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package jalview.jbgui; |
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import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; |
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import jalview.analysis.GeneticCodeI; |
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import jalview.analysis.GeneticCodes; |
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import jalview.api.SplitContainerI; |
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import jalview.bin.Cache; |
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import jalview.gui.JvSwingUtils; |
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import jalview.gui.Preferences; |
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import jalview.io.FileFormats; |
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import jalview.schemes.ResidueColourScheme; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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import java.awt.BorderLayout; |
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import java.awt.Color; |
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import java.awt.GridLayout; |
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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.FocusAdapter; |
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import java.awt.event.FocusEvent; |
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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.util.HashMap; |
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import java.util.Map; |
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import javax.swing.BorderFactory; |
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import javax.swing.ButtonGroup; |
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import javax.swing.JCheckBoxMenuItem; |
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import javax.swing.JInternalFrame; |
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import javax.swing.JLabel; |
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import javax.swing.JMenu; |
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import javax.swing.JMenuBar; |
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import javax.swing.JMenuItem; |
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import javax.swing.JPanel; |
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import javax.swing.JRadioButtonMenuItem; |
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import javax.swing.JTabbedPane; |
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import javax.swing.KeyStroke; |
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import javax.swing.event.ChangeEvent; |
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import javax.swing.event.MenuEvent; |
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import javax.swing.event.MenuListener; |
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@SuppressWarnings("serial") |
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| 59.7% |
Uncovered Elements: 404 (1,002) |
Complexity: 277 |
Complexity Density: 0.39 |
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public class GAlignFrame extends JInternalFrame |
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{ |
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protected JMenuBar alignFrameMenuBar = new JMenuBar(); |
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protected JMenuItem closeMenuItem = new JMenuItem(); |
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public JMenu webService = new JMenu(); |
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public JMenuItem webServiceNoServices; |
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protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem(); |
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protected JMenu sortByAnnotScore = new JMenu(); |
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public JLabel statusBar = new JLabel(); |
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protected JMenu outputTextboxMenu = new JMenu(); |
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protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem(); |
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protected JMenuItem undoMenuItem = new JMenuItem(); |
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protected JMenuItem redoMenuItem = new JMenuItem(); |
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protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); |
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public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); |
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JMenuItem copy = new JMenuItem(); |
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JMenuItem cut = new JMenuItem(); |
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JMenu pasteMenu = new JMenu(); |
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protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem applyToAllGroups; |
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protected JMenu colourMenu = new JMenu(); |
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protected JMenuItem textColour; |
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protected JCheckBoxMenuItem conservationMenuItem; |
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protected JMenuItem modifyConservation; |
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protected JCheckBoxMenuItem abovePIDThreshold; |
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protected JMenuItem modifyPID; |
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protected JRadioButtonMenuItem annotationColour; |
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protected JMenu sortByTreeMenu = new JMenu(); |
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protected JMenu sort = new JMenu(); |
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protected JMenuItem calculateTree = new JMenuItem(); |
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protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); |
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protected JMenu showTranslation = new JMenu(); |
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protected JMenuItem showReverse = new JMenuItem(); |
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protected JMenuItem showReverseComplement = new JMenuItem(); |
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protected JMenu showProducts = new JMenu(); |
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protected JMenuItem runGroovy = new JMenuItem(); |
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protected JMenuItem loadVcf; |
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protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem(); |
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protected JPanel statusPanel = new JPanel(); |
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protected JMenuItem showAllSeqAnnotations = new JMenuItem(); |
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protected JMenuItem hideAllSeqAnnotations = new JMenuItem(); |
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protected JMenuItem showAllAlAnnotations = new JMenuItem(); |
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protected JMenuItem hideAllAlAnnotations = new JMenuItem(); |
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protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem(); |
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protected JTabbedPane tabbedPane = new JTabbedPane(); |
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protected JMenuItem reload = new JMenuItem(); |
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protected JMenu formatMenu = new JMenu(); |
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protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem(); |
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protected JMenuItem gatherViews = new JMenuItem(); |
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protected JMenuItem expandViews = new JMenuItem(); |
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protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem(); |
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protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem(); |
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protected JMenuItem openFeatureSettings; |
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private SequenceAnnotationOrder annotationSortOrder; |
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private boolean showAutoCalculatedAbove = false; |
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private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>(); |
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private SplitContainerI splitFrame; |
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| 90% |
Uncovered Elements: 2 (20) |
Complexity: 3 |
Complexity Density: 0.17 |
|
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public GAlignFrame()... |
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{ |
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try |
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{ |
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setName("jalview-alignment"); |
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jbInit(); |
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setJMenuBar(alignFrameMenuBar); |
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for (String ff : FileFormats.getInstance().getWritableFormats(true)) |
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{ |
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JMenuItem item = new JMenuItem(ff); |
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item.addActionListener(new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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public void actionPerformed(ActionEvent e) |
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{ |
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outputText_actionPerformed(e.getActionCommand()); |
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} |
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}); |
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outputTextboxMenu.add(item); |
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} |
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} catch (Exception e) |
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{ |
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System.err.println(e.toString()); |
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} |
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if (Platform.allowMnemonics()) |
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{ |
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closeMenuItem.setMnemonic('C'); |
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outputTextboxMenu.setMnemonic('T'); |
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undoMenuItem.setMnemonic('Z'); |
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redoMenuItem.setMnemonic('0'); |
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copy.setMnemonic('C'); |
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cut.setMnemonic('U'); |
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pasteMenu.setMnemonic('P'); |
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reload.setMnemonic('R'); |
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} |
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} |
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| 99.1% |
Uncovered Elements: 5 (541) |
Complexity: 7 |
Complexity Density: 0.01 |
|
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private void jbInit() throws Exception... |
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{ |
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initColourMenu(); |
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JMenuItem saveAs = new JMenuItem( |
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MessageManager.getString("action.save_as")); |
