dialogExecutor.shutdownNow(); |
1702 |
|
} |
1703 |
|
|
1704 |
81 |
if (groovyConsole != null) |
1705 |
|
{ |
1706 |
|
|
1707 |
0 |
groovyConsole.setDirty(false); |
1708 |
|
|
1709 |
|
|
1710 |
0 |
if (((Window) groovyConsole.getFrame()) != null |
1711 |
|
&& ((Window) groovyConsole.getFrame()).isVisible()) |
1712 |
|
{ |
1713 |
|
|
1714 |
0 |
groovyConsole.exit(); |
1715 |
|
} |
1716 |
|
else |
1717 |
|
{ |
1718 |
|
|
1719 |
|
|
1720 |
|
|
1721 |
0 |
groovyConsole = null; |
1722 |
|
} |
1723 |
|
} |
1724 |
|
|
1725 |
81 |
if (terminateJvm) |
1726 |
|
{ |
1727 |
|
|
1728 |
0 |
jalview.bin.Console.debug("Force Quit selected by user"); |
1729 |
0 |
Runtime.getRuntime().halt(0); |
1730 |
|
} |
1731 |
|
|
1732 |
81 |
jalview.bin.Console.debug("Quit selected by user"); |
1733 |
81 |
if (dispose) |
1734 |
|
{ |
1735 |
0 |
instance.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); |
1736 |
|
|
1737 |
|
} |
1738 |
|
} |
1739 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
1740 |
0 |
public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag)... |
1741 |
|
{ |
1742 |
0 |
final Runnable doDesktopQuit = () -> { |
1743 |
|
|
1744 |
|
|
1745 |
0 |
if (QuitHandler.quitCancelled()) |
1746 |
|
{ |
1747 |
0 |
jalview.bin.Console |
1748 |
|
.debug("Quit was cancelled - Desktop aborting quit"); |
1749 |
0 |
return; |
1750 |
|
} |
1751 |
|
|
1752 |
|
|
1753 |
0 |
quitTheDesktop(disposeFlag, |
1754 |
|
QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT); |
1755 |
|
|
1756 |
0 |
instance.quit(); |
1757 |
|
}; |
1758 |
|
|
1759 |
0 |
return QuitHandler.getQuitResponse(ui, doDesktopQuit, doDesktopQuit, |
1760 |
|
QuitHandler.defaultCancelQuit); |
1761 |
|
} |
1762 |
|
|
1763 |
|
|
1764 |
|
|
1765 |
|
|
1766 |
|
|
1767 |
|
|
1768 |
|
|
1769 |
|
|
1770 |
|
|
1771 |
|
|
1772 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1773 |
0 |
@Override... |
1774 |
|
public void quit() |
1775 |
|
{ |
1776 |
|
|
1777 |
|
|
1778 |
|
|
1779 |
0 |
Jalview.exit("Desktop exiting.", ExitCode.OK); |
1780 |
|
} |
1781 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
1782 |
225 |
private void storeLastKnownDimensions(String string, Rectangle jc)... |
1783 |
|
{ |
1784 |
225 |
jalview.bin.Console.debug("Storing last known dimensions for " + string |
1785 |
|
+ ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width |
1786 |
|
+ " height:" + jc.height); |
1787 |
|
|
1788 |
225 |
Cache.setProperty(string + "SCREEN_X", jc.x + ""); |
1789 |
225 |
Cache.setProperty(string + "SCREEN_Y", jc.y + ""); |
1790 |
225 |
Cache.setProperty(string + "SCREEN_WIDTH", jc.width + ""); |
1791 |
225 |
Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + ""); |
1792 |
|
} |
1793 |
|
|
1794 |
|
|
1795 |
|
|
1796 |
|
|
1797 |
|
@param |
1798 |
|
|
1799 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1800 |
0 |
@Override... |
1801 |
|
public void aboutMenuItem_actionPerformed(ActionEvent e) |
1802 |
|
{ |
1803 |
0 |
new Thread(new Runnable() |
1804 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1805 |
0 |
@Override... |
1806 |
|
public void run() |
1807 |
|
{ |
1808 |
0 |
new SplashScreen(false); |
1809 |
|
} |
1810 |
|
}).start(); |
1811 |
|
} |
1812 |
|
|
1813 |
|
|
1814 |
|
|
1815 |
|
|
1816 |
|
|
1817 |
|
|
1818 |
|
@return |
1819 |
|
|
|
|
| 88% |
Uncovered Elements: 3 (25) |
Complexity: 5 |
Complexity Density: 0.29 |
|
1820 |
563 |
public String getAboutMessage()... |
1821 |
|
{ |
1822 |
563 |
StringBuilder message = new StringBuilder(1024); |
1823 |
563 |
message.append("<div style=\"font-family: sans-serif;\">") |
1824 |
|
.append("<h1><strong>Version: ") |
1825 |
|
.append(Cache.getProperty("VERSION")).append("</strong></h1>") |
1826 |
|
.append("<strong>Built: <em>") |
1827 |
|
.append(Cache.getDefault("BUILD_DATE", "unknown")) |
1828 |
|
.append("</em> from ").append(Cache.getBuildDetailsForSplash()) |
1829 |
|
.append("</strong>"); |
1830 |
|
|
1831 |
561 |
String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking"); |
1832 |
562 |
if (latestVersion.equals("Checking")) |
1833 |
|
{ |
1834 |
|
|
1835 |
|
|
1836 |
|
} |
1837 |
356 |
else if (!latestVersion.equals(Cache.getProperty("VERSION"))) |
1838 |
|
{ |
1839 |
356 |
boolean red = false; |
1840 |
356 |
if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT) |
1841 |
|
.indexOf("automated build") == -1) |
1842 |
|
{ |
1843 |
356 |
red = true; |
1844 |
|
|
1845 |
|
|
1846 |
356 |
message.append("<div style=\"color: #FF0000;font-style: bold;\">"); |
1847 |
|
} |
1848 |
|
|
1849 |
355 |
message.append("<br>!! Version ") |
1850 |
|
.append(Cache.getDefault("LATEST_VERSION", "..Checking..")) |
1851 |
|
.append(" is available for download from ") |
1852 |
|
.append(Cache.getDefault("www.jalview.org", |
1853 |
|
"https://www.jalview.org")) |
1854 |
|
.append(" !!"); |
1855 |
355 |
if (red) |
1856 |
|
{ |
1857 |
356 |
message.append("</div>"); |
1858 |
|
} |
1859 |
|
} |
1860 |
562 |
message.append("<br>Authors: "); |
1861 |
561 |
message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS)); |
1862 |
562 |
message.append(CITATION); |
1863 |
|
|
1864 |
563 |
message.append("</div>"); |
1865 |
|
|
1866 |
563 |
return message.toString(); |
1867 |
|
} |
1868 |
|
|
1869 |
|
|
1870 |
|
|
1871 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 3 |
Complexity Density: 0.6 |
|
1872 |
0 |
@Override... |
1873 |
|
public void documentationMenuItem_actionPerformed() |
1874 |
|
{ |
1875 |
0 |
try |
1876 |
|
{ |
1877 |
0 |
if (Platform.isJS()) |
1878 |
|
{ |
1879 |
0 |
BrowserLauncher.openURL("https://www.jalview.org/help.html"); |
1880 |
|
} |
1881 |
|
else |
1882 |
|
|
1883 |
|
|
1884 |
|
|
1885 |
|
|
1886 |
|
|
1887 |
|
{ |
1888 |
0 |
Help.showHelpWindow(); |
1889 |
|
} |
1890 |
|
} catch (Exception ex) |
1891 |
|
{ |
1892 |
0 |
jalview.bin.Console |
1893 |
|
.errPrintln("Error opening help: " + ex.getMessage()); |
1894 |
|
} |
1895 |
|
} |
1896 |
|
|
|
|
| 92.3% |
Uncovered Elements: 1 (13) |
Complexity: 4 |
Complexity Density: 0.44 |
|
1897 |
233 |
@Override... |
1898 |
|
public void closeAll_actionPerformed(ActionEvent e) |
1899 |
|
{ |
1900 |
|
|
1901 |
233 |
JInternalFrame[] frames = desktop.getAllFrames(); |
1902 |
471 |
for (int i = 0; i < frames.length; i++) |
1903 |
|
{ |
1904 |
238 |
try |
1905 |
|
{ |
1906 |
238 |
frames[i].setClosed(true); |
1907 |
|
} catch (java.beans.PropertyVetoException ex) |
1908 |
|
{ |
1909 |
|
} |
1910 |
|
} |
1911 |
233 |
Jalview.getInstance().setCurrentAlignFrame(null); |
1912 |
233 |
jalview.bin.Console.info("ALL CLOSED"); |
1913 |
|
|
1914 |
|
|
1915 |
|
|
1916 |
|
|
1917 |
|
|
1918 |
233 |
StructureSelectionManager ssm = StructureSelectionManager |
1919 |
|
.getStructureSelectionManager(this); |
1920 |
233 |
if (ssm != null) |
1921 |
|
{ |
1922 |
233 |
ssm.resetAll(); |
1923 |
|
} |
1924 |
|
} |
1925 |
|
|
|
|
| 61.5% |
Uncovered Elements: 5 (13) |
Complexity: 5 |
Complexity Density: 0.71 |
|
1926 |
6 |
public int structureViewersStillRunningCount()... |
1927 |
|
{ |
1928 |
6 |
int count = 0; |
1929 |
6 |
JInternalFrame[] frames = desktop.getAllFrames(); |
1930 |
12 |
for (int i = 0; i < frames.length; i++) |
1931 |
|
{ |
1932 |
6 |
if (frames[i] != null |
1933 |
|
&& frames[i] instanceof JalviewStructureDisplayI) |
1934 |
|
{ |
1935 |
0 |
if (((JalviewStructureDisplayI) frames[i]).stillRunning()) |
1936 |
0 |
count++; |
1937 |
|
} |
1938 |
|
} |
1939 |
6 |
return count; |
1940 |
|
} |
1941 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1942 |
0 |
@Override... |
1943 |
|
public void raiseRelated_actionPerformed(ActionEvent e) |
1944 |
|
{ |
1945 |
0 |
reorderAssociatedWindows(false, false); |
1946 |
|
} |
1947 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1948 |
0 |
@Override... |
1949 |
|
public void minimizeAssociated_actionPerformed(ActionEvent e) |
1950 |
|
{ |
1951 |
0 |
reorderAssociatedWindows(true, false); |
1952 |
|
} |
1953 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1954 |
0 |
void closeAssociatedWindows()... |
1955 |
|
{ |
1956 |
0 |
reorderAssociatedWindows(false, true); |
1957 |
|
} |
1958 |
|
|
1959 |
|
|
1960 |
|
|
1961 |
|
|
1962 |
|
|
1963 |
|
|
1964 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1965 |
0 |
@Override... |
1966 |
|
protected void garbageCollect_actionPerformed(ActionEvent e) |
1967 |
|
{ |
1968 |
|
|
1969 |
0 |
jalview.bin.Console.debug("Collecting garbage..."); |
1970 |
0 |
System.gc(); |
1971 |
0 |
jalview.bin.Console.debug("Finished garbage collection."); |
1972 |
|
} |
1973 |
|
|
1974 |
|
|
1975 |
|
|
1976 |
|
|
1977 |
|
@see |
1978 |
|
|
1979 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1980 |
0 |
@Override... |
1981 |
|
protected void showMemusage_actionPerformed(ActionEvent e) |
1982 |
|
{ |
1983 |
0 |
desktop.showMemoryUsage(showMemusage.isSelected()); |
1984 |
|
} |
1985 |
|
|
1986 |
|
|
1987 |
|
|
1988 |
|
|
1989 |
|
@see |
1990 |
|
|
1991 |
|
|
1992 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1993 |
0 |
@Override... |
1994 |
|
protected void showConsole_actionPerformed(ActionEvent e) |
1995 |
|
{ |
1996 |
0 |
showConsole(showConsole.isSelected()); |
1997 |
|
} |
1998 |
|
|
1999 |
|
Console jconsole = null; |
2000 |
|
|
2001 |
|
|
2002 |
|
|
2003 |
|
|
2004 |
|
@param |
2005 |
|
|
|
|
| 83.3% |
Uncovered Elements: 1 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
2006 |
75 |
void showConsole(boolean selected)... |
2007 |
|
{ |
2008 |
|
|
2009 |
75 |
if (jconsole != null) |
2010 |
|
{ |
2011 |
75 |
showConsole.setSelected(selected); |
2012 |
75 |
Cache.setProperty("SHOW_JAVA_CONSOLE", |
2013 |
|
Boolean.valueOf(selected).toString()); |
2014 |
75 |
jconsole.setVisible(selected); |
2015 |
|
} |
2016 |
|
} |
2017 |
|
|
|
|
| 0% |
Uncovered Elements: 62 (62) |
Complexity: 18 |
Complexity Density: 0.56 |
|
2018 |
0 |
void reorderAssociatedWindows(boolean minimize, boolean close)... |
2019 |
|
{ |
2020 |
0 |
JInternalFrame[] frames = desktop.getAllFrames(); |
2021 |
0 |
if (frames == null || frames.length < 1) |
2022 |
|
{ |
2023 |
0 |
return; |
2024 |
|
} |
2025 |
|
|
2026 |
0 |
AlignmentViewport source = null, target = null; |
2027 |
0 |
if (frames[0] instanceof AlignFrame) |
2028 |
|
{ |
2029 |
0 |
source = ((AlignFrame) frames[0]).getCurrentView(); |
2030 |
|
} |
2031 |
0 |
else if (frames[0] instanceof TreePanel) |
2032 |
|
{ |
2033 |
0 |
source = ((TreePanel) frames[0]).getViewPort(); |
2034 |
|
} |
2035 |
0 |
else if (frames[0] instanceof PCAPanel) |
2036 |
|
{ |
2037 |
0 |
source = ((PCAPanel) frames[0]).av; |
2038 |
|
} |
2039 |
0 |
else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) |
2040 |
|
{ |
2041 |
0 |
source = ((PairwiseAlignPanel) frames[0].getContentPane()).av; |
2042 |
|
} |
2043 |
|
|
2044 |
0 |
if (source != null) |
2045 |
|
{ |
2046 |
0 |
for (int i = 0; i < frames.length; i++) |
2047 |
|
{ |
2048 |
0 |
target = null; |
2049 |
0 |
if (frames[i] == null) |
2050 |
|
{ |
2051 |
0 |
continue; |
2052 |
|
} |
2053 |
0 |
if (frames[i] instanceof AlignFrame) |
2054 |
|
{ |
2055 |
0 |
target = ((AlignFrame) frames[i]).getCurrentView(); |
2056 |
|
} |
2057 |
0 |
else if (frames[i] instanceof TreePanel) |
2058 |
|
{ |
2059 |
0 |
target = ((TreePanel) frames[i]).getViewPort(); |
2060 |
|
} |
2061 |
0 |
else if (frames[i] instanceof PCAPanel) |
2062 |
|
{ |
2063 |
0 |
target = ((PCAPanel) frames[i]).av; |
2064 |
|
} |
2065 |
0 |
else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) |
2066 |
|
{ |
2067 |
0 |
target = ((PairwiseAlignPanel) frames[i].getContentPane()).av; |
2068 |
|
} |
2069 |
|
|
2070 |
0 |
if (source == target) |
2071 |
|
{ |
2072 |
0 |
try |
2073 |
|
{ |
2074 |
0 |
if (close) |
2075 |
|
{ |
2076 |
0 |
frames[i].setClosed(true); |
2077 |
|
} |
2078 |
|
else |
2079 |
|
{ |
2080 |
0 |
frames[i].setIcon(minimize); |
2081 |
0 |
if (!minimize) |
2082 |
|
{ |
2083 |
0 |
frames[i].toFront(); |
2084 |
|
} |
2085 |
|
} |
2086 |
|
|
2087 |
|
} catch (java.beans.PropertyVetoException ex) |
2088 |
|
{ |
2089 |
|
} |
2090 |
|
} |
2091 |
|
} |
2092 |
|
} |
2093 |
|
} |
2094 |
|
|
2095 |
|
|
2096 |
|
|
2097 |
|
|
2098 |
|
@param |
2099 |
|
|
2100 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2101 |
0 |
@Override... |
2102 |
|
protected void preferences_actionPerformed(ActionEvent e) |
2103 |
|
{ |
2104 |
0 |
Preferences.openPreferences(); |
2105 |
|
} |
2106 |
|
|
2107 |
|
|
2108 |
|
|
2109 |
|
|
2110 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2111 |
0 |
@Override... |
2112 |
|
public void saveState_actionPerformed() |
2113 |
|
{ |
2114 |
0 |
saveState_actionPerformed(false); |
2115 |
|
} |
2116 |
|
|
|
|
| 45.5% |
Uncovered Elements: 12 (22) |
Complexity: 5 |
Complexity Density: 0.31 |
|
2117 |
2 |
public void saveState_actionPerformed(boolean saveAs)... |
2118 |
|
{ |
2119 |
2 |
java.io.File projectFile = getProjectFile(); |
2120 |
|
|
2121 |
2 |
boolean autoSave = projectFile != null && !saveAs |
2122 |
|
&& BackupFiles.getEnabled(); |
2123 |
|
|
2124 |
|
|
2125 |
|
|
2126 |
|
|
2127 |
|
|
2128 |
|
|
2129 |
2 |
boolean approveSave = false; |
2130 |
2 |
if (!autoSave) |
2131 |
|
{ |
2132 |
0 |
JalviewFileChooser chooser = new JalviewFileChooser("jvp", |
2133 |
|
"Jalview Project"); |
2134 |
|
|
2135 |
0 |
chooser.setFileView(new JalviewFileView()); |
2136 |
0 |
chooser.setDialogTitle(MessageManager.getString("label.save_state")); |
2137 |
|
|
2138 |
0 |
int value = chooser.showSaveDialog(this); |
2139 |
|
|
2140 |
0 |
if (value == JalviewFileChooser.APPROVE_OPTION) |
2141 |
|
{ |
2142 |
0 |
projectFile = chooser.getSelectedFile(); |
2143 |
0 |
setProjectFile(projectFile); |
2144 |
0 |
approveSave = true; |
2145 |
|
} |
2146 |
|
} |
2147 |
|
|
2148 |
2 |
if (approveSave || autoSave) |
2149 |
|
{ |
2150 |
2 |
final Desktop me = this; |
2151 |
2 |
final java.io.File chosenFile = projectFile; |
2152 |
2 |
new Thread(new Runnable() |
2153 |
|
{ |
|
|
| 68.4% |
Uncovered Elements: 6 (19) |
Complexity: 6 |
Complexity Density: 0.46 |
|
2154 |
2 |
@Override... |
2155 |
|
public void run() |
2156 |
|
{ |
2157 |
|
|
2158 |
2 |
setProgressBar(MessageManager.formatMessage( |
2159 |
|
"label.saving_jalview_project", new Object[] |
2160 |
|
{ chosenFile.getName() }), chosenFile.hashCode()); |
2161 |
2 |
Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent()); |
2162 |
|
|
2163 |
|
|
2164 |
2 |
try |
2165 |
|
{ |
2166 |
2 |
boolean doBackup = BackupFiles.getEnabled(); |
2167 |
2 |
BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) |
2168 |
|
: null; |
2169 |
|
|
2170 |
2 |
new Jalview2XML().saveState( |
2171 |
2 |
doBackup ? backupfiles.getTempFile() : chosenFile); |
2172 |
|
|
2173 |
2 |
if (doBackup) |
2174 |
|
{ |
2175 |
2 |
backupfiles.setWriteSuccess(true); |
2176 |
2 |
backupfiles.rollBackupsAndRenameTempFile(); |
2177 |
|
} |
2178 |
|
} catch (OutOfMemoryError oom) |
2179 |
|
{ |
2180 |
0 |
new OOMWarning("Whilst saving current state to " |
2181 |
|
+ chosenFile.getName(), oom); |
2182 |
|
} catch (Exception ex) |
2183 |
|
{ |
2184 |
0 |
jalview.bin.Console.error("Problems whilst trying to save to " |
2185 |
|
+ chosenFile.getName(), ex); |
2186 |
0 |
JvOptionPane.showMessageDialog(me, |
2187 |
|
MessageManager.formatMessage( |
2188 |
|
"label.error_whilst_saving_current_state_to", |
2189 |
|
new Object[] |
2190 |
|
{ chosenFile.getName() }), |
2191 |
|
MessageManager.getString("label.couldnt_save_project"), |
2192 |
|
JvOptionPane.WARNING_MESSAGE); |
2193 |
|
} |
2194 |
2 |
setProgressBar(null, chosenFile.hashCode()); |
2195 |
|
} |
2196 |
|
}).start(); |
2197 |
|
} |
2198 |
|
} |
2199 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2200 |
0 |
@Override... |
2201 |
|
public void saveAsState_actionPerformed(ActionEvent e) |
2202 |
|
{ |
2203 |
0 |
saveState_actionPerformed(true); |
2204 |
|
} |
2205 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2206 |
7 |
protected void setProjectFile(File choice)... |
2207 |
|
{ |
2208 |
7 |
this.projectFile = choice; |
2209 |
|
} |
2210 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2211 |
2 |
public File getProjectFile()... |
2212 |
|
{ |
2213 |
2 |
return this.projectFile; |
2214 |
|
} |
2215 |
|
|
2216 |
|
|
2217 |
|
|
2218 |
|
|
2219 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
|
2220 |
0 |
@Override... |
2221 |
|
public void loadState_actionPerformed() |
2222 |
|
{ |
2223 |
0 |
final String[] suffix = new String[] { "jvp", "jar" }; |
2224 |
0 |
final String[] desc = new String[] { "Jalview Project", |
2225 |
|
"Jalview Project (old)" }; |
2226 |
0 |
JalviewFileChooser chooser = new JalviewFileChooser( |
2227 |
|
Cache.getProperty("LAST_DIRECTORY"), suffix, desc, |
2228 |
|
"Jalview Project", true, BackupFiles.getEnabled()); |
2229 |
|
|
2230 |
|
|
2231 |
|
|
2232 |
0 |
chooser.setFileView(new JalviewFileView()); |
2233 |
0 |
chooser.setDialogTitle(MessageManager.getString("label.restore_state")); |
2234 |
0 |
chooser.setResponseHandler(0, () -> { |
2235 |
0 |
File selectedFile = chooser.getSelectedFile(); |
2236 |
0 |
setProjectFile(selectedFile); |
2237 |
0 |
String choice = selectedFile.getAbsolutePath(); |
2238 |
0 |
Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); |
2239 |
0 |
new Thread(new Runnable() |
2240 |
|
{ |
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 0.6 |
|
2241 |
0 |
@Override... |
2242 |
|
public void run() |
2243 |
|
{ |
2244 |
0 |
try |
2245 |
|
{ |
2246 |
0 |
new Jalview2XML().loadJalviewAlign(selectedFile); |
2247 |
|
} catch (OutOfMemoryError oom) |
2248 |
|
{ |
2249 |
0 |
new OOMWarning("Whilst loading project from " + choice, oom); |
2250 |
|
} catch (Exception ex) |
2251 |
|
{ |
2252 |
0 |
jalview.bin.Console.error( |
2253 |
|
"Problems whilst loading project from " + choice, ex); |
2254 |
0 |
JvOptionPane.showMessageDialog(Desktop.desktop, |
2255 |
|
MessageManager.formatMessage( |
2256 |
|
"label.error_whilst_loading_project_from", |
2257 |
|
new Object[] |
2258 |
|
{ choice }), |
2259 |
|
MessageManager.getString("label.couldnt_load_project"), |
2260 |
|
JvOptionPane.WARNING_MESSAGE); |
2261 |
|
} |
2262 |
|
} |
2263 |
|
}, "Project Loader").start(); |
2264 |
|
}); |
2265 |
|
|
2266 |
0 |
chooser.showOpenDialog(this); |
2267 |
|
} |
2268 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2269 |
0 |
@Override... |
2270 |
|
public void inputSequence_actionPerformed(ActionEvent e) |
2271 |
|
{ |
2272 |
0 |
new SequenceFetcher(this); |
2273 |
|
} |
2274 |
|
|
2275 |
|
JPanel progressPanel; |
2276 |
|
|
2277 |
|
ArrayList<JPanel> fileLoadingPanels = new ArrayList<>(); |
2278 |
|
|
|
|
| 80% |
Uncovered Elements: 1 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
2279 |
293 |
public void startLoading(final Object fileName)... |
2280 |
|
{ |
2281 |
293 |
if (fileLoadingCount == 0) |
2282 |
|
{ |
2283 |
293 |
fileLoadingPanels.add(addProgressPanel(MessageManager |
2284 |
|
.formatMessage("label.loading_file", new Object[] |
2285 |
|
{ fileName }))); |
2286 |
|
} |
2287 |
293 |
fileLoadingCount++; |
2288 |
|
} |
2289 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (16) |
Complexity: 2 |
Complexity Density: 0.14 |
|
2290 |
414 |
private JPanel addProgressPanel(String string)... |
2291 |
|
{ |
2292 |
414 |
if (progressPanel == null) |
2293 |
|
{ |
2294 |
291 |
progressPanel = new JPanel(new GridLayout(1, 1)); |
2295 |
291 |
totalProgressCount = 0; |
2296 |
291 |
instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); |
2297 |
|
} |
2298 |
414 |
JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); |
2299 |
414 |
JProgressBar progressBar = new JProgressBar(); |
2300 |
414 |
progressBar.setIndeterminate(true); |
2301 |
|
|
2302 |