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ActionListener al = new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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public void actionPerformed(ActionEvent e) |
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{ |
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saveAs_actionPerformed(); |
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} |
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}; |
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KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, |
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jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() |
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| jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, |
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false); |
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241 |
addMenuActionAndAccelerator(keyStroke, saveAs, al); |
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closeMenuItem.setText(MessageManager.getString("action.close")); |
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keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, |
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jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
287 |
241 |
al = new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public void actionPerformed(ActionEvent e) |
291 |
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{ |
292 |
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closeMenuItem_actionPerformed(false); |
293 |
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} |
294 |
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}; |
295 |
241 |
addMenuActionAndAccelerator(keyStroke, closeMenuItem, al); |
296 |
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JMenu editMenu = new JMenu(MessageManager.getString("action.edit")); |
298 |
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JMenu viewMenu = new JMenu(MessageManager.getString("action.view")); |
299 |
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JMenu annotationsMenu = new JMenu( |
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MessageManager.getString("action.annotations")); |
301 |
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JMenu showMenu = new JMenu(MessageManager.getString("action.show")); |
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colourMenu.setText(MessageManager.getString("action.colour")); |
303 |
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JMenu calculateMenu = new JMenu( |
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MessageManager.getString("action.calculate")); |
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webService.setText(MessageManager.getString("action.web_service")); |
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JMenuItem selectAllSequenceMenuItem = new JMenuItem( |
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MessageManager.getString("action.select_all")); |
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keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, |
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jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
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al = new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public void actionPerformed(ActionEvent e) |
314 |
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{ |
315 |
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selectAllSequenceMenuItem_actionPerformed(e); |
316 |
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} |
317 |
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}; |
318 |
241 |
addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al); |
319 |
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JMenuItem deselectAllSequenceMenuItem = new JMenuItem( |
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MessageManager.getString("action.deselect_all")); |
322 |
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keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false); |
323 |
241 |
al = new ActionListener() |
324 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
325 |
0 |
@Override... |
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public void actionPerformed(ActionEvent e) |
327 |
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{ |
328 |
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deselectAllSequenceMenuItem_actionPerformed(e); |
329 |
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} |
330 |
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}; |
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addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al); |
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241 |
JMenuItem invertSequenceMenuItem = new JMenuItem( |
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MessageManager.getString("action.invert_sequence_selection")); |
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keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, |
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jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
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241 |
al = new ActionListener() |
338 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
339 |
0 |
@Override... |
340 |
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public void actionPerformed(ActionEvent e) |
341 |
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{ |
342 |
0 |
invertSequenceMenuItem_actionPerformed(e); |
343 |
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} |
344 |
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}; |
345 |
241 |
addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al); |
346 |
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347 |
241 |
JMenuItem grpsFromSelection = new JMenuItem( |
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MessageManager.getString("action.make_groups_selection")); |
349 |
241 |
grpsFromSelection.addActionListener(new ActionListener() |
350 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
351 |
0 |
@Override... |
352 |
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public void actionPerformed(ActionEvent e) |
353 |
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{ |
354 |
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makeGrpsFromSelection_actionPerformed(e); |
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} |
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}); |
357 |
241 |
JMenuItem expandAlignment = new JMenuItem( |
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MessageManager.getString("action.view_flanking_regions")); |
359 |
241 |
expandAlignment.setToolTipText( |
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MessageManager.getString("label.view_flanking_regions")); |
361 |
241 |
expandAlignment.addActionListener(new ActionListener() |
362 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
363 |
0 |
@Override... |
364 |
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public void actionPerformed(ActionEvent e) |
365 |
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{ |
366 |
0 |
expand_newalign(e); |
367 |
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} |
368 |
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}); |
369 |
241 |
JMenuItem remove2LeftMenuItem = new JMenuItem( |
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MessageManager.getString("action.remove_left")); |
371 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, |
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jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
373 |
241 |
al = new ActionListener() |
374 |
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{ |
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|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
375 |
0 |
@Override... |
376 |
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public void actionPerformed(ActionEvent e) |
377 |
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{ |
378 |
0 |
remove2LeftMenuItem_actionPerformed(e); |
379 |
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} |
380 |
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}; |
381 |
241 |
addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al); |
382 |
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|
383 |
241 |
JMenuItem remove2RightMenuItem = new JMenuItem( |
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MessageManager.getString("action.remove_right")); |
385 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, |
386 |
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jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
387 |
241 |
al = new ActionListener() |
388 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
389 |
0 |
@Override... |
390 |
|
public void actionPerformed(ActionEvent e) |
391 |
|
{ |
392 |
0 |
remove2RightMenuItem_actionPerformed(e); |
393 |
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} |
394 |
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}; |
395 |
241 |
addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al); |
396 |
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|
397 |
241 |
JMenuItem removeGappedColumnMenuItem = new JMenuItem( |
398 |
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MessageManager.getString("action.remove_empty_columns")); |
399 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, |
400 |
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jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
401 |
241 |
al = new ActionListener() |
402 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
403 |
0 |
@Override... |
404 |
|
public void actionPerformed(ActionEvent e) |
405 |
|
{ |
406 |
0 |
removeGappedColumnMenuItem_actionPerformed(e); |
407 |
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} |
408 |
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}; |
409 |
241 |
addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al); |
410 |
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|
411 |
241 |
JMenuItem removeAllGapsMenuItem = new JMenuItem( |
412 |
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MessageManager.getString("action.remove_all_gaps")); |
413 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, |
414 |
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jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() |
415 |
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| jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, |
416 |
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false); |
417 |
241 |
al = new ActionListener() |
418 |
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{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
419 |
0 |
@Override... |
420 |
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public void actionPerformed(ActionEvent e) |
421 |
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{ |
422 |
0 |
removeAllGapsMenuItem_actionPerformed(e); |
423 |
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} |
424 |
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}; |
425 |
241 |
addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al); |
426 |
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|
427 |
241 |
JMenuItem justifyLeftMenuItem = new JMenuItem( |
428 |
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MessageManager.getString("action.left_justify_alignment")); |
429 |
241 |
justifyLeftMenuItem.addActionListener(new ActionListener() |
430 |
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{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
431 |
0 |
@Override... |
432 |
|
public void actionPerformed(ActionEvent e) |
433 |
|
{ |
434 |
0 |
justifyLeftMenuItem_actionPerformed(e); |
435 |
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} |
436 |
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}); |
437 |
241 |
JMenuItem justifyRightMenuItem = new JMenuItem( |
438 |
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MessageManager.getString("action.right_justify_alignment")); |
439 |
241 |