414 |
thisprogress.add(new JLabel(string), BorderLayout.WEST); |
2303 |
|
|
2304 |
414 |
thisprogress.add(progressBar, BorderLayout.CENTER); |
2305 |
414 |
progressPanel.add(thisprogress); |
2306 |
413 |
((GridLayout) progressPanel.getLayout()).setRows( |
2307 |
|
((GridLayout) progressPanel.getLayout()).getRows() + 1); |
2308 |
413 |
++totalProgressCount; |
2309 |
413 |
instance.validate(); |
2310 |
413 |
return thisprogress; |
2311 |
|
} |
2312 |
|
|
2313 |
|
int totalProgressCount = 0; |
2314 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (13) |
Complexity: 3 |
Complexity Density: 0.33 |
|
2315 |
403 |
private void removeProgressPanel(JPanel progbar)... |
2316 |
|
{ |
2317 |
403 |
if (progressPanel != null) |
2318 |
|
{ |
2319 |
393 |
synchronized (progressPanel) |
2320 |
|
{ |
2321 |
393 |
progressPanel.remove(progbar); |
2322 |
393 |
GridLayout gl = (GridLayout) progressPanel.getLayout(); |
2323 |
393 |
gl.setRows(gl.getRows() - 1); |
2324 |
393 |
if (--totalProgressCount < 1) |
2325 |
|
{ |
2326 |
267 |
this.getContentPane().remove(progressPanel); |
2327 |
267 |
progressPanel = null; |
2328 |
|
} |
2329 |
|
} |
2330 |
|
} |
2331 |
403 |
validate(); |
2332 |
|
} |
2333 |
|
|
|
|
| 90.9% |
Uncovered Elements: 1 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
2334 |
319 |
public void stopLoading()... |
2335 |
|
{ |
2336 |
319 |
fileLoadingCount--; |
2337 |
319 |
if (fileLoadingCount < 1) |
2338 |
|
{ |
2339 |
608 |
while (fileLoadingPanels.size() > 0) |
2340 |
|
{ |
2341 |
289 |
removeProgressPanel(fileLoadingPanels.remove(0)); |
2342 |
|
} |
2343 |
319 |
fileLoadingPanels.clear(); |
2344 |
319 |
fileLoadingCount = 0; |
2345 |
|
} |
2346 |
319 |
validate(); |
2347 |
|
} |
2348 |
|
|
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
2349 |
10 |
public static int getViewCount(String alignmentId)... |
2350 |
|
{ |
2351 |
10 |
AlignmentViewport[] aps = getViewports(alignmentId); |
2352 |
10 |
return (aps == null) ? 0 : aps.length; |
2353 |
|
} |
2354 |
|
|
2355 |
|
|
2356 |
|
|
2357 |
|
@param |
2358 |
|
|
2359 |
|
@return |
2360 |
|
|
|
|
| 90.9% |
Uncovered Elements: 2 (22) |
Complexity: 6 |
Complexity Density: 0.43 |
|
2361 |
89 |
public static AlignmentPanel[] getAlignmentPanels(String alignmentId)... |
2362 |
|
{ |
2363 |
89 |
if (Desktop.desktop == null) |
2364 |
|
{ |
2365 |
|
|
2366 |
|
|
2367 |
0 |
return null; |
2368 |
|
} |
2369 |
89 |
List<AlignmentPanel> aps = new ArrayList<>(); |
2370 |
89 |
AlignFrame[] frames = Desktop.getDesktopAlignFrames(); |
2371 |
89 |
if (frames == null) |
2372 |
|
{ |
2373 |
21 |
return null; |
2374 |
|
} |
2375 |
68 |
for (AlignFrame af : frames) |
2376 |
|
{ |
2377 |
182 |
for (AlignmentPanel ap : af.alignPanels) |
2378 |
|
{ |
2379 |
228 |
if (alignmentId == null |
2380 |
|
|| alignmentId.equals(ap.av.getSequenceSetId())) |
2381 |
|
{ |
2382 |
138 |
aps.add(ap); |
2383 |
|
} |
2384 |
|
} |
2385 |
|
} |
2386 |
68 |
if (aps.size() == 0) |
2387 |
|
{ |
2388 |
11 |
return null; |
2389 |
|
} |
2390 |
57 |
AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]); |
2391 |
57 |
return vap; |
2392 |
|
} |
2393 |
|
|
2394 |
|
|
2395 |
|
|
2396 |
|
|
2397 |
|
@param |
2398 |
|
|
2399 |
|
|
2400 |
|
@return |
2401 |
|
|
|
|
| 73.9% |
Uncovered Elements: 6 (23) |
Complexity: 8 |
Complexity Density: 0.62 |
|
2402 |
10 |
public static AlignmentViewport[] getViewports(String sequenceSetId)... |
2403 |
|
{ |
2404 |
10 |
List<AlignmentViewport> viewp = new ArrayList<>(); |
2405 |
10 |
if (desktop != null) |
2406 |
|
{ |
2407 |
10 |
AlignFrame[] frames = Desktop.getDesktopAlignFrames(); |
2408 |
|
|
2409 |
10 |
for (AlignFrame afr : frames) |
2410 |
|
{ |
2411 |
11 |
if (sequenceSetId == null || afr.getViewport().getSequenceSetId() |
2412 |
|
.equals(sequenceSetId)) |
2413 |
|
{ |
2414 |
10 |
if (afr.alignPanels != null) |
2415 |
|
{ |
2416 |
10 |
for (AlignmentPanel ap : afr.alignPanels) |
2417 |
|
{ |
2418 |
11 |
if (sequenceSetId == null |
2419 |
|
|| sequenceSetId.equals(ap.av.getSequenceSetId())) |
2420 |
|
{ |
2421 |
11 |
viewp.add(ap.av); |
2422 |
|
} |
2423 |
|
} |
2424 |
|
} |
2425 |
|
else |
2426 |
|
{ |
2427 |
0 |
viewp.add(afr.getViewport()); |
2428 |
|
} |
2429 |
|
} |
2430 |
|
} |
2431 |
10 |
if (viewp.size() > 0) |
2432 |
|
{ |
2433 |
10 |
return viewp.toArray(new AlignmentViewport[viewp.size()]); |
2434 |
|
} |
2435 |
|
} |
2436 |
0 |
return null; |
2437 |
|
} |
2438 |
|
|
2439 |
|
|
2440 |
|
|
2441 |
|
|
2442 |
|
@param |
2443 |
|
|
|
|
| 77.8% |
Uncovered Elements: 8 (36) |
Complexity: 13 |
Complexity Density: 0.59 |
|
2444 |
1 |
public static void explodeViews(AlignFrame af)... |
2445 |
|
{ |
2446 |
1 |
int size = af.alignPanels.size(); |
2447 |
1 |
if (size < 2) |
2448 |
|
{ |
2449 |
0 |
return; |
2450 |
|
} |
2451 |
|
|
2452 |
|
|
2453 |
1 |
FeatureSettings viewFeatureSettings = (af.featureSettings != null |
2454 |
|
&& af.featureSettings.isOpen()) ? af.featureSettings : null; |
2455 |
1 |
Rectangle fsBounds = af.getFeatureSettingsGeometry(); |
2456 |
6 |
for (int i = 0; i < size; i++) |
2457 |
|
{ |
2458 |
5 |
AlignmentPanel ap = af.alignPanels.get(i); |
2459 |
|
|
2460 |
5 |
AlignFrame newaf = new AlignFrame(ap); |
2461 |
|
|
2462 |
|
|
2463 |
5 |
if (ap == af.alignPanel) |
2464 |
|
{ |
2465 |
1 |
if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap) |
2466 |
|
{ |
2467 |
0 |
newaf.featureSettings = viewFeatureSettings; |
2468 |
|
} |
2469 |
1 |
newaf.setFeatureSettingsGeometry(fsBounds); |
2470 |
|
} |
2471 |
|
|
2472 |
|
|
2473 |
|
|
2474 |
|
|
2475 |
|
|
2476 |
5 |
Rectangle geometry = ap.av.getExplodedGeometry(); |
2477 |
5 |
if (geometry != null) |
2478 |
|
{ |
2479 |
5 |
newaf.setBounds(geometry); |
2480 |
|
} |
2481 |
|
|
2482 |
5 |
ap.av.setGatherViewsHere(false); |
2483 |
|
|
2484 |
5 |
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, |
2485 |
|
AlignFrame.DEFAULT_HEIGHT); |
2486 |
|
|
2487 |
|
|
2488 |
|
|
2489 |
5 |
if (ap == af.alignPanel && newaf.featureSettings != null |
2490 |
|
&& newaf.featureSettings.isOpen() |
2491 |
|
&& af.alignPanel.getAlignViewport().isShowSequenceFeatures()) |
2492 |
|
{ |
2493 |
0 |
newaf.showFeatureSettingsUI(); |
2494 |
|
} |
2495 |
|
} |
2496 |
|
|
2497 |
1 |
af.featureSettings = null; |
2498 |
1 |
af.alignPanels.clear(); |
2499 |
1 |
af.closeMenuItem_actionPerformed(true); |
2500 |
|
|
2501 |
|
} |
2502 |
|
|
2503 |
|
|
2504 |
|
|
2505 |
|
|
2506 |
|
|
2507 |
|
|
2508 |
|
|
2509 |
|
@param |
2510 |
|
|
|
|
| 78% |
Uncovered Elements: 9 (41) |
Complexity: 12 |
Complexity Density: 0.48 |
|
2511 |
13 |
public void gatherViews(AlignFrame source)... |
2512 |
|
{ |
2513 |
13 |
source.viewport.setGatherViewsHere(true); |
2514 |
13 |
source.viewport.setExplodedGeometry(source.getBounds()); |
2515 |
13 |
JInternalFrame[] frames = desktop.getAllFrames(); |
2516 |
13 |
String viewId = source.viewport.getSequenceSetId(); |
2517 |
107 |
for (int t = 0; t < frames.length; t++) |
2518 |
|
{ |
2519 |
94 |
if (frames[t] instanceof AlignFrame && frames[t] != source) |
2520 |
|
{ |
2521 |
49 |
AlignFrame af = (AlignFrame) frames[t]; |
2522 |
49 |
boolean gatherThis = false; |
2523 |
110 |
for (int a = 0; a < af.alignPanels.size(); a++) |
2524 |
|
{ |
2525 |
61 |
AlignmentPanel ap = af.alignPanels.get(a); |
2526 |
61 |
if (viewId.equals(ap.av.getSequenceSetId())) |
2527 |
|
{ |
2528 |
35 |
gatherThis = true; |
2529 |
35 |
ap.av.setGatherViewsHere(false); |
2530 |
35 |
ap.av.setExplodedGeometry(af.getBounds()); |
2531 |
35 |
source.addAlignmentPanel(ap, false); |
2532 |
|
} |
2533 |
|
} |
2534 |
|
|
2535 |
49 |
if (gatherThis) |
2536 |
|
{ |
2537 |
35 |
if (af.featureSettings != null && af.featureSettings.isOpen()) |
2538 |
|
{ |
2539 |
0 |
if (source.featureSettings == null) |
2540 |
|
{ |
2541 |
|
|
2542 |
0 |
source.featureSettings = af.featureSettings; |
2543 |
0 |
source.setFeatureSettingsGeometry( |
2544 |
|
af.getFeatureSettingsGeometry()); |
2545 |
|
} |
2546 |
|
else |
2547 |
|
{ |
2548 |
|
|
2549 |
0 |
af.featureSettings.close(); |
2550 |
|
} |
2551 |
|
} |
2552 |
35 |
af.alignPanels.clear(); |
2553 |
35 |
af.closeMenuItem_actionPerformed(true); |
2554 |
|
} |
2555 |
|
} |
2556 |
|
} |
2557 |
|
|
2558 |
|
|
2559 |
13 |
if (source.featureSettings != null && source.featureSettings.isOpen()) |
2560 |
|
{ |
2561 |
0 |
source.showFeatureSettingsUI(); |
2562 |
|
} |
2563 |
|
|
2564 |
|
} |
2565 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2566 |
40 |
public JInternalFrame[] getAllFrames()... |
2567 |
|
{ |
2568 |
40 |
return desktop.getAllFrames(); |
2569 |
|
} |
2570 |
|
|
2571 |
|
|
2572 |
|
|
2573 |
|
|
2574 |
|
|
2575 |
|
@param |
2576 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2577 |
36 |
public void checkForQuestionnaire(String url)... |
2578 |
|
{ |
2579 |
36 |
UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url); |
2580 |
|
|
2581 |
36 |
new Thread(jvq).start(); |
2582 |
|
} |
2583 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2584 |
75 |
public void checkURLLinks()... |
2585 |
|
{ |
2586 |
|
|
2587 |
75 |
addDialogThread(new Runnable() |
2588 |
|
{ |
|
|
| 40.5% |
Uncovered Elements: 22 (37) |
Complexity: 7 |
Complexity Density: 0.26 |
|
2589 |
75 |
@Override... |
2590 |
|
public void run() |
2591 |
|
{ |
2592 |
75 |
if (Cache.getDefault("CHECKURLLINKS", true)) |
2593 |
|
{ |
2594 |
|
|
2595 |
|
|
2596 |
75 |
List<String> links = Preferences.sequenceUrlLinks |
2597 |
|
.getLinksForMenu(); |
2598 |
|
|
2599 |
|
|
2600 |
|
|
2601 |
75 |
ListIterator<String> li = links.listIterator(); |
2602 |
75 |
boolean check = false; |
2603 |
75 |
List<JLabel> urls = new ArrayList<>(); |
2604 |
222 |
while (li.hasNext()) |
2605 |
|
{ |
2606 |
147 |
String link = li.next(); |
2607 |
147 |
if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) |
2608 |
|
&& !UrlConstants.isDefaultString(link)) |
2609 |
|
{ |
2610 |
0 |
check = true; |
2611 |
0 |
int barPos = link.indexOf("|"); |
2612 |
0 |
String urlMsg = barPos == -1 ? link |
2613 |
|
: link.substring(0, barPos) + ": " |
2614 |
|
+ link.substring(barPos + 1); |
2615 |
0 |
urls.add(new JLabel(urlMsg)); |
2616 |
|
} |
2617 |
|
} |
2618 |
75 |
if (!check) |
2619 |
|
{ |
2620 |
75 |
return; |
2621 |
|
} |
2622 |
|
|
2623 |
|
|
2624 |
|
|
2625 |
0 |
JPanel msgPanel = new JPanel(); |
2626 |
0 |
msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS)); |
2627 |
0 |
msgPanel.add(Box.createVerticalGlue()); |
2628 |
0 |
JLabel msg = new JLabel(MessageManager |
2629 |
|
.getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); |
2630 |
0 |
JLabel msg2 = new JLabel(MessageManager |
2631 |
|
.getString("label.SEQUENCE_ID_for_DB_ACCESSION2")); |
2632 |
0 |
msgPanel.add(msg); |
2633 |
0 |
for (JLabel url : urls) |
2634 |
|
{ |
2635 |
0 |
msgPanel.add(url); |
2636 |
|
} |
2637 |
0 |
msgPanel.add(msg2); |
2638 |
|
|
2639 |
0 |
final JCheckBox jcb = new JCheckBox( |
2640 |
|
MessageManager.getString("label.do_not_display_again")); |
2641 |
0 |
jcb.addActionListener(new ActionListener() |
2642 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2643 |
0 |
@Override... |
2644 |
|
public void actionPerformed(ActionEvent e) |
2645 |
|
{ |
2646 |
|
|
2647 |
0 |
boolean showWarningAgain = !jcb.isSelected(); |
2648 |
0 |
Cache.setProperty("CHECKURLLINKS", |
2649 |
|
Boolean.valueOf(showWarningAgain).toString()); |
2650 |
|
} |
2651 |
|
}); |
2652 |
0 |
msgPanel.add(jcb); |
2653 |
|
|
2654 |
0 |
JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, |
2655 |
|
MessageManager |
2656 |
|
.getString("label.SEQUENCE_ID_no_longer_used"), |
2657 |
|
JvOptionPane.WARNING_MESSAGE); |
2658 |
|
} |
2659 |
|
} |
2660 |
|
}); |
2661 |
|
} |
2662 |
|
|
2663 |
|
|
2664 |
|
|
2665 |
|
|
2666 |
|
|
2667 |
|
|
2668 |
|
@author |
2669 |
|
|
|
|
| 31% |
Uncovered Elements: 29 (42) |
Complexity: 13 |
Complexity Density: 0.48 |
|
2670 |
|
public class MyDesktopPane extends JDesktopPane implements Runnable |
2671 |
|
{ |
2672 |
|
private static final float ONE_MB = 1048576f; |
2673 |
|
|
2674 |
|
boolean showMemoryUsage = false; |
2675 |
|
|
2676 |
|
Runtime runtime; |
2677 |
|
|
2678 |
|
java.text.NumberFormat df; |
2679 |
|
|
2680 |
|
float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, |
2681 |
|
percentUsage; |
2682 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2683 |
75 |
public MyDesktopPane(boolean showMemoryUsage)... |
2684 |
|
{ |
2685 |
75 |
showMemoryUsage(showMemoryUsage); |
2686 |
|
} |
2687 |
|
|
|
|
| 57.1% |
Uncovered Elements: 3 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
2688 |
75 |
public void showMemoryUsage(boolean showMemory)... |
2689 |
|
{ |
2690 |
75 |
this.showMemoryUsage = showMemory; |
2691 |
75 |
if (showMemory) |
2692 |
|
{ |
2693 |
0 |
Thread worker = new Thread(this); |
2694 |
0 |
worker.start(); |
2695 |
|
} |
2696 |
75 |
repaint(); |
2697 |
|
} |
2698 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2699 |
582 |
public boolean isShowMemoryUsage()... |
2700 |
|
{ |
2701 |
582 |
return showMemoryUsage; |
2702 |
|
} |
2703 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 3 |
Complexity Density: 0.23 |
|
2704 |
0 |
@Override... |
2705 |
|
public void run() |
2706 |
|
{ |
2707 |
0 |
df = java.text.NumberFormat.getNumberInstance(); |
2708 |
0 |
df.setMaximumFractionDigits(2); |
2709 |
0 |
runtime = Runtime.getRuntime(); |
2710 |
|
|
2711 |
0 |
while (showMemoryUsage) |
2712 |
|
{ |
2713 |
0 |
try |
2714 |
|
{ |
2715 |
0 |
maxMemory = runtime.maxMemory() / ONE_MB; |
2716 |
0 |
allocatedMemory = runtime.totalMemory() / ONE_MB; |
2717 |
0 |
freeMemory = runtime.freeMemory() / ONE_MB; |
2718 |
0 |
totalFreeMemory = freeMemory + (maxMemory - allocatedMemory); |
2719 |
|
|
2720 |
0 |
percentUsage = (totalFreeMemory / maxMemory) * 100; |
2721 |
|
|
2722 |
|
|
2723 |
|
{ |
2724 |
|
|
2725 |
|
|
2726 |
|
|
2727 |
|
} |
2728 |
0 |
repaint(); |
2729 |
|
|
2730 |
0 |
Thread.sleep(3000); |
2731 |
|
} catch (Exception ex) |
2732 |
|
{ |
2733 |
0 |
ex.printStackTrace(); |
2734 |
|
} |
2735 |
|
} |
2736 |
|
} |
2737 |
|
|
|
|
| 23.1% |
Uncovered Elements: 10 (13) |
Complexity: 6 |
Complexity Density: 0.86 |
|
2738 |
2904 |
@Override... |
2739 |
|
public void paintComponent(Graphics g) |
2740 |
|
{ |
2741 |
2904 |
if (showMemoryUsage && g != null && df != null) |
2742 |
|
{ |
2743 |
0 |
if (percentUsage < 20) |
2744 |
|
{ |
2745 |
0 |
g.setColor(Color.red); |
2746 |
|
} |
2747 |
0 |
FontMetrics fm = g.getFontMetrics(); |
2748 |
0 |
if (fm != null) |
2749 |
|
{ |
2750 |
0 |
g.drawString(MessageManager.formatMessage("label.memory_stats", |
2751 |
|
new Object[] |
2752 |
|
{ df.format(totalFreeMemory), df.format(maxMemory), |
2753 |
|
df.format(percentUsage) }), |
2754 |
|
10, getHeight() - fm.getHeight()); |
2755 |
|
} |
2756 |
|
} |
2757 |
|
|
2758 |
|
|
2759 |
2904 |
Desktop.debugScaleMessage(Desktop.getDesktop().getGraphics()); |
2760 |
|
} |
2761 |
|
} |
2762 |
|
|
2763 |
|
|
2764 |
|
|
2765 |
|
|
2766 |
|
@return |
2767 |
|
|
|
|
| 82.9% |
Uncovered Elements: 6 (35) |
Complexity: 9 |
Complexity Density: 0.47 |
|
2768 |
305 |
@Override... |
2769 |
|
public AlignFrame[] getAlignFrames() |
2770 |
|
{ |
2771 |
305 |
if (desktop == null) |
2772 |
|
{ |
2773 |
0 |
return null; |
2774 |
|
} |
2775 |
|
|
2776 |
305 |
JInternalFrame[] frames = Desktop.desktop.getAllFrames(); |
2777 |
|
|
2778 |
305 |
if (frames == null) |
2779 |
|
{ |
2780 |
0 |
return null; |
2781 |
|
} |
2782 |
305 |
List<AlignFrame> avp = new ArrayList<>(); |
2783 |
|
|
2784 |
1010 |
for (int i = frames.length - 1; i > -1; i--) |
2785 |
|
{ |
2786 |
705 |
if (frames[i] instanceof AlignFrame) |
2787 |
|
{ |
2788 |
423 |
avp.add((AlignFrame) frames[i]); |
2789 |
|
} |
2790 |
282 |
else if (frames[i] instanceof SplitFrame) |
2791 |
|
{ |
2792 |
|
|
2793 |
|
|
2794 |
|
|
2795 |
48 |
GSplitFrame sf = (GSplitFrame) frames[i]; |
2796 |
48 |
if (sf.getTopFrame() instanceof AlignFrame) |
2797 |
|
{ |
2798 |
48 |
avp.add((AlignFrame) sf.getTopFrame()); |
2799 |
|
} |
2800 |
48 |
if (sf.getBottomFrame() instanceof AlignFrame) |
2801 |
|
{ |
2802 |
48 |
avp.add((AlignFrame) sf.getBottomFrame()); |
2803 |
|
} |
2804 |
|
} |
2805 |
|
} |
2806 |
305 |
if (avp.size() == 0) |
2807 |
|
{ |
2808 |
50 |
return null; |
2809 |
|
} |
2810 |
255 |
AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]); |
2811 |
255 |
return afs; |
2812 |
|
} |
2813 |
|
|
2814 |
|
|
2815 |
|
|
2816 |
|
|
|
|
| 55.6% |
Uncovered Elements: 4 (9) |
Complexity: 4 |
Complexity Density: 0.8 |
|
2817 |
305 |
public static AlignFrame[] getDesktopAlignFrames()... |
2818 |
|
{ |
2819 |
305 |
if (Jalview.isHeadlessMode()) |
2820 |
|
{ |
2821 |
|
|
2822 |
0 |
return Jalview.getInstance().getAlignFrames(); |
2823 |
|
} |
2824 |
|
|
2825 |
305 |
if (instance != null && desktop != null) |
2826 |
|
{ |
2827 |
305 |
return instance.getAlignFrames(); |
2828 |
|
} |
2829 |
|
|
2830 |
0 |
return null; |
2831 |
|
} |
2832 |
|
|
2833 |
|
|
2834 |
|
|
2835 |
|
|
2836 |
|
@return |
2837 |
|
|
|
|
| 0% |
Uncovered Elements: 20 (20) |
Complexity: 5 |
Complexity Density: 0.42 |
|
2838 |
0 |
public GStructureViewer[] getJmols()... |
2839 |
|
{ |
2840 |
0 |
JInternalFrame[] frames = Desktop.desktop.getAllFrames(); |
2841 |
|
|
2842 |
0 |
if (frames == null) |
2843 |
|
{ |
2844 |
0 |
return null; |
2845 |
|
} |
2846 |
0 |
List<GStructureViewer> avp = new ArrayList<>(); |
2847 |
|
|
2848 |
0 |
for (int i = frames.length - 1; i > -1; i--) |
2849 |
|
{ |
2850 |
0 |
if (frames[i] instanceof AppJmol) |
2851 |
|
{ |
2852 |
0 |
GStructureViewer af = (GStructureViewer) frames[i]; |
2853 |
0 |
avp.add(af); |
2854 |
|
} |
2855 |
|
} |
2856 |
0 |
if (avp.size() == 0) |
2857 |
|
{ |
2858 |
0 |
return null; |
2859 |
|
} |
2860 |
0 |
GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]); |
2861 |
0 |
return afs; |
2862 |
|
} |
2863 |
|
|
2864 |
|
|
2865 |
|
|
2866 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
2867 |
0 |
@Override... |
2868 |
|
public void groovyShell_actionPerformed() |
2869 |
|
{ |
2870 |
0 |
try |
2871 |
|
{ |
2872 |
0 |
openGroovyConsole(); |
2873 |
|
} catch (Exception ex) |
2874 |
|
{ |
2875 |
0 |
jalview.bin.Console.error("Groovy Console creation failed.", ex); |
2876 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
2877 |
|
|
2878 |
|
MessageManager.getString("label.couldnt_create_groovy_shell"), |
2879 |
|
MessageManager.getString("label.groovy_support_failed"), |
2880 |
|
JvOptionPane.ERROR_MESSAGE); |
2881 |
|
} |
2882 |
|
} |
2883 |
|
|
2884 |
|
|
2885 |
|
|
2886 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 2 |
Complexity Density: 0.2 |
|
2887 |
0 |
void openGroovyConsole()... |
2888 |
|
{ |
2889 |
0 |
if (groovyConsole == null) |
2890 |
|
{ |
2891 |
0 |
JalviewObjectI j = new JalviewObject(this); |
2892 |
0 |
groovyConsole = new groovy.console.ui.Console(); |
2893 |
0 |
groovyConsole.setVariable(JalviewObjectI.jalviewObjectName, j); |
2894 |
0 |
groovyConsole.setVariable(JalviewObjectI.currentAlFrameName, |
2895 |
|
getCurrentAlignFrame()); |
2896 |
0 |
groovyConsole.run(); |
2897 |
|
|
2898 |
|
|
2899 |
|
|
2900 |
|
|
2901 |
|
|
2902 |
|
|
2903 |
|
|
2904 |
0 |
Window window = (Window) groovyConsole.getFrame(); |
2905 |
0 |
window.addWindowListener(new WindowAdapter() |
2906 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2907 |
0 |
@Override... |
2908 |
|
public void windowClosed(WindowEvent e) |
2909 |
|
{ |
2910 |
|
|
2911 |
|
|
2912 |
|
|
2913 |
0 |
addQuitHandler(); |
2914 |
0 |
enableExecuteGroovy(false); |
2915 |
|
} |
2916 |
|
}); |
2917 |
|
} |
2918 |
|
|
2919 |
|
|
2920 |
|
|
2921 |
|
|
2922 |
0 |