justifyRightMenuItem.addActionListener(new ActionListener() |
440 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
441 |
0 |
@Override... |
442 |
|
public void actionPerformed(ActionEvent e) |
443 |
|
{ |
444 |
0 |
justifyRightMenuItem_actionPerformed(e); |
445 |
|
} |
446 |
|
}); |
447 |
241 |
viewBoxesMenuItem.setText(MessageManager.getString("action.boxes")); |
448 |
241 |
viewBoxesMenuItem.setState(true); |
449 |
241 |
viewBoxesMenuItem.addActionListener(new ActionListener() |
450 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
451 |
0 |
@Override... |
452 |
|
public void actionPerformed(ActionEvent e) |
453 |
|
{ |
454 |
0 |
viewBoxesMenuItem_actionPerformed(e); |
455 |
|
} |
456 |
|
}); |
457 |
241 |
viewTextMenuItem.setText(MessageManager.getString("action.text")); |
458 |
241 |
viewTextMenuItem.setState(true); |
459 |
241 |
viewTextMenuItem.addActionListener(new ActionListener() |
460 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
461 |
0 |
@Override... |
462 |
|
public void actionPerformed(ActionEvent e) |
463 |
|
{ |
464 |
0 |
viewTextMenuItem_actionPerformed(e); |
465 |
|
} |
466 |
|
}); |
467 |
241 |
showNonconservedMenuItem |
468 |
|
.setText(MessageManager.getString("label.show_non_conserved")); |
469 |
241 |
showNonconservedMenuItem.setState(false); |
470 |
241 |
showNonconservedMenuItem.addActionListener(new ActionListener() |
471 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
472 |
0 |
@Override... |
473 |
|
public void actionPerformed(ActionEvent e) |
474 |
|
{ |
475 |
0 |
showUnconservedMenuItem_actionPerformed(e); |
476 |
|
} |
477 |
|
}); |
478 |
241 |
JMenuItem sortPairwiseMenuItem = new JMenuItem( |
479 |
|
MessageManager.getString("action.by_pairwise_id")); |
480 |
241 |
sortPairwiseMenuItem.addActionListener(new ActionListener() |
481 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
482 |
0 |
@Override... |
483 |
|
public void actionPerformed(ActionEvent e) |
484 |
|
{ |
485 |
0 |
sortPairwiseMenuItem_actionPerformed(e); |
486 |
|
} |
487 |
|
}); |
488 |
241 |
JMenuItem sortIDMenuItem = new JMenuItem( |
489 |
|
MessageManager.getString("action.by_id")); |
490 |
241 |
sortIDMenuItem.addActionListener(new ActionListener() |
491 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
492 |
0 |
@Override... |
493 |
|
public void actionPerformed(ActionEvent e) |
494 |
|
{ |
495 |
0 |
sortIDMenuItem_actionPerformed(e); |
496 |
|
} |
497 |
|
}); |
498 |
241 |
JMenuItem sortLengthMenuItem = new JMenuItem( |
499 |
|
MessageManager.getString("action.by_length")); |
500 |
241 |
sortLengthMenuItem.addActionListener(new ActionListener() |
501 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
502 |
0 |
@Override... |
503 |
|
public void actionPerformed(ActionEvent e) |
504 |
|
{ |
505 |
0 |
sortLengthMenuItem_actionPerformed(e); |
506 |
|
} |
507 |
|
}); |
508 |
241 |
JMenuItem sortGroupMenuItem = new JMenuItem( |
509 |
|
MessageManager.getString("action.by_group")); |
510 |
241 |
sortGroupMenuItem.addActionListener(new ActionListener() |
511 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
512 |
0 |
@Override... |
513 |
|
public void actionPerformed(ActionEvent e) |
514 |
|
{ |
515 |
0 |
sortGroupMenuItem_actionPerformed(e); |
516 |
|
} |
517 |
|
}); |
518 |
|
|
519 |
241 |
JMenuItem removeRedundancyMenuItem = new JMenuItem( |
520 |
|
MessageManager.getString("action.remove_redundancy")); |
521 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, |
522 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
523 |
241 |
al = new ActionListener() |
524 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
525 |
0 |
@Override... |
526 |
|
public void actionPerformed(ActionEvent e) |
527 |
|
{ |
528 |
0 |
removeRedundancyMenuItem_actionPerformed(e); |
529 |
|
} |
530 |
|
}; |
531 |
241 |
addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al); |
532 |
|
|
533 |
241 |
JMenuItem pairwiseAlignmentMenuItem = new JMenuItem( |
534 |
|
MessageManager.getString("action.pairwise_alignment")); |
535 |
241 |
pairwiseAlignmentMenuItem.addActionListener(new ActionListener() |
536 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
537 |
0 |
@Override... |
538 |
|
public void actionPerformed(ActionEvent e) |
539 |
|
{ |
540 |
0 |
pairwiseAlignmentMenuItem_actionPerformed(e); |
541 |
|
} |
542 |
|
}); |
543 |
|
|
544 |
241 |
this.getContentPane().setLayout(new BorderLayout()); |
545 |
241 |
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); |
546 |
241 |
statusBar.setBackground(Color.white); |
547 |
241 |
statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); |
548 |
241 |
statusBar.setBorder(BorderFactory.createLineBorder(Color.black)); |
549 |
241 |
statusBar.setText(MessageManager.getString("label.status_bar")); |
550 |
241 |
outputTextboxMenu |
551 |
|
.setText(MessageManager.getString("label.out_to_textbox")); |
552 |
|
|
553 |
241 |
annotationPanelMenuItem.setActionCommand(""); |
554 |
241 |
annotationPanelMenuItem |
555 |
|
.setText(MessageManager.getString("label.show_annotations")); |
556 |
241 |
annotationPanelMenuItem |
557 |
|
.setState(Cache.getDefault("SHOW_ANNOTATIONS", true)); |
558 |
241 |
annotationPanelMenuItem.addActionListener(new ActionListener() |
559 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
560 |
0 |
@Override... |
561 |
|
public void actionPerformed(ActionEvent e) |
562 |
|
{ |
563 |
0 |
annotationPanelMenuItem_actionPerformed(e); |
564 |
|
} |
565 |
|
}); |
566 |
241 |
showAllAlAnnotations.setText( |
567 |
|
MessageManager.getString("label.show_all_al_annotations")); |
568 |
241 |
final boolean isAnnotationPanelShown = annotationPanelMenuItem |
569 |
|
.getState(); |
570 |
241 |
showAllAlAnnotations.setEnabled(isAnnotationPanelShown); |
571 |
241 |
showAllAlAnnotations.addActionListener(new ActionListener() |
572 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
573 |
0 |
@Override... |
574 |
|
public void actionPerformed(ActionEvent e) |
575 |
|
{ |
576 |
0 |
showAllAnnotations_actionPerformed(false, true); |
577 |
|
} |
578 |
|
}); |
579 |
241 |
hideAllAlAnnotations.setText( |
580 |
|
MessageManager.getString("label.hide_all_al_annotations")); |
581 |
241 |
hideAllAlAnnotations.setEnabled(isAnnotationPanelShown); |
582 |
241 |
hideAllAlAnnotations.addActionListener(new ActionListener() |
583 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
584 |
0 |
@Override... |
585 |
|
public void actionPerformed(ActionEvent e) |
586 |
|
{ |
587 |
0 |
hideAllAnnotations_actionPerformed(false, true); |
588 |
|
} |
589 |
|
}); |
590 |
241 |
showAllSeqAnnotations.setText( |
591 |
|
MessageManager.getString("label.show_all_seq_annotations")); |
592 |
241 |
showAllSeqAnnotations.setEnabled(isAnnotationPanelShown); |
593 |
241 |
showAllSeqAnnotations.addActionListener(new ActionListener() |
594 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
595 |
0 |
@Override... |
596 |
|
public void actionPerformed(ActionEvent e) |
597 |
|
{ |
598 |
0 |
showAllAnnotations_actionPerformed(true, false); |
599 |
|
} |
600 |
|
}); |
601 |
241 |
hideAllSeqAnnotations.setText( |
602 |
|
MessageManager.getString("label.hide_all_seq_annotations")); |
603 |
241 |
hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown); |
604 |
241 |
hideAllSeqAnnotations.addActionListener(new ActionListener() |
605 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
606 |
0 |
@Override... |
607 |
|
public void actionPerformed(ActionEvent e) |
608 |
|
{ |
609 |
0 |
hideAllAnnotations_actionPerformed(true, false); |
610 |
|
} |
611 |
|
}); |
612 |
241 |
SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder |
613 |
|
.valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, |
614 |
|
SequenceAnnotationOrder.NONE.name())); |
615 |
241 |
final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem( |
616 |
|
MessageManager.getString("label.sort_annotations_by_sequence")); |
617 |
241 |
final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem( |
618 |
|
MessageManager.getString("label.sort_annotations_by_label")); |
619 |
|
|
620 |
241 |
sortAnnBySequence.setSelected( |
621 |
|
sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL); |
622 |
241 |
sortAnnBySequence.addActionListener(new ActionListener() |
623 |
|
{ |
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
624 |
0 |
@Override... |
625 |
|
public void actionPerformed(ActionEvent e) |
626 |
|
{ |
627 |
0 |
boolean newState = sortAnnBySequence.getState(); |
628 |
0 |
sortAnnByLabel.setSelected(false); |
629 |
0 |
setAnnotationSortOrder( |
630 |
0 |
newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL |
631 |
|
: SequenceAnnotationOrder.NONE); |
632 |
0 |
sortAnnotations_actionPerformed(); |
633 |
|
} |
634 |
|
}); |
635 |
241 |
sortAnnByLabel.setSelected( |
636 |
|
sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE); |
637 |
241 |
sortAnnByLabel.addActionListener(new ActionListener() |
638 |
|
{ |
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
639 |
0 |
@Override... |
640 |
|
public void actionPerformed(ActionEvent e) |
641 |
|
{ |
642 |
0 |
boolean newState = sortAnnByLabel.getState(); |
643 |
0 |
sortAnnBySequence.setSelected(false); |
644 |
0 |
setAnnotationSortOrder( |
645 |
0 |
newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE |
646 |
|
: SequenceAnnotationOrder.NONE); |
647 |
0 |
sortAnnotations_actionPerformed(); |
648 |
|
} |
649 |
|
}); |
650 |
241 |
colourTextMenuItem = new JCheckBoxMenuItem( |
651 |
|
MessageManager.getString("label.colour_text")); |
652 |
241 |
colourTextMenuItem.addActionListener(new ActionListener() |
653 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
654 |
0 |
@Override... |
655 |
|
public void actionPerformed(ActionEvent e) |
656 |
|
{ |
657 |
0 |
colourTextMenuItem_actionPerformed(e); |
658 |
|
} |
659 |
|
}); |
660 |
|
|
661 |
241 |
JMenuItem htmlMenuItem = new JMenuItem( |
662 |
|
MessageManager.getString("label.html")); |
663 |
241 |
htmlMenuItem.addActionListener(new ActionListener() |
664 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
665 |
0 |
@Override... |
666 |
|
public void actionPerformed(ActionEvent e) |
667 |
|
{ |
668 |
0 |
htmlMenuItem_actionPerformed(e); |
669 |
|
} |
670 |
|
}); |
671 |
|
|
672 |
241 |
JMenuItem createBioJS = new JMenuItem( |
673 |
|
MessageManager.getString("label.biojs_html_export")); |
674 |
241 |
createBioJS.addActionListener(new java.awt.event.ActionListener() |
675 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
676 |
0 |
@Override... |
677 |
|
public void actionPerformed(ActionEvent e) |
678 |
|
{ |
679 |
0 |
bioJSMenuItem_actionPerformed(e); |
680 |
|
} |
681 |
|
}); |
682 |
|
|
683 |
241 |
JMenuItem overviewMenuItem = new JMenuItem( |
684 |
|
MessageManager.getString("label.overview_window")); |
685 |
241 |
overviewMenuItem.addActionListener(new ActionListener() |
686 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
687 |
0 |
@Override... |
688 |
|
public void actionPerformed(ActionEvent e) |
689 |
|
{ |
690 |
0 |
overviewMenuItem_actionPerformed(e); |
691 |
|
} |
692 |
|
}); |
693 |
|
|
694 |
241 |
undoMenuItem.setEnabled(false); |
695 |
241 |
undoMenuItem.setText(MessageManager.getString("action.undo")); |
696 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, |
697 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
698 |
241 |
al = new ActionListener() |
699 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
700 |
0 |
@Override... |
701 |
|
public void actionPerformed(ActionEvent e) |
702 |
|
{ |
703 |
0 |
undoMenuItem_actionPerformed(e); |
704 |
|
} |
705 |
|
}; |
706 |
241 |
addMenuActionAndAccelerator(keyStroke, undoMenuItem, al); |
707 |
|
|
708 |
241 |
redoMenuItem.setEnabled(false); |
709 |
241 |
redoMenuItem.setText(MessageManager.getString("action.redo")); |
710 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, |
711 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
712 |
241 |
al = new ActionListener() |
713 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
714 |
0 |
@Override... |
715 |
|
public void actionPerformed(ActionEvent e) |
716 |
|
{ |
717 |
0 |
redoMenuItem_actionPerformed(e); |
718 |
|
} |
719 |
|
}; |
720 |
241 |
addMenuActionAndAccelerator(keyStroke, redoMenuItem, al); |
721 |
|
|
722 |
241 |
wrapMenuItem.setText(MessageManager.getString("label.wrap")); |
723 |
241 |
wrapMenuItem.addActionListener(new ActionListener() |
724 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
725 |
0 |
@Override... |
726 |
|
public void actionPerformed(ActionEvent e) |
727 |
|
{ |
728 |
0 |
wrapMenuItem_actionPerformed(e); |
729 |
|
} |
730 |
|
}); |
731 |
|
|
732 |
241 |
JMenuItem printMenuItem = new JMenuItem( |
733 |
|
MessageManager.getString("action.print")); |
734 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, |
735 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
736 |
241 |
al = new ActionListener() |
737 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
738 |
0 |
@Override... |
739 |
|
public void actionPerformed(ActionEvent e) |
740 |
|
{ |
741 |
0 |
printMenuItem_actionPerformed(e); |
742 |
|
} |
743 |
|
}; |
744 |
241 |
addMenuActionAndAccelerator(keyStroke, printMenuItem, al); |
745 |
|
|
746 |
241 |
renderGapsMenuItem |
747 |
|
.setText(MessageManager.getString("action.show_gaps")); |
748 |
241 |
renderGapsMenuItem.setState(true); |
749 |
241 |
renderGapsMenuItem.addActionListener(new ActionListener() |
750 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
751 |
0 |
@Override... |
752 |
|
public void actionPerformed(ActionEvent e) |
753 |
|
{ |
754 |
0 |
renderGapsMenuItem_actionPerformed(e); |
755 |
|
} |
756 |
|
}); |
757 |
|
|
758 |
241 |
JMenuItem findMenuItem = new JMenuItem( |
759 |
|
MessageManager.getString("action.find")); |
760 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, |
761 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
762 |
241 |
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true, |
763 |
|
MessageManager.getString("label.find_tip"))); |
764 |
241 |
al = new ActionListener() |
765 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
766 |
0 |
@Override... |
767 |
|
public void actionPerformed(ActionEvent e) |
768 |
|
{ |
769 |
0 |
findMenuItem_actionPerformed(e); |
770 |
|
} |
771 |
|
}; |
772 |
241 |
addMenuActionAndAccelerator(keyStroke, findMenuItem, al); |
773 |
|
|
774 |
241 |
showSeqFeatures.setText( |
775 |
|
MessageManager.getString("label.show_sequence_features")); |
776 |
241 |
showSeqFeatures.addActionListener(new ActionListener() |
777 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
778 |
0 |
@Override... |
779 |
|
public void actionPerformed(ActionEvent actionEvent) |
780 |
|
{ |
781 |
0 |
showSeqFeatures_actionPerformed(actionEvent); |
782 |
|
} |
783 |
|
}); |
784 |
|
|
785 |
|
|
786 |
|
|
787 |
|
|
788 |
|
|
789 |
|
|
790 |
241 |
showDbRefsMenuitem |
791 |
|
.setText(MessageManager.getString("label.show_database_refs")); |
792 |
241 |
showDbRefsMenuitem.addActionListener(new ActionListener() |
793 |
|
{ |
794 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
795 |
0 |
@Override... |
796 |
|
public void actionPerformed(ActionEvent e) |
797 |
|
{ |
798 |
0 |
showDbRefs_actionPerformed(e); |
799 |
|
} |
800 |
|
|
801 |
|
}); |
802 |
241 |
showNpFeatsMenuitem.setText( |
803 |
|
MessageManager.getString("label.show_non_positional_features")); |
804 |
241 |
showNpFeatsMenuitem.addActionListener(new ActionListener() |
805 |
|
{ |
806 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
807 |
0 |
@Override... |
808 |
|
public void actionPerformed(ActionEvent e) |
809 |
|
{ |
810 |
0 |
showNpFeats_actionPerformed(e); |
811 |
|
} |
812 |
|
|
813 |
|
}); |
814 |
241 |
showGroupConservation |
815 |
|
.setText(MessageManager.getString("label.group_conservation")); |
816 |
241 |
showGroupConservation.addActionListener(new ActionListener() |
817 |
|
{ |
818 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
819 |
0 |
@Override... |
820 |
|
public void actionPerformed(ActionEvent e) |
821 |
|
{ |
822 |
0 |
showGroupConservation_actionPerformed(e); |
823 |
|
} |
824 |
|
|
825 |
|
}); |
826 |
|
|
827 |
241 |
showGroupConsensus |
828 |
|
.setText(MessageManager.getString("label.group_consensus")); |
829 |
241 |
showGroupConsensus.addActionListener(new ActionListener() |
830 |
|
{ |
831 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
832 |
0 |
@Override... |
833 |
|
public void actionPerformed(ActionEvent e) |
834 |
|
{ |
835 |
0 |
showGroupConsensus_actionPerformed(e); |
836 |
|
} |
837 |
|
|
838 |
|
}); |
839 |
241 |
showConsensusHistogram.setText( |
840 |
|
MessageManager.getString("label.show_consensus_histogram")); |
841 |
241 |
showConsensusHistogram.addActionListener(new ActionListener() |
842 |
|
{ |
843 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
844 |
0 |
@Override... |
845 |
|
public void actionPerformed(ActionEvent e) |
846 |
|
{ |
847 |
0 |
showConsensusHistogram_actionPerformed(e); |
848 |
|
} |
849 |
|
|
850 |
|
}); |
851 |
241 |
showSequenceLogo |
852 |
|
.setText(MessageManager.getString("label.show_consensus_logo")); |
853 |
241 |
showSequenceLogo.addActionListener(new ActionListener() |
854 |
|
{ |
855 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
856 |
0 |
@Override... |
857 |
|
public void actionPerformed(ActionEvent e) |
858 |
|
{ |
859 |
0 |
showSequenceLogo_actionPerformed(e); |
860 |
|
} |
861 |
|
|
862 |
|
}); |
863 |
241 |
normaliseSequenceLogo |
864 |
|
.setText(MessageManager.getString("label.norm_consensus_logo")); |
865 |
241 |
normaliseSequenceLogo.addActionListener(new ActionListener() |
866 |
|
{ |
867 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
868 |
0 |
@Override... |
869 |
|
public void actionPerformed(ActionEvent e) |
870 |
|
{ |
871 |
0 |
normaliseSequenceLogo_actionPerformed(e); |
872 |
|
} |
873 |
|
|
874 |
|
}); |
875 |
241 |
applyAutoAnnotationSettings |
876 |
|
.setText(MessageManager.getString("label.apply_all_groups")); |
877 |
241 |
applyAutoAnnotationSettings.setState(false); |
878 |
241 |
applyAutoAnnotationSettings.setVisible(true); |
879 |
241 |
applyAutoAnnotationSettings.addActionListener(new ActionListener() |
880 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
881 |
0 |
@Override... |
882 |
|
public void actionPerformed(ActionEvent e) |
883 |
|
{ |
884 |
0 |
applyAutoAnnotationSettings_actionPerformed(e); |
885 |
|
} |
886 |
|
}); |
887 |
|
|
888 |
241 |
ButtonGroup buttonGroup = new ButtonGroup(); |
889 |
241 |
final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem( |
890 |
|
MessageManager.getString("label.show_first")); |
891 |
241 |
final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem( |
892 |
|
MessageManager.getString("label.show_last")); |
893 |
241 |
buttonGroup.add(showAutoFirst); |
894 |
241 |
buttonGroup.add(showAutoLast); |
895 |
241 |
final boolean autoFirst = Cache |
896 |
|
.getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); |
897 |
241 |
showAutoFirst.setSelected(autoFirst); |
898 |
241 |
setShowAutoCalculatedAbove(autoFirst); |
899 |
241 |
showAutoFirst.addActionListener(new ActionListener() |
900 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
901 |
0 |
@Override... |
902 |
|
public void actionPerformed(ActionEvent e) |
903 |
|
{ |
904 |
0 |
setShowAutoCalculatedAbove(showAutoFirst.isSelected()); |
905 |
0 |
sortAnnotations_actionPerformed(); |
906 |
|
} |
907 |
|
}); |
908 |
241 |
showAutoLast.setSelected(!showAutoFirst.isSelected()); |
909 |
241 |
showAutoLast.addActionListener(new ActionListener() |
910 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
911 |
0 |
@Override... |
912 |
|
public void actionPerformed(ActionEvent e) |
913 |
|
{ |
914 |
0 |
setShowAutoCalculatedAbove(!showAutoLast.isSelected()); |
915 |
0 |
sortAnnotations_actionPerformed(); |
916 |
|
} |
917 |
|
}); |
918 |
|
|
919 |
241 |
JMenuItem deleteGroups = new JMenuItem( |
920 |
|
MessageManager.getString("action.undefine_groups")); |
921 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, |
922 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
923 |
241 |
al = new ActionListener() |
924 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
925 |
0 |
@Override... |
926 |
|
public void actionPerformed(ActionEvent e) |
927 |
|
{ |
928 |
0 |
deleteGroups_actionPerformed(e); |
929 |
|
} |
930 |
|
}; |
931 |
241 |
addMenuActionAndAccelerator(keyStroke, deleteGroups, al); |
932 |
|
|
933 |
241 |
JMenuItem annotationColumn = new JMenuItem( |
934 |
|
MessageManager.getString("action.select_by_annotation")); |
935 |
241 |
annotationColumn.addActionListener(new ActionListener() |
936 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
937 |
0 |
@Override... |
938 |
|
public void actionPerformed(ActionEvent e) |
939 |
|
{ |
940 |
0 |
annotationColumn_actionPerformed(e); |
941 |
|
} |
942 |
|
}); |
943 |
|
|
944 |
241 |
JMenuItem createGroup = new JMenuItem( |
945 |
|
MessageManager.getString("action.create_group")); |
946 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, |
947 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
948 |
241 |
al = new ActionListener() |
949 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
950 |
0 |
@Override... |
951 |
|
public void actionPerformed(ActionEvent e) |
952 |
|
{ |
953 |
0 |
createGroup_actionPerformed(e); |
954 |
|
} |
955 |
|
}; |
956 |
241 |
addMenuActionAndAccelerator(keyStroke, createGroup, al); |
957 |
|
|
958 |
241 |
JMenuItem unGroup = new JMenuItem( |
959 |
|
MessageManager.getString("action.remove_group")); |
960 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, |
961 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() |
962 |
|
| jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, |
963 |
|
false); |
964 |
241 |
al = new ActionListener() |
965 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
966 |
0 |
@Override... |
967 |
|
public void actionPerformed(ActionEvent e) |
968 |
|
{ |
969 |
0 |
unGroup_actionPerformed(e); |
970 |
|
} |
971 |
|
}; |
972 |
241 |
addMenuActionAndAccelerator(keyStroke, unGroup, al); |
973 |
|
|
974 |
241 |
copy.setText(MessageManager.getString("action.copy")); |
975 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, |
976 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
977 |
|
|
978 |
241 |
al = new ActionListener() |
979 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
980 |
0 |
@Override... |
981 |
|
public void actionPerformed(ActionEvent e) |
982 |
|
{ |
983 |
0 |
copy_actionPerformed(); |
984 |
|
} |
985 |
|
}; |
986 |
241 |
addMenuActionAndAccelerator(keyStroke, copy, al); |
987 |
|
|
988 |
241 |
cut.setText(MessageManager.getString("action.cut")); |
989 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, |
990 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
991 |
241 |
al = new ActionListener() |
992 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
993 |
0 |
@Override... |
994 |
|
public void actionPerformed(ActionEvent e) |
995 |
|
{ |
996 |
0 |
cut_actionPerformed(); |
997 |
|
} |
998 |
|
}; |
999 |
241 |
addMenuActionAndAccelerator(keyStroke, cut, al); |
1000 |
|
|
1001 |
241 |
JMenuItem delete = new JMenuItem( |
1002 |
|
MessageManager.getString("action.delete")); |
1003 |
241 |
delete.addActionListener(new ActionListener() |
1004 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1005 |
0 |
@Override... |
1006 |
|
public void actionPerformed(ActionEvent e) |
1007 |
|
{ |
1008 |
0 |
delete_actionPerformed(); |
1009 |
|
} |
1010 |
|
}); |
1011 |
|
|
1012 |
241 |
pasteMenu.setText(MessageManager.getString("action.paste")); |
1013 |
241 |
JMenuItem pasteNew = new JMenuItem( |
1014 |
|
MessageManager.getString("label.to_new_alignment")); |
1015 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, |
1016 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() |
1017 |
|
| jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK, |
1018 |
|
false); |
1019 |
241 |
al = new ActionListener() |
1020 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1021 |
0 |
@Override... |
1022 |
|
public void actionPerformed(ActionEvent e) |
1023 |
|
{ |
1024 |
0 |
pasteNew_actionPerformed(e); |
1025 |
|
} |
1026 |
|
}; |
1027 |
241 |
addMenuActionAndAccelerator(keyStroke, pasteNew, al); |
1028 |
|
|
1029 |
241 |
JMenuItem pasteThis = new JMenuItem( |
1030 |
|
MessageManager.getString("label.to_this_alignment")); |
1031 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, |
1032 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
1033 |
241 |
al = new ActionListener() |
1034 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1035 |
0 |
@Override... |
1036 |
|
public void actionPerformed(ActionEvent e) |