((Window) groovyConsole.getFrame()).setVisible(true); |
2923 |
|
|
2924 |
|
|
2925 |
|
|
2926 |
|
|
2927 |
|
|
2928 |
0 |
enableExecuteGroovy(true); |
2929 |
|
} |
2930 |
|
|
2931 |
|
|
2932 |
|
|
2933 |
|
|
2934 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2935 |
0 |
protected void addQuitHandler()... |
2936 |
|
{ |
2937 |
0 |
getRootPane() |
2938 |
|
.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( |
2939 |
|
KeyStroke |
2940 |
|
.getKeyStroke(KeyEvent.VK_Q, |
2941 |
|
jalview.util.ShortcutKeyMaskExWrapper |
2942 |
|
.getMenuShortcutKeyMaskEx()), |
2943 |
|
"Quit"); |
2944 |
0 |
getRootPane().getActionMap().put("Quit", new AbstractAction() |
2945 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2946 |
0 |
@Override... |
2947 |
|
public void actionPerformed(ActionEvent e) |
2948 |
|
{ |
2949 |
0 |
desktopQuit(); |
2950 |
|
} |
2951 |
|
}); |
2952 |
|
} |
2953 |
|
|
2954 |
|
|
2955 |
|
|
2956 |
|
|
2957 |
|
@param |
2958 |
|
|
2959 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
2960 |
0 |
public void enableExecuteGroovy(boolean enabled)... |
2961 |
|
{ |
2962 |
|
|
2963 |
|
|
2964 |
|
|
2965 |
|
|
2966 |
0 |
groovyShell.setEnabled(!enabled); |
2967 |
|
|
2968 |
0 |
AlignFrame[] alignFrames = getDesktopAlignFrames(); |
2969 |
0 |
if (alignFrames != null) |
2970 |
|
{ |
2971 |
0 |
for (AlignFrame af : alignFrames) |
2972 |
|
{ |
2973 |
0 |
af.setGroovyEnabled(enabled); |
2974 |
|
} |
2975 |
|
} |
2976 |
|
} |
2977 |
|
|
2978 |
|
|
2979 |
|
|
2980 |
|
|
2981 |
|
|
2982 |
|
private Hashtable<Long, JPanel> progressBars; |
2983 |
|
|
2984 |
|
private Hashtable<Long, IProgressIndicatorHandler> progressBarHandlers; |
2985 |
|
|
2986 |
|
private Hashtable<Long, String> progressBarMessages; |
2987 |
|
|
2988 |
|
|
2989 |
|
|
2990 |
|
|
2991 |
|
@see |
2992 |
|
|
|
|
| 90.5% |
Uncovered Elements: 2 (21) |
Complexity: 5 |
Complexity Density: 0.38 |
|
2993 |
235 |
@Override... |
2994 |
|
public void setProgressBar(String message, long id) |
2995 |
|
{ |
2996 |
235 |
if (progressBars == null) |
2997 |
|
{ |
2998 |
45 |
progressBars = new Hashtable<>(); |
2999 |
45 |
progressBarHandlers = new Hashtable<>(); |
3000 |
45 |
progressBarMessages = new Hashtable<>(); |
3001 |
|
} |
3002 |
|
|
3003 |
235 |
if (progressBars.get(Long.valueOf(id)) != null) |
3004 |
|
{ |
3005 |
114 |
JPanel panel = progressBars.remove(Long.valueOf(id)); |
3006 |
114 |
if (progressBarHandlers.contains(Long.valueOf(id))) |
3007 |
|
{ |
3008 |
0 |
progressBarHandlers.remove(Long.valueOf(id)); |
3009 |
|
} |
3010 |
114 |
removeProgressPanel(panel); |
3011 |
|
} |
3012 |
|
else |
3013 |
|
{ |
3014 |
121 |
progressBars.put(Long.valueOf(id), addProgressPanel(message)); |
3015 |
120 |
if (message != null) |
3016 |
|
{ |
3017 |
117 |
progressBarMessages.put(id, message); |
3018 |
|
} |
3019 |
|
else |
3020 |
|
{ |
3021 |
3 |
progressBarMessages.remove(id); |
3022 |
|
} |
3023 |
|
} |
3024 |
|
} |
3025 |
|
|
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 4 |
Complexity Density: 0.5 |
|
3026 |
0 |
@Override... |
3027 |
|
public JProgressBar getProgressBar(long id) |
3028 |
|
{ |
3029 |
0 |
if (progressBars == null) |
3030 |
0 |
return null; |
3031 |
|
|
3032 |
0 |
if (progressBars.get(Long.valueOf(id)) == null) |
3033 |
0 |
return null; |
3034 |
|
|
3035 |
0 |
for (Component c : progressBars.get(Long.valueOf(id)).getComponents()) |
3036 |
|
{ |
3037 |
0 |
if (c.getClass() == JProgressBar.class) |
3038 |
0 |
return (JProgressBar) c; |
3039 |
|
} |
3040 |
0 |
return null; |
3041 |
|
} |
3042 |
|
|
3043 |
|
|
3044 |
|
|
3045 |
|
|
3046 |
|
@see |
3047 |
|
|
3048 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 4 |
Complexity Density: 0.44 |
|
3049 |
0 |
@Override... |
3050 |
|
public void registerHandler(final long id, |
3051 |
|
final IProgressIndicatorHandler handler) |
3052 |
|
{ |
3053 |
0 |
if (progressBarHandlers == null |
3054 |
|
|| !progressBars.containsKey(Long.valueOf(id))) |
3055 |
|
{ |
3056 |
0 |
throw new Error(MessageManager.getString( |
3057 |
|
"error.call_setprogressbar_before_registering_handler")); |
3058 |
|
} |
3059 |
0 |
progressBarHandlers.put(Long.valueOf(id), handler); |
3060 |
0 |
final JPanel progressPanel = progressBars.get(Long.valueOf(id)); |
3061 |
0 |
if (handler.canCancel()) |
3062 |
|
{ |
3063 |
0 |
JButton cancel = new JButton( |
3064 |
|
MessageManager.getString("action.cancel")); |
3065 |
0 |
final IProgressIndicator us = this; |
3066 |
0 |
cancel.addActionListener(new ActionListener() |
3067 |
|
{ |
3068 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
3069 |
0 |
@Override... |
3070 |
|
public void actionPerformed(ActionEvent e) |
3071 |
|
{ |
3072 |
0 |
handler.cancelActivity(id); |
3073 |
0 |
us.setProgressBar(MessageManager |
3074 |
|
.formatMessage("label.cancelled_params", new Object[] |
3075 |
|
{ ((JLabel) progressPanel.getComponent(0)).getText() }), |
3076 |
|
id); |
3077 |
|
} |
3078 |
|
}); |
3079 |
0 |
progressPanel.add(cancel, BorderLayout.EAST); |
3080 |
|
} |
3081 |
|
} |
3082 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3083 |
0 |
@Override... |
3084 |
|
public String getMessage(long id) |
3085 |
|
{ |
3086 |
0 |
return progressBarMessages.get(id); |
3087 |
|
} |
3088 |
|
|
3089 |
|
|
3090 |
|
|
3091 |
|
|
3092 |
|
@param |
3093 |
|
@param |
3094 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 4 |
Complexity Density: 0.5 |
|
3095 |
0 |
@Override... |
3096 |
|
public void setProgressBarMessage(long id, String message) |
3097 |
|
{ |
3098 |
0 |
Container progBar = progressBars.get(id); |
3099 |
0 |
if (progBar == null || progBar.getComponentCount() == 0) |
3100 |
|
{ |
3101 |
0 |
return; |
3102 |
|
} |
3103 |
0 |
for (Component component : progBar.getComponents()) |
3104 |
|
{ |
3105 |
0 |
if (component.getClass().equals(JLabel.class)) |
3106 |
|
{ |
3107 |
0 |
((JLabel) component).setText(message); |
3108 |
0 |
; |
3109 |
0 |
progBar.revalidate(); |
3110 |
|
} |
3111 |
|
} |
3112 |
|
} |
3113 |
|
|
3114 |
|
|
3115 |
|
|
3116 |
|
@return |
3117 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
3118 |
10 |
@Override... |
3119 |
|
public boolean operationInProgress() |
3120 |
|
{ |
3121 |
10 |
if (progressBars != null && progressBars.size() > 0) |
3122 |
|
{ |
3123 |
0 |
return true; |
3124 |
|
} |
3125 |
10 |
return false; |
3126 |
|
} |
3127 |
|
|
3128 |
|
|
3129 |
|
|
3130 |
|
|
3131 |
|
|
3132 |
|
|
3133 |
|
@param |
3134 |
|
@return |
3135 |
|
|
|
|
| 66.7% |
Uncovered Elements: 4 (12) |
Complexity: 6 |
Complexity Density: 1 |
|
3136 |
1 |
public static AlignFrame getAlignFrameFor(AlignViewportI viewport)... |
3137 |
|
{ |
3138 |
1 |
if (desktop != null) |
3139 |
|
{ |
3140 |
1 |
AlignmentPanel[] aps = getAlignmentPanels( |
3141 |
|
viewport.getSequenceSetId()); |
3142 |
1 |
for (int panel = 0; aps != null && panel < aps.length; panel++) |
3143 |
|
{ |
3144 |
1 |
if (aps[panel] != null && aps[panel].av == viewport) |
3145 |
|
{ |
3146 |
1 |
return aps[panel].alignFrame; |
3147 |
|
} |
3148 |
|
} |
3149 |
|
} |
3150 |
0 |
return null; |
3151 |
|
} |
3152 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3153 |
0 |
public VamsasApplication getVamsasApplication()... |
3154 |
|
{ |
3155 |
|
|
3156 |
0 |
return null; |
3157 |
|
|
3158 |
|
} |
3159 |
|
|
3160 |
|
|
3161 |
|
|
3162 |
|
|
3163 |
|
private boolean inBatchMode = false; |
3164 |
|
|
3165 |
|
|
3166 |
|
|
3167 |
|
|
3168 |
|
@return |
3169 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3170 |
27 |
public boolean isInBatchMode()... |
3171 |
|
{ |
3172 |
27 |
return inBatchMode; |
3173 |
|
} |
3174 |
|
|
3175 |
|
|
3176 |
|
|
3177 |
|
|
3178 |
|
@param |
3179 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3180 |
145 |
public void setInBatchMode(boolean inBatchMode)... |
3181 |
|
{ |
3182 |
145 |
this.inBatchMode = inBatchMode; |
3183 |
|
} |
3184 |
|
|
3185 |
|
|
3186 |
|
|
3187 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3188 |
65 |
public void startServiceDiscovery()... |
3189 |
|
{ |
3190 |
65 |
startServiceDiscovery(false); |
3191 |
|
} |
3192 |
|
|
3193 |
|
|
3194 |
|
|
3195 |
|
|
3196 |
|
@param |
3197 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3198 |
65 |
public void startServiceDiscovery(boolean blocking)... |
3199 |
|
{ |
3200 |
65 |
startServiceDiscovery(blocking, false); |
3201 |
|
} |
3202 |
|
|
3203 |
|
|
3204 |
|
|
3205 |
|
|
3206 |
|
@param |
3207 |
|
|
3208 |
|
@param |
3209 |
|
|
3210 |
|
|
3211 |
|
|
|
|
| 65.2% |
Uncovered Elements: 8 (23) |
Complexity: 7 |
Complexity Density: 0.47 |
|
3212 |
65 |
public void startServiceDiscovery(boolean blocking,... |
3213 |
|
boolean ignore_SHOW_JWS2_SERVICES_preference) |
3214 |
|
{ |
3215 |
65 |
boolean alive = true; |
3216 |
65 |
Thread t0 = null, t1 = null, t2 = null; |
3217 |
|
|
3218 |
65 |
if (true) |
3219 |
|
{ |
3220 |
|
|
3221 |
65 |
if (discoverer == null) |
3222 |
|
{ |
3223 |
6 |
discoverer = new jalview.ws.jws1.Discoverer(); |
3224 |
|
|
3225 |
6 |
discoverer.addPropertyChangeListener(changeSupport); |
3226 |
|
} |
3227 |
|
|
3228 |
|
|
3229 |
65 |
(t0 = new Thread(discoverer)).start(); |
3230 |
|
} |
3231 |
|
|
3232 |
65 |
if (ignore_SHOW_JWS2_SERVICES_preference |
3233 |
|
|| Cache.getDefault("SHOW_JWS2_SERVICES", true)) |
3234 |
|
{ |
3235 |
65 |
t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() |
3236 |
|
.startDiscoverer(changeSupport); |
3237 |
|
} |
3238 |
65 |
Thread t3 = null; |
3239 |
|
{ |
3240 |
|
|
3241 |
|
} |
3242 |
65 |
if (blocking) |
3243 |
|
{ |
3244 |
0 |
while (alive) |
3245 |
|
{ |
3246 |
0 |
try |
3247 |
|
{ |
3248 |
0 |
Thread.sleep(15); |
3249 |
|
} catch (Exception e) |
3250 |
|
{ |
3251 |
|
} |
3252 |
0 |
alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) |
3253 |
|
|| (t3 != null && t3.isAlive()) |
3254 |
|
|| (t0 != null && t0.isAlive()); |
3255 |
|
} |
3256 |
|
} |
3257 |
|
} |
3258 |
|
|
3259 |
|
|
3260 |
|
|
3261 |
|
|
3262 |
|
@param |
3263 |
|
|
|
|
| 33.3% |
Uncovered Elements: 10 (15) |
Complexity: 6 |
Complexity Density: 0.86 |
|
3264 |
1341 |
protected void JalviewServicesChanged(PropertyChangeEvent evt)... |
3265 |
|
{ |
3266 |
1341 |
if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) |
3267 |
|
{ |
3268 |
1341 |
final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() |
3269 |
|
.getErrorMessages(); |
3270 |
1341 |
if (ermsg != null) |
3271 |
|
{ |
3272 |
0 |
if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) |
3273 |
|
{ |
3274 |
0 |
if (serviceChangedDialog == null) |
3275 |
|
{ |
3276 |
|
|
3277 |
0 |
addDialogThread(serviceChangedDialog = new Runnable() |
3278 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
3279 |
0 |
@Override... |
3280 |
|
public void run() |
3281 |
|
{ |
3282 |
|
|
3283 |
|
|
3284 |
|
|
3285 |
|
|
3286 |
|
|
3287 |
|
|
3288 |
|
|
3289 |
|
|
3290 |
|
|
3291 |
|
|
3292 |
|
|
3293 |
|
|
3294 |
|
|
3295 |
|
|
3296 |
|
|
3297 |
|
|
3298 |
|
|
3299 |
|
|
3300 |
|
|
3301 |
|
|
3302 |
0 |
JvOptionPane.showConfirmDialog(Desktop.desktop, |
3303 |
|
new JLabel("<html><table width=\"450\"><tr><td>" |
3304 |
|
+ ermsg + "</td></tr></table>" |
3305 |
|
+ "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences," |
3306 |
|
+ "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>" |
3307 |
|
+ "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the" |
3308 |
|
+ " Tools->Preferences dialog box to change them.</p></html>"), |
3309 |
|
"Web Service Configuration Problem", |
3310 |
|
JvOptionPane.DEFAULT_OPTION, |
3311 |
|
JvOptionPane.ERROR_MESSAGE); |
3312 |
0 |
serviceChangedDialog = null; |
3313 |
|
|
3314 |
|
} |
3315 |
|
}); |
3316 |
|
} |
3317 |
|
} |
3318 |
|
else |
3319 |
|
{ |
3320 |
0 |
jalview.bin.Console.error( |
3321 |
|
"Errors reported by JABA discovery service. Check web services preferences.\n" |
3322 |
|
+ ermsg); |
3323 |
|
} |
3324 |
|
} |
3325 |
|
} |
3326 |
|
} |
3327 |
|
|
3328 |
|
private Runnable serviceChangedDialog = null; |
3329 |
|
|
3330 |
|
|
3331 |
|
|
3332 |
|
|
3333 |
|
|
3334 |
|
|
3335 |
|
@param |
3336 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
3337 |
0 |
public static void showUrl(final String url)... |
3338 |
|
{ |
3339 |
0 |
if (url != null && !url.trim().equals("")) |
3340 |
|
{ |
3341 |
0 |
jalview.bin.Console.info("Opening URL: " + url); |
3342 |
0 |
showUrl(url, Desktop.instance); |
3343 |
|
} |
3344 |
|
else |
3345 |
|
{ |
3346 |
0 |
jalview.bin.Console.warn("Ignoring attempt to show an empty URL."); |
3347 |
|
} |
3348 |
|
|
3349 |
|
} |
3350 |
|
|
3351 |
|
|
3352 |
|
|
3353 |
|
|
3354 |
|
@param |
3355 |
|
@param |
3356 |
|
|
3357 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3358 |
0 |
public static void showUrl(final String url,... |
3359 |
|
final IProgressIndicator progress) |
3360 |
|
{ |
3361 |
0 |
new Thread(new Runnable() |
3362 |
|
{ |
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 4 |
Complexity Density: 0.5 |
|
3363 |
0 |
@Override... |
3364 |
|
public void run() |
3365 |
|
{ |
3366 |
0 |
try |
3367 |
|
{ |
3368 |
0 |
if (progress != null) |
3369 |
|
{ |
3370 |
0 |
progress.setProgressBar(MessageManager |
3371 |
|
.formatMessage("status.opening_params", new Object[] |
3372 |
|
{ url }), this.hashCode()); |
3373 |
|
} |
3374 |
0 |
jalview.util.BrowserLauncher.openURL(url); |
3375 |
|
} catch (Exception ex) |
3376 |
|
{ |
3377 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
3378 |
|
MessageManager |
3379 |
|
.getString("label.web_browser_not_found_unix"), |
3380 |
|
MessageManager.getString("label.web_browser_not_found"), |
3381 |
|
JvOptionPane.WARNING_MESSAGE); |
3382 |
|
|
3383 |
0 |
ex.printStackTrace(); |
3384 |
|
} |
3385 |
0 |
if (progress != null) |
3386 |
|
{ |
3387 |
0 |
progress.setProgressBar(null, this.hashCode()); |
3388 |
|
} |
3389 |
|
} |
3390 |
|
}).start(); |
3391 |
|
} |
3392 |
|
|
3393 |
|
public static WsParamSetManager wsparamManager = null; |
3394 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
3395 |
259 |
public static ParamManager getUserParameterStore()... |
3396 |
|
{ |
3397 |
259 |
if (wsparamManager == null) |
3398 |
|
{ |
3399 |
6 |
wsparamManager = new WsParamSetManager(); |
3400 |
|
} |
3401 |
259 |
return wsparamManager; |
3402 |
|
} |
3403 |
|
|
3404 |
|
|
3405 |
|
|
3406 |
|
|
3407 |
|
@param |
3408 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 4 |
Complexity Density: 0.57 |
|
3409 |
0 |
public static void hyperlinkUpdate(HyperlinkEvent e)... |
3410 |
|
{ |
3411 |
0 |
if (e.getEventType() == EventType.ACTIVATED) |
3412 |
|
{ |
3413 |
0 |
String url = null; |
3414 |
0 |
try |
3415 |
|
{ |
3416 |
0 |
url = e.getURL().toString(); |
3417 |
0 |
Desktop.showUrl(url); |
3418 |
|
} catch (Exception x) |
3419 |
|
{ |
3420 |
0 |
if (url != null) |
3421 |
|
{ |
3422 |
0 |
jalview.bin.Console |
3423 |
|
.error("Couldn't handle string " + url + " as a URL."); |
3424 |
|
} |
3425 |
|
|
3426 |
|
} |
3427 |
|
|
3428 |
|
} |
3429 |
|
} |
3430 |
|
|
3431 |
|
|
3432 |
|
|
3433 |
|
|
3434 |
|
ExecutorService dialogExecutor = Executors.newFixedThreadPool(3); |
3435 |
|
|
3436 |
|
|
3437 |
|
|
3438 |
|
|
3439 |
|
private volatile boolean dialogPause = true; |
3440 |
|
|
3441 |
|
|
3442 |
|
|
3443 |
|
|
3444 |
|
private Semaphore block = new Semaphore(0); |
3445 |
|
|
3446 |
|
private static groovy.console.ui.Console groovyConsole; |
3447 |
|
|
3448 |
|
|
3449 |
|
|
3450 |
|
|
3451 |
|
@param |
3452 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3453 |
144 |
public void addDialogThread(final Runnable prompter)... |
3454 |
|
{ |
3455 |
144 |
dialogExecutor.submit(new Runnable() |
3456 |
|
{ |
|
|
| 81.8% |
Uncovered Elements: 2 (11) |
Complexity: 4 |
Complexity Density: 0.57 |
|
3457 |
144 |
@Override... |
3458 |
|
public void run() |
3459 |
|
{ |
3460 |
144 |
if (dialogPause) |
3461 |
|
{ |
3462 |
51 |
acquireDialogQueue(); |
3463 |
|
} |
3464 |
134 |
if (instance == null) |
3465 |
|
{ |
3466 |
0 |
return; |
3467 |
|
} |
3468 |
134 |
try |
3469 |
|
{ |
3470 |
134 |
SwingUtilities.invokeAndWait(prompter); |
3471 |
|
} catch (Exception q) |
3472 |
|
{ |
3473 |
14 |
jalview.bin.Console.warn("Unexpected Exception in dialog thread.", |
3474 |
|
q); |
3475 |
|
} |
3476 |
|
} |
3477 |
|
}); |
3478 |
|
} |
3479 |
|
|
3480 |
|
private boolean dialogQueueStarted = false; |
3481 |
|
|
|
|
| 66.7% |
Uncovered Elements: 2 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
3482 |
75 |
public void startDialogQueue()... |
3483 |
|
{ |
3484 |
75 |
if (dialogQueueStarted) |
3485 |
|
{ |
3486 |
0 |
return; |
3487 |
|
} |
3488 |
|
|
3489 |
|
|
3490 |
75 |
releaseDialogQueue(); |
3491 |
75 |
dialogQueueStarted = true; |
3492 |
|
} |
3493 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
3494 |
176 |
public void acquireDialogQueue()... |
3495 |
|
{ |
3496 |
176 |
try |
3497 |
|
{ |
3498 |
176 |
block.acquire(); |
3499 |
134 |
dialogPause = true; |
3500 |
|
} catch (InterruptedException e) |
3501 |
|
{ |
3502 |
32 |
jalview.bin.Console.debug("Interruption when acquiring DialogueQueue", |
3503 |
|
e); |
3504 |
|
} |
3505 |
|
} |
3506 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
3507 |
199 |
public void releaseDialogQueue()... |
3508 |
|
{ |
3509 |
199 |
if (!dialogPause) |
3510 |
|
{ |
3511 |
30 |
return; |
3512 |
|
} |
3513 |
169 |
block.release(); |
3514 |
169 |
dialogPause = false; |
3515 |
|
} |
3516 |
|
|
3517 |
|
|
3518 |
|
|
3519 |
|
|
3520 |
|
|
3521 |
|
|
3522 |
|
|
3523 |
|
|
3524 |
|
|
3525 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.2 |
|
3526 |
0 |
@Override... |
3527 |
|
protected void snapShotWindow_actionPerformed(ActionEvent e) |
3528 |
|
{ |
3529 |
|
|
3530 |
0 |
invalidate(); |
3531 |
|
|
3532 |
0 |
int width = getWidth(); |
3533 |
0 |
int height = getHeight(); |
3534 |
0 |
File of = new File( |
3535 |
|
"Jalview_snapshot_" + System.currentTimeMillis() + ".eps"); |
3536 |
0 |
ImageWriterI writer = new ImageWriterI() |
3537 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
3538 |
0 |
@Override... |
3539 |
|
public void exportImage(Graphics g) throws Exception |
3540 |
|
{ |
3541 |
0 |
paintAll(g); |
3542 |
0 |
jalview.bin.Console.info("Successfully written snapshot to file " |
3543 |
|
+ of.getAbsolutePath()); |
3544 |
|
} |
3545 |
|
}; |
3546 |
0 |
String title = "View of desktop"; |
3547 |
0 |
ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, |
3548 |
|
title); |
3549 |
0 |
try |
3550 |
|
{ |
3551 |
0 |
exporter.doExport(of, this, width, height, title); |
3552 |
|
} catch (ImageOutputException ioex) |
3553 |
|
{ |
3554 |
0 |
jalview.bin.Console.error( |
3555 |
|
"Unexpected error whilst writing Jalview desktop snapshot as EPS", |
3556 |
|
ioex); |
3557 |
|
} |
3558 |
|
} |
3559 |
|
|
3560 |
|
|
3561 |
|
|
3562 |
|
|
3563 |
|
|
3564 |
|
|
3565 |
|
|
3566 |
|
|
3567 |
|
@param |
3568 |
|
|
|
|
| 0% |
Uncovered Elements: 41 (41) |
Complexity: 6 |
Complexity Density: 0.19 |
|
3569 |
0 |
public void explodeViews(SplitFrame sf)... |
3570 |
|
{ |
3571 |
0 |
AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame(); |
3572 |
0 |
AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame(); |
3573 |
0 |
List<? extends AlignmentViewPanel> topPanels = oldTopFrame |
3574 |
|
.getAlignPanels(); |
3575 |
0 |
List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame |
3576 |
|
.getAlignPanels(); |
3577 |
0 |
int viewCount = topPanels.size(); |
3578 |
0 |
if (viewCount < 2) |
3579 |
|
{ |
3580 |
0 |
return; |
3581 |
|
} |
3582 |
|
|
3583 |
|
|
3584 |
|
|
3585 |
|
|
3586 |
|
|
3587 |
0 |
for (int i = viewCount - 1; i >= 0; i--) |
3588 |
|
{ |
3589 |
|
|
3590 |
|
|
3591 |
|
|
3592 |
|
|
3593 |
|
|
3594 |
|
|
3595 |
|
|
3596 |
|
|
3597 |