1037 |
|
{ |
1038 |
0 |
pasteThis_actionPerformed(e); |
1039 |
|
} |
1040 |
|
}; |
1041 |
241 |
addMenuActionAndAccelerator(keyStroke, pasteThis, al); |
1042 |
|
|
1043 |
241 |
JMenuItem createPNG = new JMenuItem("PNG"); |
1044 |
241 |
createPNG.addActionListener(new ActionListener() |
1045 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1046 |
0 |
@Override... |
1047 |
|
public void actionPerformed(ActionEvent e) |
1048 |
|
{ |
1049 |
0 |
createPNG(null); |
1050 |
|
} |
1051 |
|
}); |
1052 |
241 |
createPNG.setActionCommand( |
1053 |
|
MessageManager.getString("label.save_png_image")); |
1054 |
|
|
1055 |
241 |
JMenuItem font = new JMenuItem(MessageManager.getString("action.font")); |
1056 |
241 |
font.addActionListener(new ActionListener() |
1057 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1058 |
0 |
@Override... |
1059 |
|
public void actionPerformed(ActionEvent e) |
1060 |
|
{ |
1061 |
0 |
font_actionPerformed(e); |
1062 |
|
} |
1063 |
|
}); |
1064 |
241 |
seqLimits.setText( |
1065 |
|
MessageManager.getString("label.show_sequence_limits")); |
1066 |
241 |
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); |
1067 |
241 |
seqLimits.addActionListener(new ActionListener() |
1068 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1069 |
0 |
@Override... |
1070 |
|
public void actionPerformed(ActionEvent e) |
1071 |
|
{ |
1072 |
0 |
seqLimit_actionPerformed(e); |
1073 |
|
} |
1074 |
|
}); |
1075 |
241 |
JMenuItem epsFile = new JMenuItem("EPS"); |
1076 |
241 |
epsFile.addActionListener(new ActionListener() |
1077 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1078 |
0 |
@Override... |
1079 |
|
public void actionPerformed(ActionEvent e) |
1080 |
|
{ |
1081 |
0 |
createEPS(null); |
1082 |
|
} |
1083 |
|
}); |
1084 |
|
|
1085 |
241 |
JMenuItem createSVG = new JMenuItem("SVG"); |
1086 |
241 |
createSVG.addActionListener(new ActionListener() |
1087 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1088 |
0 |
@Override... |
1089 |
|
public void actionPerformed(ActionEvent e) |
1090 |
|
{ |
1091 |
0 |
createSVG(null); |
1092 |
|
} |
1093 |
|
}); |
1094 |
|
|
1095 |
241 |
JMenuItem loadTreeMenuItem = new JMenuItem( |
1096 |
|
MessageManager.getString("label.load_associated_tree")); |
1097 |
241 |
loadTreeMenuItem.setActionCommand( |
1098 |
|
MessageManager.getString("label.load_tree_for_sequence_set")); |
1099 |
241 |
loadTreeMenuItem.addActionListener(new ActionListener() |
1100 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1101 |
0 |
@Override... |
1102 |
|
public void actionPerformed(ActionEvent e) |
1103 |
|
{ |
1104 |
0 |
loadTreeMenuItem_actionPerformed(e); |
1105 |
|
} |
1106 |
|
}); |
1107 |
|
|
1108 |
241 |
scaleAbove.setVisible(false); |
1109 |
241 |
scaleAbove.setText(MessageManager.getString("action.scale_above")); |
1110 |
241 |
scaleAbove.addActionListener(new ActionListener() |
1111 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1112 |
0 |
@Override... |
1113 |
|
public void actionPerformed(ActionEvent e) |
1114 |
|
{ |
1115 |
0 |
scaleAbove_actionPerformed(e); |
1116 |
|
} |
1117 |
|
}); |
1118 |
241 |
scaleLeft.setVisible(false); |
1119 |
241 |
scaleLeft.setSelected(true); |
1120 |
241 |
scaleLeft.setText(MessageManager.getString("action.scale_left")); |
1121 |
241 |
scaleLeft.addActionListener(new ActionListener() |
1122 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1123 |
0 |
@Override... |
1124 |
|
public void actionPerformed(ActionEvent e) |
1125 |
|
{ |
1126 |
0 |
scaleLeft_actionPerformed(e); |
1127 |
|
} |
1128 |
|
}); |
1129 |
241 |
scaleRight.setVisible(false); |
1130 |
241 |
scaleRight.setSelected(true); |
1131 |
241 |
scaleRight.setText(MessageManager.getString("action.scale_right")); |
1132 |
241 |
scaleRight.addActionListener(new ActionListener() |
1133 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1134 |
0 |
@Override... |
1135 |
|
public void actionPerformed(ActionEvent e) |
1136 |
|
{ |
1137 |
0 |
scaleRight_actionPerformed(e); |
1138 |
|
} |
1139 |
|
}); |
1140 |
241 |
centreColumnLabelsMenuItem.setVisible(true); |
1141 |
241 |
centreColumnLabelsMenuItem.setState(false); |
1142 |
241 |
centreColumnLabelsMenuItem.setText( |
1143 |
|
MessageManager.getString("label.centre_column_labels")); |
1144 |
241 |
centreColumnLabelsMenuItem.addActionListener(new ActionListener() |
1145 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1146 |
0 |
@Override... |
1147 |
|
public void actionPerformed(ActionEvent e) |
1148 |
|
{ |
1149 |
0 |
centreColumnLabels_actionPerformed(e); |
1150 |
|
} |
1151 |
|
}); |
1152 |
241 |
followHighlightMenuItem.setVisible(true); |
1153 |
241 |
followHighlightMenuItem.setState(true); |
1154 |
241 |
followHighlightMenuItem |
1155 |
|
.setText(MessageManager.getString("label.automatic_scrolling")); |
1156 |
241 |
followHighlightMenuItem.addActionListener(new ActionListener() |
1157 |
|
{ |
1158 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1159 |
0 |
@Override... |
1160 |
|
public void actionPerformed(ActionEvent e) |
1161 |
|
{ |
1162 |
0 |
followHighlight_actionPerformed(); |
1163 |
|
} |
1164 |
|
|
1165 |
|
}); |
1166 |
|
|
1167 |
241 |
sortByTreeMenu |
1168 |
|
.setText(MessageManager.getString("action.by_tree_order")); |
1169 |
241 |
sort.setText(MessageManager.getString("action.sort")); |
1170 |
241 |
sort.addMenuListener(new MenuListener() |
1171 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1172 |
0 |
@Override... |
1173 |
|
public void menuSelected(MenuEvent e) |
1174 |
|
{ |
1175 |
0 |
buildTreeSortMenu(); |
1176 |
|
} |
1177 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1178 |
0 |
@Override... |
1179 |
|
public void menuDeselected(MenuEvent e) |
1180 |
|
{ |
1181 |
|
} |
1182 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1183 |
0 |
@Override... |
1184 |
|
public void menuCanceled(MenuEvent e) |
1185 |
|
{ |
1186 |
|
} |
1187 |
|
}); |
1188 |
241 |
sortByAnnotScore |
1189 |
|
.setText(MessageManager.getString("label.sort_by_score")); |
1190 |
241 |
sort.add(sortByAnnotScore); |
1191 |
241 |
sort.addMenuListener(new javax.swing.event.MenuListener() |
1192 |
|
{ |
1193 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1194 |
0 |
@Override... |
1195 |
|
public void menuCanceled(MenuEvent e) |
1196 |
|
{ |
1197 |
|
} |
1198 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1199 |
0 |
@Override... |
1200 |
|
public void menuDeselected(MenuEvent e) |
1201 |
|
{ |
1202 |
|
} |
1203 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1204 |
0 |
@Override... |
1205 |
|
public void menuSelected(MenuEvent e) |
1206 |
|
{ |
1207 |
0 |
buildSortByAnnotationScoresMenu(); |
1208 |
|
} |
1209 |
|
}); |
1210 |
241 |
sortByAnnotScore.setVisible(false); |
1211 |
|
|
1212 |
241 |
calculateTree |
1213 |
|
.setText(MessageManager.getString("action.calculate_tree_pca")); |
1214 |
|
|
1215 |
241 |
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps")); |
1216 |
241 |
padGapsMenuitem |
1217 |
|
.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false)); |
1218 |
241 |
padGapsMenuitem.addActionListener(new ActionListener() |
1219 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1220 |
0 |
@Override... |
1221 |
|
public void actionPerformed(ActionEvent e) |
1222 |
|
{ |
1223 |
0 |
padGapsMenuitem_actionPerformed(e); |
1224 |
|
} |
1225 |
|
}); |
1226 |
241 |
JMenuItem vamsasStore = new JMenuItem( |
1227 |
|
MessageManager.getString("label.vamsas_store")); |
1228 |
241 |
vamsasStore.setVisible(false); |
1229 |
241 |
vamsasStore.addActionListener(new ActionListener() |
1230 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1231 |
0 |
@Override... |
1232 |
|
public void actionPerformed(ActionEvent e) |
1233 |
|
{ |
1234 |
0 |
vamsasStore_actionPerformed(e); |
1235 |
|
} |
1236 |
|
}); |
1237 |
|
|
1238 |
|
|
1239 |
|
|
1240 |
|
|
1241 |
241 |
showTranslation |
1242 |
|
.setText(MessageManager.getString("label.translate_cDNA")); |
1243 |
241 |
boolean first = true; |
1244 |
241 |
for (final GeneticCodeI table : GeneticCodes.getInstance() |
1245 |
|
.getCodeTables()) |
1246 |
|
{ |
1247 |
6025 |
JMenuItem item = new JMenuItem(table.getId() + " " + table.getName()); |
1248 |
6025 |
showTranslation.add(item); |
1249 |
6025 |
item.addActionListener(new ActionListener() |
1250 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1251 |
0 |
@Override... |
1252 |
|
public void actionPerformed(ActionEvent e) |
1253 |
|
{ |
1254 |
0 |
showTranslation_actionPerformed(table); |
1255 |
|
} |
1256 |
|
}); |
1257 |
6025 |
if (first) |
1258 |
|
{ |
1259 |
241 |
showTranslation.addSeparator(); |
1260 |
|
} |
1261 |
6025 |
first = false; |
1262 |
|
} |
1263 |
|
|
1264 |
241 |
showReverse.setText(MessageManager.getString("label.reverse")); |
1265 |
241 |
showReverse.addActionListener(new ActionListener() |
1266 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1267 |
0 |
@Override... |
1268 |
|
public void actionPerformed(ActionEvent e) |
1269 |
|
{ |
1270 |
0 |
showReverse_actionPerformed(false); |
1271 |
|
} |
1272 |
|
}); |
1273 |
241 |
showReverseComplement |
1274 |
|
.setText(MessageManager.getString("label.reverse_complement")); |
1275 |
241 |
showReverseComplement.addActionListener(new ActionListener() |
1276 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1277 |
0 |
@Override... |
1278 |
|
public void actionPerformed(ActionEvent e) |
1279 |
|
{ |
1280 |
0 |
showReverse_actionPerformed(true); |
1281 |
|
} |
1282 |
|
}); |
1283 |
|
|
1284 |
241 |
JMenuItem extractScores = new JMenuItem( |
1285 |
|
MessageManager.getString("label.extract_scores")); |
1286 |
241 |
extractScores.addActionListener(new ActionListener() |
1287 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1288 |
0 |
@Override... |
1289 |
|
public void actionPerformed(ActionEvent e) |
1290 |
|
{ |
1291 |
0 |
extractScores_actionPerformed(e); |
1292 |
|
} |
1293 |
|
}); |
1294 |
241 |
extractScores.setVisible(true); |
1295 |
|
|
1296 |
|
|
1297 |
|
|
1298 |
241 |
showProducts.setText(MessageManager.getString("label.get_cross_refs")); |
1299 |
|
|
1300 |
241 |
runGroovy.setText(MessageManager.getString("label.run_groovy")); |
1301 |
241 |
runGroovy.setToolTipText( |
1302 |
|
MessageManager.getString("label.run_groovy_tip")); |
1303 |
241 |
runGroovy.addActionListener(new ActionListener() |
1304 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1305 |
0 |
@Override... |
1306 |
|
public void actionPerformed(ActionEvent e) |
1307 |
|
{ |
1308 |
0 |
runGroovy_actionPerformed(); |
1309 |
|
} |
1310 |
|
}); |
1311 |
|
|
1312 |
241 |
openFeatureSettings = new JMenuItem( |
1313 |
|
MessageManager.getString("action.feature_settings")); |
1314 |
241 |
openFeatureSettings.addActionListener(new ActionListener() |
1315 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1316 |
0 |
@Override... |
1317 |
|
public void actionPerformed(ActionEvent e) |
1318 |
|
{ |
1319 |
0 |
featureSettings_actionPerformed(e); |
1320 |
|
} |
1321 |
|
}); |
1322 |
|
|
1323 |
|
|
1324 |
|
|
1325 |
|
|
1326 |
241 |
JMenuItem fetchSequence = new JMenuItem( |
1327 |
|
MessageManager.getString("label.fetch_sequences")); |
1328 |
241 |
fetchSequence.addActionListener(new ActionListener() |
1329 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1330 |
0 |
@Override... |
1331 |
|
public void actionPerformed(ActionEvent e) |
1332 |
|
{ |
1333 |
0 |
fetchSequence_actionPerformed(); |
1334 |
|
} |
1335 |
|
}); |
1336 |
|
|
1337 |
241 |
JMenuItem associatedData = new JMenuItem( |
1338 |
|
MessageManager.getString("label.load_features_annotations")); |
1339 |
241 |
associatedData.addActionListener(new ActionListener() |
1340 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1341 |
0 |
@Override... |
1342 |
|
public void actionPerformed(ActionEvent e) |
1343 |
|
{ |
1344 |
0 |
associatedData_actionPerformed(e); |
1345 |
|
} |
1346 |
|
}); |
1347 |
241 |
loadVcf = new JMenuItem( |
1348 |
|
MessageManager.getString("label.load_vcf_file")); |
1349 |
241 |
loadVcf.setToolTipText(MessageManager.getString("label.load_vcf")); |
1350 |
241 |
loadVcf.addActionListener(new ActionListener() |
1351 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1352 |
0 |
@Override... |
1353 |
|
public void actionPerformed(ActionEvent e) |
1354 |
|
{ |
1355 |
0 |
loadVcf_actionPerformed(); |
1356 |
|
} |
1357 |
|
}); |