0 |
AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i); |
3598 |
0 |
AlignFrame newTopFrame = new AlignFrame(topPanel); |
3599 |
0 |
newTopFrame.setSize(oldTopFrame.getSize()); |
3600 |
0 |
newTopFrame.setVisible(true); |
3601 |
0 |
Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()) |
3602 |
|
.getExplodedGeometry(); |
3603 |
0 |
if (geometry != null) |
3604 |
|
{ |
3605 |
0 |
newTopFrame.setSize(geometry.getSize()); |
3606 |
|
} |
3607 |
|
|
3608 |
0 |
AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i); |
3609 |
0 |
AlignFrame newBottomFrame = new AlignFrame(bottomPanel); |
3610 |
0 |
newBottomFrame.setSize(oldBottomFrame.getSize()); |
3611 |
0 |
newBottomFrame.setVisible(true); |
3612 |
0 |
geometry = ((AlignViewport) bottomPanel.getAlignViewport()) |
3613 |
|
.getExplodedGeometry(); |
3614 |
0 |
if (geometry != null) |
3615 |
|
{ |
3616 |
0 |
newBottomFrame.setSize(geometry.getSize()); |
3617 |
|
} |
3618 |
|
|
3619 |
0 |
topPanel.av.setGatherViewsHere(false); |
3620 |
0 |
bottomPanel.av.setGatherViewsHere(false); |
3621 |
0 |
JInternalFrame splitFrame = new SplitFrame(newTopFrame, |
3622 |
|
newBottomFrame); |
3623 |
0 |
if (geometry != null) |
3624 |
|
{ |
3625 |
0 |
splitFrame.setLocation(geometry.getLocation()); |
3626 |
|
} |
3627 |
0 |
Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1); |
3628 |
|
} |
3629 |
|
|
3630 |
|
|
3631 |
|
|
3632 |
|
|
3633 |
|
|
3634 |
0 |
topPanels.clear(); |
3635 |
0 |
bottomPanels.clear(); |
3636 |
0 |
sf.close(); |
3637 |
|
} |
3638 |
|
|
3639 |
|
|
3640 |
|
|
3641 |
|
|
3642 |
|
|
3643 |
|
|
3644 |
|
@param |
3645 |
|
|
|
|
| 0% |
Uncovered Elements: 39 (39) |
Complexity: 7 |
Complexity Density: 0.23 |
|
3646 |
0 |
public void gatherViews(GSplitFrame source)... |
3647 |
|
{ |
3648 |
|
|
3649 |
|
|
3650 |
|
|
3651 |
|
|
3652 |
|
|
3653 |
0 |
AlignFrame myTopFrame = (AlignFrame) source.getTopFrame(); |
3654 |
0 |
AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame(); |
3655 |
0 |
myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(), |
3656 |
|
source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight())); |
3657 |
0 |
myBottomFrame.viewport |
3658 |
|
.setExplodedGeometry(new Rectangle(source.getX(), source.getY(), |
3659 |
|
myBottomFrame.getWidth(), myBottomFrame.getHeight())); |
3660 |
0 |
myTopFrame.viewport.setGatherViewsHere(true); |
3661 |
0 |
myBottomFrame.viewport.setGatherViewsHere(true); |
3662 |
0 |
String topViewId = myTopFrame.viewport.getSequenceSetId(); |
3663 |
0 |
String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); |
3664 |
|
|
3665 |
0 |
JInternalFrame[] frames = desktop.getAllFrames(); |
3666 |
0 |
for (JInternalFrame frame : frames) |
3667 |
|
{ |
3668 |
0 |
if (frame instanceof SplitFrame && frame != source) |
3669 |
|
{ |
3670 |
0 |
SplitFrame sf = (SplitFrame) frame; |
3671 |
0 |
AlignFrame topFrame = (AlignFrame) sf.getTopFrame(); |
3672 |
0 |
AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame(); |
3673 |
0 |
boolean gatherThis = false; |
3674 |
0 |
for (int a = 0; a < topFrame.alignPanels.size(); a++) |
3675 |
|
{ |
3676 |
0 |
AlignmentPanel topPanel = topFrame.alignPanels.get(a); |
3677 |
0 |
AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a); |
3678 |
0 |
if (topViewId.equals(topPanel.av.getSequenceSetId()) |
3679 |
|
&& bottomViewId.equals(bottomPanel.av.getSequenceSetId())) |
3680 |
|
{ |
3681 |
0 |
gatherThis = true; |
3682 |
0 |
topPanel.av.setGatherViewsHere(false); |
3683 |
0 |
bottomPanel.av.setGatherViewsHere(false); |
3684 |
0 |
topPanel.av.setExplodedGeometry( |
3685 |
|
new Rectangle(sf.getLocation(), topFrame.getSize())); |
3686 |
0 |
bottomPanel.av.setExplodedGeometry( |
3687 |
|
new Rectangle(sf.getLocation(), bottomFrame.getSize())); |
3688 |
0 |
myTopFrame.addAlignmentPanel(topPanel, false); |
3689 |
0 |
myBottomFrame.addAlignmentPanel(bottomPanel, false); |
3690 |
|
} |
3691 |
|
} |
3692 |
|
|
3693 |
0 |
if (gatherThis) |
3694 |
|
{ |
3695 |
0 |
topFrame.getAlignPanels().clear(); |
3696 |
0 |
bottomFrame.getAlignPanels().clear(); |
3697 |
0 |
sf.close(); |
3698 |
|
} |
3699 |
|
} |
3700 |
|
} |
3701 |
|
|
3702 |
|
|
3703 |
|
|
3704 |
|
|
3705 |
0 |
myTopFrame.setDisplayedView(myTopFrame.alignPanel); |
3706 |
|
} |
3707 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3708 |
671 |
public static groovy.console.ui.Console getGroovyConsole()... |
3709 |
|
{ |
3710 |
671 |
return groovyConsole; |
3711 |
|
} |
3712 |
|
|
3713 |
|
|
3714 |
|
|
3715 |
|
|
3716 |
|
|
3717 |
|
|
3718 |
|
@param |
3719 |
|
|
3720 |
|
@param |
3721 |
|
|
3722 |
|
@param |
3723 |
|
|
3724 |
|
@param |
3725 |
|
|
3726 |
|
@throws |
3727 |
|
|
|
|
| 0% |
Uncovered Elements: 115 (115) |
Complexity: 31 |
Complexity Density: 0.42 |
|
3728 |
0 |
public static void transferFromDropTarget(List<Object> files,... |
3729 |
|
List<DataSourceType> protocols, DropTargetDropEvent evt, |
3730 |
|
Transferable t) throws Exception |
3731 |
|
{ |
3732 |
|
|
3733 |
0 |
DataFlavor uriListFlavor = new DataFlavor( |
3734 |
|
"text/uri-list;class=java.lang.String"), urlFlavour = null; |
3735 |
0 |
try |
3736 |
|
{ |
3737 |
0 |
urlFlavour = new DataFlavor( |
3738 |
|
"application/x-java-url; class=java.net.URL"); |
3739 |
|
} catch (ClassNotFoundException cfe) |
3740 |
|
{ |
3741 |
0 |
jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.", |
3742 |
|
cfe); |
3743 |
|
} |
3744 |
|
|
3745 |
0 |
if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) |
3746 |
|
{ |
3747 |
|
|
3748 |
0 |
try |
3749 |
|
{ |
3750 |
0 |
java.net.URL url = (URL) t.getTransferData(urlFlavour); |
3751 |
|
|
3752 |
|
|
3753 |
0 |
if (url != null) |
3754 |
|
{ |
3755 |
0 |
protocols.add(DataSourceType.URL); |
3756 |
0 |
files.add(url.toString()); |
3757 |
0 |
jalview.bin.Console.debug("Drop handled as URL dataflavor " |
3758 |
|
+ files.get(files.size() - 1)); |
3759 |
0 |
return; |
3760 |
|
} |
3761 |
|
else |
3762 |
|
{ |
3763 |
0 |
if (Platform.isAMacAndNotJS()) |
3764 |
|
{ |
3765 |
0 |
jalview.bin.Console.errPrintln( |
3766 |
|
"Please ignore plist error - occurs due to problem with java 8 on OSX"); |
3767 |
|
} |
3768 |
|
} |
3769 |
|
} catch (Throwable ex) |
3770 |
|
{ |
3771 |
0 |
jalview.bin.Console.debug("URL drop handler failed.", ex); |
3772 |
|
} |
3773 |
|
} |
3774 |
0 |
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) |
3775 |
|
{ |
3776 |
|
|
3777 |
0 |
jalview.bin.Console.debug("Drop handled as javaFileListFlavor"); |
3778 |
0 |
for (Object file : (List) t |
3779 |
|
.getTransferData(DataFlavor.javaFileListFlavor)) |
3780 |
|
{ |
3781 |
0 |
files.add(file); |
3782 |
0 |
protocols.add(DataSourceType.FILE); |
3783 |
|
} |
3784 |
|
} |
3785 |
|
else |
3786 |
|
{ |
3787 |
|
|
3788 |
0 |
boolean added = false; |
3789 |
0 |
String data = null; |
3790 |
0 |
if (t.isDataFlavorSupported(uriListFlavor)) |
3791 |
|
{ |
3792 |
0 |
jalview.bin.Console.debug("Drop handled as uriListFlavor"); |
3793 |
|
|
3794 |
0 |
data = (String) t.getTransferData(uriListFlavor); |
3795 |
|
} |
3796 |
0 |
if (data == null) |
3797 |
|
{ |
3798 |
|
|
3799 |
0 |
jalview.bin.Console |
3800 |
|
.debug("standard URIListFlavor failed. Trying text"); |
3801 |
|
|
3802 |
0 |
DataFlavor textDf = new DataFlavor( |
3803 |
|
"text/plain;class=java.lang.String"); |
3804 |
0 |
if (t.isDataFlavorSupported(textDf)) |
3805 |
|
{ |
3806 |
0 |
data = (String) t.getTransferData(textDf); |
3807 |
|
} |
3808 |
|
|
3809 |
0 |
jalview.bin.Console.debug("Plain text drop content returned " |
3810 |
0 |
+ (data == null ? "Null - failed" : data)); |
3811 |
|
|
3812 |
|
} |
3813 |
0 |
if (data != null) |
3814 |
|
{ |
3815 |
0 |
while (protocols.size() < files.size()) |
3816 |
|
{ |
3817 |
0 |
jalview.bin.Console.debug("Adding missing FILE protocol for " |
3818 |
|
+ files.get(protocols.size())); |
3819 |
0 |
protocols.add(DataSourceType.FILE); |
3820 |
|
} |
3821 |
0 |
for (java.util.StringTokenizer st = new java.util.StringTokenizer( |
3822 |
0 |
data, "\r\n"); st.hasMoreTokens();) |
3823 |
|
{ |
3824 |
0 |
added = true; |
3825 |
0 |
String s = st.nextToken(); |
3826 |
0 |
if (s.startsWith("#")) |
3827 |
|
{ |
3828 |
|
|
3829 |
0 |
continue; |
3830 |
|
} |
3831 |
0 |
java.net.URI uri = new java.net.URI(s); |
3832 |
0 |
if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http")) |
3833 |
|
{ |
3834 |
0 |
protocols.add(DataSourceType.URL); |
3835 |
0 |
files.add(uri.toString()); |
3836 |
|
} |
3837 |
|
else |
3838 |
|
{ |
3839 |
|
|
3840 |
0 |
java.io.File file = new java.io.File(uri); |
3841 |
0 |
protocols.add(DataSourceType.FILE); |
3842 |
0 |
files.add(file.toString()); |
3843 |
|
} |
3844 |
|
} |
3845 |
|
} |
3846 |
|
|
3847 |
0 |
if (jalview.bin.Console.isDebugEnabled()) |
3848 |
|
{ |
3849 |
0 |
if (data == null || !added) |
3850 |
|
{ |
3851 |
|
|
3852 |
0 |
if (t.getTransferDataFlavors() != null |
3853 |
|
&& t.getTransferDataFlavors().length > 0) |
3854 |
|
{ |
3855 |
0 |
jalview.bin.Console.debug( |
3856 |
|
"Couldn't resolve drop data. Here are the supported flavors:"); |
3857 |
0 |
for (DataFlavor fl : t.getTransferDataFlavors()) |
3858 |
|
{ |
3859 |
0 |
jalview.bin.Console.debug( |
3860 |
|
"Supported transfer dataflavor: " + fl.toString()); |
3861 |
0 |
Object df = t.getTransferData(fl); |
3862 |
0 |
if (df != null) |
3863 |
|
{ |
3864 |
0 |
jalview.bin.Console.debug("Retrieves: " + df); |
3865 |
|
} |
3866 |
|
else |
3867 |
|
{ |
3868 |
0 |
jalview.bin.Console.debug("Retrieved nothing"); |
3869 |
|
} |
3870 |
|
} |
3871 |
|
} |
3872 |
|
else |
3873 |
|
{ |
3874 |
0 |
jalview.bin.Console |
3875 |
|
.debug("Couldn't resolve dataflavor for drop: " |
3876 |
|
+ t.toString()); |
3877 |
|
} |
3878 |
|
} |
3879 |
|
} |
3880 |
|
} |
3881 |
0 |
if (Platform.isWindowsAndNotJS()) |
3882 |
|
{ |
3883 |
0 |
jalview.bin.Console |
3884 |
|
.debug("Scanning dropped content for Windows Link Files"); |
3885 |
|
|
3886 |
|
|
3887 |
0 |
for (int f = 0; f < files.size(); f++) |
3888 |
|
{ |
3889 |
0 |
String source = files.get(f).toString().toLowerCase(Locale.ROOT); |
3890 |
0 |
if (protocols.get(f).equals(DataSourceType.FILE) |
3891 |
|
&& (source.endsWith(".lnk") || source.endsWith(".url") |
3892 |
|
|| source.endsWith(".site"))) |
3893 |
|
{ |
3894 |
0 |
try |
3895 |
|
{ |
3896 |
0 |
Object obj = files.get(f); |
3897 |
0 |
File lf = (obj instanceof File ? (File) obj |
3898 |
|
: new File((String) obj)); |
3899 |
|
|
3900 |
0 |
jalview.bin.Console.debug("Found potential link file: " + lf); |
3901 |
0 |
WindowsShortcut wscfile = new WindowsShortcut(lf); |
3902 |
0 |
String fullname = wscfile.getRealFilename(); |
3903 |
0 |
protocols.set(f, FormatAdapter.checkProtocol(fullname)); |
3904 |
0 |
files.set(f, fullname); |
3905 |
0 |
jalview.bin.Console.debug("Parsed real filename " + fullname |
3906 |
|
+ " to extract protocol: " + protocols.get(f)); |
3907 |
|
} catch (Exception ex) |
3908 |
|
{ |
3909 |
0 |
jalview.bin.Console.error( |
3910 |
|
"Couldn't parse " + files.get(f) + " as a link file.", |
3911 |
|
ex); |
3912 |
|
} |
3913 |
|
} |
3914 |
|
} |
3915 |
|
} |
3916 |
|
} |
3917 |
|
|
3918 |
|
|
3919 |
|
|
3920 |
|
|
3921 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
3922 |
0 |
@Override... |
3923 |
|
protected void showExperimental_actionPerformed(boolean selected) |
3924 |
|
{ |
3925 |
0 |
Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected)); |
3926 |
|
} |
3927 |
|
|
3928 |
|
|
3929 |
|
|
3930 |
|
|
3931 |
|
|
3932 |
|
|
3933 |
|
|
3934 |
|
@param |
3935 |
|
|
3936 |
|
@param |
3937 |
|
|
3938 |
|
@return |
3939 |
|
|
|
|
| 85.7% |
Uncovered Elements: 2 (14) |
Complexity: 6 |
Complexity Density: 0.75 |
|
3940 |
19 |
public List<StructureViewerBase> getStructureViewers(... |
3941 |
|
AlignmentPanel apanel, |
3942 |
|
Class<? extends StructureViewerBase> structureViewerClass) |
3943 |
|
{ |
3944 |
19 |
List<StructureViewerBase> result = new ArrayList<>(); |
3945 |
19 |
JInternalFrame[] frames = Desktop.instance.getAllFrames(); |
3946 |
|
|
3947 |
19 |
for (JInternalFrame frame : frames) |
3948 |
|
{ |
3949 |
45 |
if (frame instanceof StructureViewerBase) |
3950 |
|
{ |
3951 |
17 |
if (structureViewerClass == null |
3952 |
|
|| structureViewerClass.isInstance(frame)) |
3953 |
|
{ |
3954 |
17 |
if (apanel == null |
3955 |
|
|| ((StructureViewerBase) frame).isLinkedWith(apanel)) |
3956 |
|
{ |
3957 |
17 |
result.add((StructureViewerBase) frame); |
3958 |
|
} |
3959 |
|
} |
3960 |
|
} |
3961 |
|
} |
3962 |
19 |
return result; |
3963 |
|
} |
3964 |
|
|
3965 |
|
public static final String debugScaleMessage = "Desktop graphics transform scale="; |
3966 |
|
|
3967 |
|
private static boolean debugScaleMessageDone = false; |
3968 |
|
|
|
|
| 82.4% |
Uncovered Elements: 3 (17) |
Complexity: 4 |
Complexity Density: 0.31 |
|
3969 |
2904 |
public static void debugScaleMessage(Graphics g)... |
3970 |
|
{ |
3971 |
2904 |
if (debugScaleMessageDone) |
3972 |
|
{ |
3973 |
2894 |
return; |
3974 |
|
} |
3975 |
|
|
3976 |
10 |
try |
3977 |
|
{ |
3978 |
10 |
Graphics2D gg = (Graphics2D) g; |
3979 |
10 |
if (gg != null) |
3980 |
|
{ |
3981 |
10 |
AffineTransform t = gg.getTransform(); |
3982 |
10 |
double scaleX = t.getScaleX(); |
3983 |
10 |
double scaleY = t.getScaleY(); |
3984 |
10 |
jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)"); |
3985 |
10 |
jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)"); |
3986 |
10 |
debugScaleMessageDone = true; |
3987 |
|
} |
3988 |
|
else |
3989 |
|
{ |
3990 |
0 |
jalview.bin.Console.debug("Desktop graphics null"); |
3991 |
|
} |
3992 |
|
} catch (Exception e) |
3993 |
|
{ |
3994 |
0 |
jalview.bin.Console.debug(Cache.getStackTraceString(e)); |
3995 |
|
} |
3996 |
|
} |
3997 |
|
|
3998 |
|
|
3999 |
|
|
4000 |
|
|
4001 |
|
|
4002 |
|
|
|
|
| 77.8% |
Uncovered Elements: 2 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
4003 |
81 |
public static void closeDesktop()... |
4004 |
|
{ |
4005 |
81 |
if (Desktop.instance != null) |
4006 |
|
{ |
4007 |
81 |
Desktop us = Desktop.instance; |
4008 |
81 |
Desktop.instance.quitTheDesktop(false, false); |
4009 |
|
|
4010 |
81 |
if (us != null) |
4011 |
|
{ |
4012 |
81 |
new Thread(new Runnable() |
4013 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
4014 |
81 |
@Override... |
4015 |
|
public void run() |
4016 |
|
{ |
4017 |
81 |
ExecutorService dex = us.dialogExecutor; |
4018 |
81 |
if (dex != null) |
4019 |
|
{ |
4020 |
38 |
dex.shutdownNow(); |
4021 |
38 |
us.dialogExecutor = null; |
4022 |
38 |
us.block.drainPermits(); |
4023 |
|
} |
4024 |
81 |
us.dispose(); |
4025 |
|
} |
4026 |
|
}).start(); |
4027 |
|
} |
4028 |
|
} |
4029 |
|
} |
4030 |
|
|
4031 |
|
|
4032 |
|
|
4033 |
|
|
4034 |
|
|
4035 |
|
@return |
4036 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
4037 |
20 |
public boolean operationsAreInProgress()... |
4038 |
|
{ |
4039 |
20 |
JInternalFrame[] frames = getAllFrames(); |
4040 |
20 |
for (JInternalFrame frame : frames) |
4041 |
|
{ |
4042 |
45 |
if (frame instanceof IProgressIndicator) |
4043 |
|
{ |
4044 |
20 |
if (((IProgressIndicator) frame).operationInProgress()) |
4045 |
|
{ |
4046 |
10 |
return true; |
4047 |
|
} |
4048 |
|
} |
4049 |
|
} |
4050 |
10 |
return operationInProgress(); |
4051 |
|
} |
4052 |
|
|
4053 |
|
|
4054 |
|
|
4055 |
|
|
4056 |
|
|
4057 |
|
|
4058 |
|
private static Map<AlignFrame, JInternalFrame> alignFrameModalMap = new HashMap<>(); |
4059 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4060 |
0 |
protected static void addModal(AlignFrame af, JInternalFrame jif)... |
4061 |
|
{ |
4062 |
0 |
alignFrameModalMap.put(af, jif); |
4063 |
|
} |
4064 |
|
|
|
|
| 25% |
Uncovered Elements: 9 (12) |
Complexity: 4 |
Complexity Density: 0.5 |
|
4065 |
382 |
protected static void closeModal(AlignFrame af)... |
4066 |
|
{ |
4067 |
382 |
if (!alignFrameModalMap.containsKey(af)) |
4068 |
|
{ |
4069 |
382 |
return; |
4070 |
|
} |
4071 |
0 |
JInternalFrame jif = alignFrameModalMap.get(af); |
4072 |
0 |
if (jif != null) |
4073 |
|
{ |
4074 |
0 |
try |
4075 |
|
{ |
4076 |
0 |
jif.setClosed(true); |
4077 |
|
} catch (PropertyVetoException e) |
4078 |
|
{ |
4079 |
0 |
e.printStackTrace(); |
4080 |
|
} |
4081 |
|
} |
4082 |
0 |
alignFrameModalMap.remove(af); |
4083 |
|
} |
4084 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4085 |
0 |
public void nonBlockingDialog(String title, String message, String button,... |
4086 |
|
int type, boolean scrollable, boolean modal) |
4087 |
|
{ |
4088 |
0 |
nonBlockingDialog(title, message, null, button, type, scrollable, false, |
4089 |
|
modal, -1); |
4090 |
|
} |
4091 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4092 |
1 |
public void nonBlockingDialog(String title, String message,... |
4093 |
|
String boxtext, String button, int type, boolean scrollable, |
4094 |
|
boolean html, boolean modal, int timeout) |
4095 |
|
{ |
4096 |
1 |
nonBlockingDialog(32, 2, title, message, boxtext, button, type, |
4097 |
|
scrollable, html, modal, timeout); |
4098 |
|
} |
4099 |
|
|
|
|
| 67.4% |
Uncovered Elements: 15 (46) |
Complexity: 7 |
Complexity Density: 0.21 |
|
4100 |
1 |
public void nonBlockingDialog(int width, int height, String title,... |
4101 |
|
String message, String boxtext, String button, int type, |
4102 |
|
boolean scrollable, boolean html, boolean modal, int timeout) |
4103 |
|
{ |
4104 |
1 |
if (type < 0) |
4105 |
|
{ |
4106 |
0 |
type = JvOptionPane.WARNING_MESSAGE; |
4107 |
|
} |
4108 |
1 |
JLabel jl = new JLabel(message); |
4109 |
|
|
4110 |
1 |
JTextComponent jtc = null; |
4111 |
1 |
if (html) |
4112 |
|
{ |
4113 |
1 |
JTextPane jtp = new JTextPane(); |
4114 |
1 |
jtp.setContentType("text/html"); |
4115 |
1 |
jtp.setEditable(false); |
4116 |
1 |
jtp.setAutoscrolls(true); |
4117 |
1 |
jtp.setText(boxtext); |
4118 |
|
|
4119 |
1 |
jtc = jtp; |
4120 |
|
} |
4121 |
|
else |
4122 |
|
{ |
4123 |
0 |
JTextArea jta = new JTextArea(height, width); |
4124 |
|
|
4125 |
0 |
jta.setEditable(false); |
4126 |
0 |
jta.setWrapStyleWord(true); |
4127 |
0 |
jta.setAutoscrolls(true); |
4128 |
0 |
jta.setText(boxtext); |
4129 |
|
|
4130 |
0 |
jtc = jta; |
4131 |
|
} |
4132 |
|
|
4133 |
1 |
JScrollPane jsp = scrollable |
4134 |
|
? new JScrollPane(jtc, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, |
4135 |
|
JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED) |
4136 |
|
: null; |
4137 |
|
|
4138 |
1 |
JvOptionPane jvp = JvOptionPane.newOptionDialog(this); |
4139 |
|
|
4140 |
1 |
JPanel jp = new JPanel(); |
4141 |
1 |
jp.setLayout(new BoxLayout(jp, BoxLayout.Y_AXIS)); |
4142 |
|
|
4143 |
1 |
if (message != null) |
4144 |
|
{ |
4145 |
1 |
jl.setAlignmentX(Component.LEFT_ALIGNMENT); |
4146 |
1 |
jp.add(jl); |
4147 |
|
} |
4148 |
1 |
if (boxtext != null) |
4149 |
|
{ |
4150 |
1 |
if (scrollable) |
4151 |
|
{ |
4152 |
0 |
jsp.setAlignmentX(Component.LEFT_ALIGNMENT); |
4153 |
0 |
jp.add(jsp); |
4154 |
|
} |
4155 |
|
else |
4156 |
|
{ |
4157 |
1 |
jtc.setAlignmentX(Component.LEFT_ALIGNMENT); |
4158 |
1 |
jp.add(jtc); |
4159 |
|
} |
4160 |
|
} |
4161 |
|
|
4162 |
1 |
jvp.setResponseHandler(JOptionPane.YES_OPTION, () -> { |
4163 |
|
}); |
4164 |
1 |
jvp.setTimeout(timeout); |
4165 |
1 |
JButton jb = new JButton(button); |
4166 |
1 |
jvp.showDialogOnTopAsync(this, jp, title, JOptionPane.YES_OPTION, type, |
4167 |
|
null, new Object[] |
4168 |
|
{ button }, button, modal, new JButton[] { jb }, false); |
4169 |
|
} |
4170 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
4171 |
0 |
@Override... |
4172 |
|
public AlignFrame getCurrentAlignFrame() |
4173 |
|
{ |
4174 |
0 |
return Jalview.getInstance().getCurrentAlignFrame(); |
4175 |
|
} |
4176 |
|
} |