1358 |
241 |
autoCalculate.setText( |
1359 |
|
MessageManager.getString("label.autocalculate_consensus")); |
1360 |
241 |
autoCalculate.setState( |
1361 |
|
jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true)); |
1362 |
241 |
autoCalculate.addActionListener(new ActionListener() |
1363 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1364 |
0 |
@Override... |
1365 |
|
public void actionPerformed(ActionEvent e) |
1366 |
|
{ |
1367 |
0 |
autoCalculate_actionPerformed(e); |
1368 |
|
} |
1369 |
|
}); |
1370 |
241 |
sortByTree.setText( |
1371 |
|
MessageManager.getString("label.sort_alignment_new_tree")); |
1372 |
241 |
sortByTree.setToolTipText("<html>" + MessageManager.getString( |
1373 |
|
"label.enable_automatically_sort_alignment_when_open_new_tree")); |
1374 |
241 |
sortByTree |
1375 |
|
.setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false)); |
1376 |
241 |
sortByTree.addActionListener(new ActionListener() |
1377 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1378 |
0 |
@Override... |
1379 |
|
public void actionPerformed(ActionEvent e) |
1380 |
|
{ |
1381 |
0 |
sortByTreeOption_actionPerformed(e); |
1382 |
|
} |
1383 |
|
}); |
1384 |
|
|
1385 |
241 |
listenToViewSelections.setText( |
1386 |
|
MessageManager.getString("label.listen_for_selections")); |
1387 |
241 |
listenToViewSelections |
1388 |
|
.setToolTipText("<html>" + MessageManager.getString( |
1389 |
|
"label.selections_mirror_selections_made_same_sequences_other_views")); |
1390 |
241 |
listenToViewSelections.setState(false); |
1391 |
241 |
listenToViewSelections.addActionListener(new ActionListener() |
1392 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1393 |
0 |
@Override... |
1394 |
|
public void actionPerformed(ActionEvent e) |
1395 |
|
{ |
1396 |
0 |
listenToViewSelections_actionPerformed(e); |
1397 |
|
} |
1398 |
|
}); |
1399 |
|
|
1400 |
241 |
JMenu addSequenceMenu = new JMenu( |
1401 |
|
MessageManager.getString("label.add_sequences")); |
1402 |
241 |
JMenuItem addFromFile = new JMenuItem( |
1403 |
|
MessageManager.getString("label.from_file")); |
1404 |
241 |
addFromFile.addActionListener(new ActionListener() |
1405 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1406 |
0 |
@Override... |
1407 |
|
public void actionPerformed(ActionEvent e) |
1408 |
|
{ |
1409 |
0 |
addFromFile_actionPerformed(e); |
1410 |
|
} |
1411 |
|
}); |
1412 |
241 |
JMenuItem addFromText = new JMenuItem( |
1413 |
|
MessageManager.getString("label.from_textbox")); |
1414 |
241 |
addFromText.addActionListener(new ActionListener() |
1415 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1416 |
0 |
@Override... |
1417 |
|
public void actionPerformed(ActionEvent e) |
1418 |
|
{ |
1419 |
0 |
addFromText_actionPerformed(e); |
1420 |
|
} |
1421 |
|
}); |
1422 |
241 |
JMenuItem addFromURL = new JMenuItem( |
1423 |
|
MessageManager.getString("label.from_url")); |
1424 |
241 |
addFromURL.addActionListener(new ActionListener() |
1425 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1426 |
0 |
@Override... |
1427 |
|
public void actionPerformed(ActionEvent e) |
1428 |
|
{ |
1429 |
0 |
addFromURL_actionPerformed(e); |
1430 |
|
} |
1431 |
|
}); |
1432 |
241 |
JMenuItem exportFeatures = new JMenuItem( |
1433 |
|
MessageManager.getString("label.export_features")); |
1434 |
241 |
exportFeatures.addActionListener(new ActionListener() |
1435 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1436 |
0 |
@Override... |
1437 |
|
public void actionPerformed(ActionEvent e) |
1438 |
|
{ |
1439 |
0 |
exportFeatures_actionPerformed(e); |
1440 |
|
} |
1441 |
|
}); |
1442 |
241 |
JMenuItem exportAnnotations = new JMenuItem( |
1443 |
|
MessageManager.getString("label.export_annotations")); |
1444 |
241 |
exportAnnotations.addActionListener(new ActionListener() |
1445 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1446 |
0 |
@Override... |
1447 |
|
public void actionPerformed(ActionEvent e) |
1448 |
|
{ |
1449 |
0 |
exportAnnotations_actionPerformed(e); |
1450 |
|
} |
1451 |
|
}); |
1452 |
241 |
statusPanel.setLayout(new GridLayout()); |
1453 |
241 |
JMenuItem showAllSeqs = new JMenuItem( |
1454 |
|
MessageManager.getString("label.all_sequences")); |
1455 |
241 |
showAllSeqs.setToolTipText( |
1456 |
|
MessageManager.getString("label.toggle_sequence_visibility")); |
1457 |
241 |
showAllSeqs.addActionListener(new ActionListener() |
1458 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1459 |
0 |
@Override... |
1460 |
|
public void actionPerformed(ActionEvent e) |
1461 |
|
{ |
1462 |
0 |
showAllSeqs_actionPerformed(e); |
1463 |
|
} |
1464 |
|
}); |
1465 |
241 |
JMenuItem showAllColumns = new JMenuItem( |
1466 |
|
MessageManager.getString("label.all_columns")); |
1467 |
241 |
showAllColumns.setToolTipText( |
1468 |
|
MessageManager.getString("label.toggle_columns_visibility")); |
1469 |
241 |
showAllColumns.addActionListener(new ActionListener() |
1470 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1471 |
0 |
@Override... |
1472 |
|
public void actionPerformed(ActionEvent e) |
1473 |
|
{ |
1474 |
0 |
showAllColumns_actionPerformed(e); |
1475 |
|
} |
1476 |
|
}); |
1477 |
241 |
JMenu hideMenu = new JMenu(MessageManager.getString("action.hide")); |
1478 |
241 |
JMenuItem hideSelSequences = new JMenuItem( |
1479 |
|
MessageManager.getString("label.selected_sequences")); |
1480 |
241 |
hideSelSequences.setToolTipText( |
1481 |
|
MessageManager.getString("label.toggle_sequence_visibility")); |
1482 |
241 |
hideSelSequences.addActionListener(new ActionListener() |
1483 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1484 |
0 |
@Override... |
1485 |
|
public void actionPerformed(ActionEvent e) |
1486 |
|
{ |
1487 |
0 |
hideSelSequences_actionPerformed(e); |
1488 |
|
} |
1489 |
|
}); |
1490 |
241 |
JMenuItem hideSelColumns = new JMenuItem( |
1491 |
|
MessageManager.getString("label.selected_columns")); |
1492 |
241 |
hideSelColumns.setToolTipText( |
1493 |
|
MessageManager.getString("label.toggle_columns_visibility")); |
1494 |
241 |
hideSelColumns.addActionListener(new ActionListener() |
1495 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1496 |
0 |
@Override... |
1497 |
|
public void actionPerformed(ActionEvent e) |
1498 |
|
{ |
1499 |
0 |
hideSelColumns_actionPerformed(e); |
1500 |
|
} |
1501 |
|
}); |
1502 |
241 |
JMenuItem hideAllSelection = new JMenuItem( |
1503 |
|
MessageManager.getString("label.selected_region")); |
1504 |
241 |
hideAllSelection.addActionListener(new ActionListener() |
1505 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1506 |
0 |
@Override... |
1507 |
|
public void actionPerformed(ActionEvent e) |
1508 |
|
{ |
1509 |
0 |
hideAllSelection_actionPerformed(e); |
1510 |
|
} |
1511 |
|
}); |
1512 |
|
|
1513 |
241 |
JMenuItem hideAllButSelection = new JMenuItem( |
1514 |
|
MessageManager.getString("label.all_but_selected_region")); |
1515 |
241 |
hideAllButSelection.addActionListener(new ActionListener() |
1516 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1517 |
0 |
@Override... |
1518 |
|
public void actionPerformed(ActionEvent e) |
1519 |
|
{ |
1520 |
0 |
hideAllButSelection_actionPerformed(e); |
1521 |
|
} |
1522 |
|
}); |
1523 |
241 |
JMenuItem showAllhidden = new JMenuItem( |
1524 |
|
MessageManager.getString("label.all_sequences_columns")); |
1525 |
241 |
showAllhidden.setToolTipText(MessageManager |
1526 |
|
.getString("label.toggles_visibility_hidden_selected_regions")); |
1527 |
241 |
showAllhidden.addActionListener(new ActionListener() |
1528 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1529 |
0 |
@Override... |
1530 |
|
public void actionPerformed(ActionEvent e) |
1531 |
|
{ |
1532 |
0 |
showAllhidden_actionPerformed(e); |
1533 |
|
} |
1534 |
|
}); |
1535 |
241 |
hiddenMarkers.setText( |
1536 |
|
MessageManager.getString("action.show_hidden_markers")); |
1537 |
241 |
hiddenMarkers.addActionListener(new ActionListener() |
1538 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1539 |
0 |
@Override... |
1540 |
|
public void actionPerformed(ActionEvent e) |
1541 |
|
{ |
1542 |
0 |
hiddenMarkers_actionPerformed(e); |
1543 |
|
} |
1544 |
|
}); |
1545 |
|
|
1546 |
241 |
JMenuItem invertColSel = new JMenuItem( |
1547 |
|
MessageManager.getString("action.invert_column_selection")); |
1548 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, |
1549 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() |
1550 |
|
| jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK, |
1551 |
|
false); |
1552 |
241 |
al = new ActionListener() |
1553 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1554 |
0 |
@Override... |
1555 |
|
public void actionPerformed(ActionEvent e) |
1556 |
|
{ |
1557 |
0 |
invertColSel_actionPerformed(e); |
1558 |
|
} |
1559 |
|
}; |
1560 |
241 |
addMenuActionAndAccelerator(keyStroke, invertColSel, al); |
1561 |
|
|
1562 |
241 |
showComplementMenuItem.setVisible(false); |
1563 |
241 |
showComplementMenuItem.addActionListener(new ActionListener() |
1564 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1565 |
0 |
@Override... |
1566 |
|
public void actionPerformed(ActionEvent e) |
1567 |
|
{ |
1568 |
0 |
showComplement_actionPerformed(showComplementMenuItem.getState()); |
1569 |
|
} |
1570 |
|
}); |
1571 |
|
|
1572 |
241 |
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() |
1573 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1574 |
139 |
@Override... |
1575 |
|
public void stateChanged(ChangeEvent evt) |
1576 |
|
{ |
1577 |
139 |
JTabbedPane pane = (JTabbedPane) evt.getSource(); |
1578 |
139 |
int sel = pane.getSelectedIndex(); |
1579 |
139 |
tabSelectionChanged(sel); |
1580 |
|
} |
1581 |
|
}); |
1582 |
241 |
tabbedPane.addMouseListener(new MouseAdapter() |
1583 |
|
{ |
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1584 |
0 |
@Override... |
1585 |
|
public void mousePressed(MouseEvent e) |
1586 |
|
{ |
1587 |
0 |
if (e.isPopupTrigger()) |
1588 |
|
{ |
1589 |
0 |
tabbedPane_mousePressed(e); |
1590 |
|
} |
1591 |
|
} |
1592 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1593 |
0 |
@Override... |
1594 |
|
public void mouseReleased(MouseEvent e) |
1595 |
|
{ |
1596 |
0 |
if (e.isPopupTrigger()) |
1597 |
|
{ |
1598 |
0 |
tabbedPane_mousePressed(e); |
1599 |
|
} |
1600 |
|
} |
1601 |
|
}); |
1602 |
241 |
tabbedPane.addFocusListener(new FocusAdapter() |
1603 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1604 |
59 |
@Override... |
1605 |
|
public void focusGained(FocusEvent e) |
1606 |
|
{ |
1607 |
59 |
tabbedPane_focusGained(e); |
1608 |
|
} |
1609 |
|
}); |
1610 |
|
|
1611 |
241 |
JMenuItem save = new JMenuItem(MessageManager.getString("action.save")); |
1612 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, |
1613 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
1614 |
241 |
al = new ActionListener() |
1615 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1616 |
0 |
@Override... |
1617 |
|
public void actionPerformed(ActionEvent e) |
1618 |
|
{ |
1619 |
0 |
save_actionPerformed(e); |
1620 |
|
} |
1621 |
|
}; |
1622 |
241 |
addMenuActionAndAccelerator(keyStroke, save, al); |
1623 |
|
|
1624 |
241 |
reload.setEnabled(false); |
1625 |
241 |
reload.setText(MessageManager.getString("action.reload")); |
1626 |
241 |
reload.addActionListener(new ActionListener() |
1627 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1628 |
0 |
@Override... |
1629 |
|
public void actionPerformed(ActionEvent e) |
1630 |
|
{ |
1631 |
0 |
reload_actionPerformed(e); |
1632 |
|
} |
1633 |
|
}); |
1634 |
|
|
1635 |
241 |
JMenuItem newView = new JMenuItem( |
1636 |
|
MessageManager.getString("action.new_view")); |
1637 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, |
1638 |
|
jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false); |
1639 |
241 |
al = new ActionListener() |
1640 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1641 |
0 |
@Override... |
1642 |
|
public void actionPerformed(ActionEvent e) |
1643 |
|
{ |
1644 |
0 |
newView_actionPerformed(e); |
1645 |
|
} |
1646 |
|
}; |
1647 |
241 |
addMenuActionAndAccelerator(keyStroke, newView, al); |
1648 |
|
|
1649 |
241 |
tabbedPane.setToolTipText("<html><i>" |
1650 |
|
+ MessageManager.getString("label.rename_tab_eXpand_reGroup") |
1651 |
|
+ "</i></html>"); |
1652 |
|
|
1653 |
241 |
formatMenu.setText(MessageManager.getString("action.format")); |
1654 |
241 |
JMenu selectMenu = new JMenu(MessageManager.getString("action.select")); |
1655 |
|
|
1656 |
241 |
idRightAlign.setText( |
1657 |
|
MessageManager.getString("label.right_align_sequence_id")); |
1658 |
241 |
idRightAlign.addActionListener(new ActionListener() |
1659 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1660 |
0 |
@Override... |
1661 |
|
public void actionPerformed(ActionEvent e) |
1662 |
|
{ |
1663 |
0 |
idRightAlign_actionPerformed(e); |
1664 |
|
} |
1665 |
|
}); |
1666 |
|
|
1667 |
241 |
gatherViews.setEnabled(false); |
1668 |
241 |
gatherViews.setText(MessageManager.getString("action.gather_views")); |
1669 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false); |
1670 |
241 |
al = new ActionListener() |
1671 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1672 |
0 |
@Override... |
1673 |
|
public void actionPerformed(ActionEvent e) |
1674 |
|
{ |
1675 |
0 |
gatherViews_actionPerformed(e); |
1676 |
|
} |
1677 |
|
}; |
1678 |
241 |
addMenuActionAndAccelerator(keyStroke, gatherViews, al); |
1679 |
|
|
1680 |
241 |
expandViews.setEnabled(false); |
1681 |
241 |
expandViews.setText(MessageManager.getString("action.expand_views")); |
1682 |
241 |
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false); |
1683 |
241 |
al = new ActionListener() |
1684 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1685 |
0 |
@Override... |
1686 |
|
public void actionPerformed(ActionEvent e) |
1687 |
|
{ |
1688 |
0 |
expandViews_actionPerformed(e); |
1689 |
|
} |
1690 |
|
}; |
1691 |
241 |
addMenuActionAndAccelerator(keyStroke, expandViews, al); |
1692 |
|
|
1693 |
241 |
JMenuItem pageSetup = new JMenuItem( |
1694 |
|
MessageManager.getString("action.page_setup")); |
1695 |
241 |
pageSetup.addActionListener(new ActionListener() |
1696 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1697 |
0 |
@Override... |
1698 |
|
public void actionPerformed(ActionEvent e) |
1699 |
|
{ |
1700 |
0 |
pageSetup_actionPerformed(e); |
1701 |
|
} |
1702 |
|
}); |
1703 |
241 |
JMenuItem alignmentProperties = new JMenuItem( |
1704 |
|
MessageManager.getString("label.alignment_props")); |
1705 |
241 |
alignmentProperties.addActionListener(new ActionListener() |
1706 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1707 |
0 |
@Override... |
1708 |
|
public void actionPerformed(ActionEvent actionEvent) |
1709 |
|
{ |
1710 |
0 |
alignmentProperties(); |
1711 |
|
} |
1712 |
|
}); |
1713 |
241 |
JMenuItem selectHighlighted = new JMenuItem( |
1714 |
|
MessageManager.getString("action.select_highlighted_columns")); |
1715 |
241 |
selectHighlighted.setToolTipText( |
1716 |
|
MessageManager.getString("tooltip.select_highlighted_columns")); |
1717 |
241 |
al = new ActionListener() |
1718 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1719 |
0 |
@Override... |
1720 |
|
public void actionPerformed(ActionEvent actionEvent) |
1721 |
|
{ |
1722 |
0 |
selectHighlightedColumns_actionPerformed(actionEvent); |
1723 |
|
} |
1724 |
|
}; |
1725 |
241 |
selectHighlighted.addActionListener(al); |
1726 |
241 |
JMenu tooltipSettingsMenu = new JMenu( |
1727 |
|
MessageManager.getString("label.sequence_id_tooltip")); |
1728 |
241 |
JMenu autoAnnMenu = new JMenu( |
1729 |
|
MessageManager.getString("label.autocalculated_annotation")); |
1730 |
|
|
1731 |
241 |
JMenu exportImageMenu = new JMenu( |
1732 |
|
MessageManager.getString("label.export_image")); |
1733 |
241 |
JMenu fileMenu = new JMenu(MessageManager.getString("action.file")); |
1734 |
241 |
alignFrameMenuBar.add(fileMenu); |
1735 |
241 |
alignFrameMenuBar.add(editMenu); |
1736 |
241 |
alignFrameMenuBar.add(selectMenu); |
1737 |
241 |
alignFrameMenuBar.add(viewMenu); |
1738 |
241 |
alignFrameMenuBar.add(annotationsMenu); |
1739 |
241 |
alignFrameMenuBar.add(formatMenu); |
1740 |
241 |
alignFrameMenuBar.add(colourMenu); |
1741 |
241 |
alignFrameMenuBar.add(calculateMenu); |
1742 |
241 |
if (!Platform.isJS()) |
1743 |
|
{ |
1744 |
241 |
alignFrameMenuBar.add(webService); |
1745 |
|
} |
1746 |
|
|
1747 |
241 |
fileMenu.add(fetchSequence); |
1748 |
241 |
fileMenu.add(addSequenceMenu); |
1749 |
241 |
fileMenu.add(reload); |
1750 |
241 |
fileMenu.addSeparator(); |
1751 |
241 |
fileMenu.add(vamsasStore); |
1752 |
241 |
fileMenu.add(save); |
1753 |
241 |
fileMenu.add(saveAs); |
1754 |
241 |
fileMenu.add(outputTextboxMenu); |
1755 |
241 |
fileMenu.add(pageSetup); |
1756 |
241 |
fileMenu.add(printMenuItem); |
1757 |
241 |
fileMenu.addSeparator(); |
1758 |
241 |
fileMenu.add(exportImageMenu); |
1759 |
241 |
fileMenu.add(exportFeatures); |
1760 |
241 |
fileMenu.add(exportAnnotations); |
1761 |
241 |
fileMenu.add(loadTreeMenuItem); |
1762 |
241 |
fileMenu.add(associatedData); |
1763 |
241 |
if (!Platform.isJS()) |
1764 |
|
{ |
1765 |
241 |
fileMenu.add(loadVcf); |
1766 |
|
} |
1767 |
241 |
fileMenu.addSeparator(); |
1768 |
241 |
fileMenu.add(closeMenuItem); |
1769 |
|
|
1770 |
241 |
pasteMenu.add(pasteNew); |
1771 |
241 |
pasteMenu.add(pasteThis); |
1772 |
241 |
editMenu.add(undoMenuItem); |
1773 |
241 |
editMenu.add(redoMenuItem); |
1774 |
241 |
editMenu.add(cut); |
1775 |
241 |
editMenu.add(copy); |
1776 |
241 |
editMenu.add(pasteMenu); |
1777 |
241 |
editMenu.add(delete); |
1778 |
241 |
editMenu.addSeparator(); |
1779 |
241 |
editMenu.add(remove2LeftMenuItem); |
1780 |
241 |
editMenu.add(remove2RightMenuItem); |
1781 |
241 |
editMenu.add(removeGappedColumnMenuItem); |
1782 |
241 |
editMenu.add(removeAllGapsMenuItem); |
1783 |
241 |
editMenu.add(removeRedundancyMenuItem); |
1784 |
241 |
editMenu.addSeparator(); |
1785 |
|
|
1786 |
|
|
1787 |
|
|
1788 |
|
|
1789 |
|
|
1790 |
241 |
editMenu.add(padGapsMenuitem); |
1791 |
|
|
1792 |
241 |
showMenu.add(showAllColumns); |
1793 |
241 |
showMenu.add(showAllSeqs); |
1794 |
241 |
showMenu.add(showAllhidden); |
1795 |
241 |
hideMenu.add(hideSelColumns); |
1796 |
241 |
hideMenu.add(hideSelSequences); |
1797 |
241 |
hideMenu.add(hideAllSelection); |
1798 |
241 |
hideMenu.add(hideAllButSelection); |
1799 |
241 |
viewMenu.add(newView); |
1800 |
241 |
viewMenu.add(expandViews); |
1801 |
241 |
viewMenu.add(gatherViews); |
1802 |
241 |
viewMenu.addSeparator(); |
1803 |
241 |
viewMenu.add(showMenu); |
1804 |
241 |
viewMenu.add(hideMenu); |
1805 |
241 |
viewMenu.add(showComplementMenuItem); |
1806 |
241 |
viewMenu.addSeparator(); |
1807 |
241 |
viewMenu.add(followHighlightMenuItem); |
1808 |
241 |
viewMenu.addSeparator(); |
1809 |
241 |
viewMenu.add(showSeqFeatures); |
1810 |
|
|
1811 |
241 |
viewMenu.add(openFeatureSettings); |
1812 |
241 |
tooltipSettingsMenu.add(showDbRefsMenuitem); |
1813 |
241 |
tooltipSettingsMenu.add(showNpFeatsMenuitem); |
1814 |
241 |
viewMenu.add(tooltipSettingsMenu); |
1815 |
241 |
viewMenu.addSeparator(); |
1816 |
241 |
viewMenu.add(alignmentProperties); |
1817 |
241 |
viewMenu.addSeparator(); |
1818 |
241 |
viewMenu.add(overviewMenuItem); |
1819 |
|
|
1820 |
241 |
annotationsMenu.add(annotationPanelMenuItem); |
1821 |
241 |
annotationsMenu.addSeparator(); |
1822 |
241 |
annotationsMenu.add(showAllAlAnnotations); |
1823 |
241 |
annotationsMenu.add(hideAllAlAnnotations); |
1824 |
241 |
annotationsMenu.addSeparator(); |
1825 |
241 |
annotationsMenu.add(showAllSeqAnnotations); |
1826 |
241 |
annotationsMenu.add(hideAllSeqAnnotations); |
1827 |
241 |
annotationsMenu.add(sortAnnBySequence); |
1828 |
241 |
annotationsMenu.add(sortAnnByLabel); |
1829 |
241 |
annotationsMenu.addSeparator(); |
1830 |
241 |
autoAnnMenu.add(showAutoFirst); |
1831 |
241 |
autoAnnMenu.add(showAutoLast); |
1832 |
241 |
autoAnnMenu.addSeparator(); |
1833 |
241 |
autoAnnMenu.add(applyAutoAnnotationSettings); |
1834 |
241 |
autoAnnMenu.add(showConsensusHistogram); |
1835 |
241 |
autoAnnMenu.add(showSequenceLogo); |
1836 |
241 |
autoAnnMenu.add(normaliseSequenceLogo); |
1837 |
241 |
autoAnnMenu.addSeparator(); |
1838 |
241 |
autoAnnMenu.add(showGroupConservation); |
1839 |
241 |
autoAnnMenu.add(showGroupConsensus); |
1840 |
241 |
annotationsMenu.add(autoAnnMenu); |
1841 |
|
|
1842 |
241 |
sort.add(sortIDMenuItem); |
1843 |
241 |
sort.add(sortLengthMenuItem); |
1844 |
241 |
sort.add(sortGroupMenuItem); |
1845 |
241 |
sort.add(sortPairwiseMenuItem); |
1846 |
241 |
sort.add(sortByTreeMenu); |
1847 |
241 |
calculateMenu.add(sort); |
1848 |
241 |
calculateMenu.add(calculateTree); |
1849 |
241 |
calculateMenu.addSeparator(); |
1850 |
241 |
calculateMenu.add(pairwiseAlignmentMenuItem); |
1851 |
241 |
calculateMenu.addSeparator(); |
1852 |
241 |
calculateMenu.add(showTranslation); |
1853 |
241 |
calculateMenu.add(showReverse); |
1854 |
241 |
calculateMenu.add(showReverseComplement); |
1855 |
241 |
calculateMenu.add(showProducts); |
1856 |
241 |
calculateMenu.add(autoCalculate); |
1857 |
241 |
calculateMenu.add(sortByTree); |
1858 |
241 |
calculateMenu.addSeparator(); |
1859 |
241 |
calculateMenu.add(expandAlignment); |
1860 |
241 |
calculateMenu.add(extractScores); |
1861 |
241 |
if (!Platform.isJS()) |
1862 |
|
{ |
1863 |
241 |
calculateMenu.addSeparator(); |
1864 |
241 |
calculateMenu.add(runGroovy); |
1865 |
|
} |
1866 |
|
|
1867 |
241 |
webServiceNoServices = new JMenuItem( |
1868 |
|
MessageManager.getString("label.no_services")); |
1869 |
241 |
webService.add(webServiceNoServices); |
1870 |
241 |
if (!Platform.isJS()) |
1871 |
|
{ |
1872 |
241 |
exportImageMenu.add(htmlMenuItem); |
1873 |
|
} |
1874 |
241 |
exportImageMenu.add(epsFile); |
1875 |
241 |
exportImageMenu.add(createPNG); |
1876 |
241 |
if (!Platform.isJS()) |
1877 |
|
{ |
1878 |
241 |
exportImageMenu.add(createBioJS); |
1879 |
241 |
exportImageMenu.add(createSVG); |
1880 |
|
} |
1881 |
241 |
addSequenceMenu.add(addFromFile); |
1882 |
241 |
addSequenceMenu.add(addFromText); |
1883 |
241 |
addSequenceMenu.add(addFromURL); |
1884 |
241 |
this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH); |
1885 |
241 |
statusPanel.add(statusBar, null); |
1886 |
241 |
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER); |
1887 |
|
|
1888 |
241 |
formatMenu.add(font); |
1889 |
241 |
formatMenu.addSeparator(); |
1890 |
241 |
formatMenu.add(wrapMenuItem); |
1891 |
241 |
formatMenu.add(scaleAbove); |
1892 |
241 |
formatMenu.add(scaleLeft); |
1893 |
241 |
formatMenu.add(scaleRight); |
1894 |
241 |
formatMenu.add(seqLimits); |
1895 |
241 |
formatMenu.add(idRightAlign); |
1896 |
241 |
formatMenu.add(hiddenMarkers); |
1897 |
241 |
formatMenu.add(viewBoxesMenuItem); |
1898 |
241 |
formatMenu.add(viewTextMenuItem); |
1899 |
241 |
formatMenu.add(colourTextMenuItem); |
1900 |
241 |
formatMenu.add(renderGapsMenuItem); |
1901 |
241 |
formatMenu.add(centreColumnLabelsMenuItem); |
1902 |
241 |
formatMenu.add(showNonconservedMenuItem); |
1903 |
241 |
selectMenu.add(findMenuItem); |
1904 |
241 |
selectMenu.addSeparator(); |
1905 |
241 |
selectMenu.add(selectAllSequenceMenuItem); |
1906 |
241 |
selectMenu.add(deselectAllSequenceMenuItem); |
1907 |
241 |
selectMenu.add(invertSequenceMenuItem); |
1908 |
241 |
selectMenu.add(invertColSel); |
1909 |
241 |
selectMenu.add(createGroup); |
1910 |
241 |
selectMenu.add(unGroup); |
1911 |
241 |
selectMenu.add(grpsFromSelection); |
1912 |
241 |
selectMenu.add(deleteGroups); |
1913 |
241 |
selectMenu.add(annotationColumn); |
1914 |
241 |
selectMenu.add(selectHighlighted); |
1915 |
|
|
1916 |
|
|
1917 |
|
|
1918 |
|
|
1919 |
|
} |
1920 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
1921 |
0 |
protected void loadVcf_actionPerformed()... |
1922 |
|
{ |
1923 |
|
} |
1924 |
|
|
1925 |
|
|
1926 |
|
|
1927 |
|
|
1928 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
|
1929 |
241 |
protected void initColourMenu()... |
1930 |
|
{ |
1931 |
241 |
applyToAllGroups = new JCheckBoxMenuItem( |
1932 |
|
MessageManager.getString("label.apply_colour_to_all_groups")); |
1933 |
241 |
applyToAllGroups.addActionListener(new ActionListener() |
1934 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1935 |
0 |
@Override... |
1936 |
|
public void actionPerformed(ActionEvent e) |
1937 |
|
{ |
1938 |
0 |
applyToAllGroups_actionPerformed(applyToAllGroups.isSelected()); |
1939 |
|
} |
1940 |
|
}); |
1941 |
|
|
1942 |
241 |
textColour = new JMenuItem( |
1943 |
|
MessageManager.getString("label.text_colour")); |
1944 |
241 |
textColour.addActionListener(new ActionListener() |
1945 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1946 |
0 |
@Override... |
1947 |
|
public void actionPerformed(ActionEvent e) |
1948 |
|
{ |
1949 |
0 |
textColour_actionPerformed(); |
1950 |
|
} |
1951 |
|
}); |
1952 |
|
|
1953 |
241 |
conservationMenuItem = new JCheckBoxMenuItem( |
1954 |
|
MessageManager.getString("action.by_conservation")); |
1955 |
241 |
conservationMenuItem.addActionListener(new ActionListener() |
1956 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1957 |
0 |
@Override... |
1958 |
|
public void actionPerformed(ActionEvent e) |
1959 |
|
{ |
1960 |
0 |
conservationMenuItem_actionPerformed( |
1961 |
|
conservationMenuItem.isSelected()); |
1962 |
|
} |
1963 |
|
}); |
1964 |
|
|
1965 |
241 |
abovePIDThreshold = new JCheckBoxMenuItem( |
1966 |
|
MessageManager.getString("label.above_identity_threshold")); |
1967 |
241 |
abovePIDThreshold.addActionListener(new ActionListener() |
1968 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1969 |
0 |
@Override... |
1970 |
|
public void actionPerformed(ActionEvent e) |
1971 |
|
{ |
1972 |
0 |
abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected()); |
1973 |
|
} |
1974 |
|
}); |
1975 |
241 |
modifyPID = new JMenuItem( |
1976 |
|
MessageManager.getString("label.modify_identity_threshold")); |
1977 |
241 |
modifyPID.addActionListener(new ActionListener() |
1978 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1979 |
0 |
@Override... |
1980 |
|
public void actionPerformed(ActionEvent e) |
1981 |
|
{ |
1982 |
0 |
modifyPID_actionPerformed(); |
1983 |
|
} |
1984 |
|
}); |
1985 |
241 |
modifyConservation = new JMenuItem(MessageManager |
1986 |
|
.getString("label.modify_conservation_threshold")); |
1987 |
241 |
modifyConservation.addActionListener(new ActionListener() |
1988 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1989 |
0 |
@Override... |
1990 |
|
public void actionPerformed(ActionEvent e) |
1991 |
|
{ |
1992 |
0 |
modifyConservation_actionPerformed(); |
1993 |
|
} |
1994 |
|
}); |
1995 |
|
|
1996 |
241 |
annotationColour = new JRadioButtonMenuItem( |
1997 |
|
MessageManager.getString("action.by_annotation")); |
1998 |
241 |
annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR); |
1999 |
241 |
annotationColour.addActionListener(new ActionListener() |
2000 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2001 |
0 |
@Override... |
2002 |
|
public void actionPerformed(ActionEvent e) |
2003 |
|
{ |
2004 |
0 |
annotationColour_actionPerformed(); |
2005 |
|
} |
2006 |
|
}); |
2007 |
|
} |
2008 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2009 |
0 |
protected void selectHighlightedColumns_actionPerformed(... |
2010 |
|
ActionEvent actionEvent) |
2011 |
|
{ |
2012 |
|
|
2013 |
|
|
2014 |
|
} |
2015 |
|
|
2016 |
|
|
2017 |
|
|
2018 |
|
|
2019 |
|
|
2020 |
|
@param |
2021 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2022 |
0 |
protected void showReverse_actionPerformed(boolean complement)... |
2023 |
|
{ |
2024 |
|
} |
2025 |
|
|
2026 |
|
|
2027 |
|
|
2028 |
|
|
2029 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2030 |
0 |
protected void runGroovy_actionPerformed()... |
2031 |
|
{ |
2032 |
|
|
2033 |
|
} |
2034 |
|
|
2035 |
|
|
2036 |
|
|
2037 |
|
|
2038 |
|
|
2039 |
|
@param |
2040 |
|
@param |
2041 |
|
@param |
2042 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
2043 |
6266 |
protected void addMenuActionAndAccelerator(KeyStroke keyStroke,... |
2044 |
|
JMenuItem menuItem, ActionListener actionListener) |
2045 |
|
{ |
2046 |
6266 |
menuItem.setAccelerator(keyStroke); |
2047 |
6266 |
accelerators.put(keyStroke, menuItem); |
2048 |
6266 |
menuItem.addActionListener(actionListener); |
2049 |
|
} |
2050 |
|
|
2051 |
|
|
2052 |
|
|
2053 |
|
|
2054 |
|
@param |
2055 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2056 |
0 |
protected void sortAnnotations_actionPerformed()... |
2057 |
|
{ |
2058 |
|
} |
2059 |
|
|
2060 |
|
|
2061 |
|
|
2062 |
|
|
2063 |
|
@param |
2064 |
|
|
2065 |
|
@param |
2066 |
|
|
2067 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2068 |
0 |
protected void showAllAnnotations_actionPerformed(boolean forSequences,... |
2069 |
|
boolean forAlignment) |
2070 |
|
{ |
2071 |
0 |
setAnnotationsVisibility(true, forSequences, forAlignment); |
2072 |
|
} |
2073 |
|
|
2074 |
|
|
2075 |
|
|
2076 |
|
|
2077 |
|
@param |
2078 |
|
|
2079 |
|
@param |
2080 |
|
|
2081 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2082 |
0 |
protected void hideAllAnnotations_actionPerformed(boolean forSequences,... |
2083 |
|
boolean forAlignment) |
2084 |
|
{ |
2085 |
0 |
setAnnotationsVisibility(false, forSequences, forAlignment); |
2086 |
|
} |
2087 |
|
|
2088 |
|
|
2089 |
|
|
2090 |
|
|
2091 |
|
|
2092 |
|
@param |
2093 |
|
@param |
2094 |
|
|
2095 |
|
@param |
2096 |
|
|
2097 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2098 |
0 |
protected void setAnnotationsVisibility(boolean visible,... |
2099 |
|
boolean forSequences, boolean forAlignment) |
2100 |
|
{ |
2101 |
|
|
2102 |
|
} |
2103 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2104 |
0 |
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)... |
2105 |
|
{ |
2106 |
|
|
2107 |
|
|
2108 |
|
} |
2109 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2110 |
0 |
protected void listenToViewSelections_actionPerformed(ActionEvent e)... |
2111 |
|
{ |
2112 |
|
|
2113 |
|
|
2114 |
|
} |
2115 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2116 |
0 |
protected void showAllhidden_actionPerformed(ActionEvent e)... |
2117 |
|
{ |
2118 |
|
|
2119 |
|
|
2120 |
|
} |
2121 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2122 |
0 |
protected void hideAllButSelection_actionPerformed(ActionEvent e)... |
2123 |
|
{ |
2124 |
|
|
2125 |
|
|
2126 |
|
} |
2127 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2128 |
0 |
protected void hideAllSelection_actionPerformed(ActionEvent e)... |
2129 |
|
{ |
2130 |
|
|
2131 |
|
|
2132 |
|
} |
2133 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2134 |
0 |
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)... |
2135 |
|
{ |
2136 |
|
|
2137 |
|
|
2138 |
|
} |
2139 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2140 |
0 |
protected void showConsensusHistogram_actionPerformed(ActionEvent e)... |
2141 |
|
{ |
2142 |
|
|
2143 |
|
|
2144 |
|
} |
2145 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2146 |
0 |
protected void showSequenceLogo_actionPerformed(ActionEvent e)... |
2147 |
|
{ |
2148 |
|
|
2149 |
|
|
2150 |
|
} |
2151 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2152 |
0 |
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)... |
2153 |
|
{ |
2154 |
|
|
2155 |
|
|
2156 |
|
} |
2157 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2158 |
0 |
protected void showGroupConsensus_actionPerformed(ActionEvent e)... |
2159 |
|
{ |
2160 |
|
|
2161 |
|
|
2162 |
|
} |
2163 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2164 |
0 |
protected void showGroupConservation_actionPerformed(ActionEvent e)... |
2165 |
|
{ |
2166 |
|
|
2167 |
|
|
2168 |
|
} |
2169 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2170 |
0 |
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)... |
2171 |
|
{ |
2172 |
|
|
2173 |
|
|
2174 |
|
} |
2175 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2176 |
0 |
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)... |
2177 |
|
{ |
2178 |
|
|
2179 |
|
|
2180 |
|
} |
2181 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2182 |
0 |
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)... |
2183 |
|
{ |
2184 |
|
|
2185 |
|
|
2186 |
|
} |
2187 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2188 |
0 |
protected void followHighlight_actionPerformed()... |
2189 |
|
{ |
2190 |
|
|
2191 |
|
|
2192 |
|
} |
2193 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2194 |
0 |
protected void showNpFeats_actionPerformed(ActionEvent e)... |
2195 |
|
{ |
2196 |
|
|
2197 |
|
|
2198 |
|
} |
2199 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2200 |
0 |
protected void showDbRefs_actionPerformed(ActionEvent e)... |
2201 |
|
{ |
2202 |
|
|
2203 |
|
|
2204 |
|
} |
2205 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2206 |
0 |
protected void centreColumnLabels_actionPerformed(ActionEvent e)... |
2207 |
|
{ |
2208 |
|
} |
2209 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2210 |
0 |
protected void buildSortByAnnotationScoresMenu()... |
2211 |
|
{ |
2212 |
|
} |
2213 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2214 |
0 |
protected void extractScores_actionPerformed(ActionEvent e)... |
2215 |
|
{ |
2216 |
|
} |
2217 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2218 |
0 |
protected void outputText_actionPerformed(String formatName)... |
2219 |
|
{ |
2220 |
|
} |
2221 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2222 |
0 |
public void addFromFile_actionPerformed(ActionEvent e)... |
2223 |
|
{ |
2224 |
|
|
2225 |
|
} |
2226 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2227 |
0 |
public void addFromText_actionPerformed(ActionEvent e)... |
2228 |
|
{ |
2229 |
|
|
2230 |
|
} |
2231 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2232 |
0 |
public void addFromURL_actionPerformed(ActionEvent e)... |
2233 |
|
{ |
2234 |
|
|
2235 |
|
} |
2236 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2237 |
0 |
public void exportFeatures_actionPerformed(ActionEvent e)... |
2238 |
|
{ |
2239 |
|
|
2240 |
|
} |
2241 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2242 |
0 |
public void exportAnnotations_actionPerformed(ActionEvent e)... |
2243 |
|
{ |
2244 |
|
|
2245 |
|
} |
2246 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2247 |
0 |
protected void htmlMenuItem_actionPerformed(ActionEvent e)... |
2248 |
|
{ |
2249 |
|
} |
2250 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2251 |
0 |
protected void bioJSMenuItem_actionPerformed(ActionEvent e)... |
2252 |
|
{ |
2253 |
|
|
2254 |
|
} |
2255 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2256 |
0 |
protected void closeMenuItem_actionPerformed(boolean b)... |
2257 |
|
{ |
2258 |
|
} |
2259 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2260 |
0 |
protected void redoMenuItem_actionPerformed(ActionEvent e)... |
2261 |
|
{ |
2262 |
|
} |
2263 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2264 |
0 |
protected void undoMenuItem_actionPerformed(ActionEvent e)... |
2265 |
|
{ |
2266 |
|
} |
2267 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2268 |
0 |
protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)... |
2269 |
|
{ |
2270 |
|
} |
2271 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2272 |
0 |
protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)... |
2273 |
|
{ |
2274 |
|
} |
2275 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2276 |
0 |
protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)... |
2277 |
|
{ |
2278 |
|
} |
2279 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2280 |
0 |
protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)... |
2281 |
|
{ |
2282 |
|
} |
2283 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2284 |
0 |
protected void remove2RightMenuItem_actionPerformed(ActionEvent e)... |
2285 |
|
{ |
2286 |
|
} |
2287 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2288 |
0 |
protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)... |
2289 |
|
{ |
2290 |
|
} |
2291 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2292 |
0 |
protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)... |
2293 |
|
{ |
2294 |
|
} |
2295 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2296 |
0 |
protected void wrapMenuItem_actionPerformed(ActionEvent e)... |
2297 |
|
{ |
2298 |
|
} |
2299 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2300 |
0 |
protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)... |
2301 |
|
{ |
2302 |
|
} |
2303 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2304 |
0 |
protected void viewTextMenuItem_actionPerformed(ActionEvent e)... |
2305 |
|
{ |
2306 |
|
} |
2307 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2308 |
0 |
protected void colourTextMenuItem_actionPerformed(ActionEvent e)... |
2309 |
|
{ |
2310 |
|
} |
2311 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2312 |
0 |
protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)... |
2313 |
|
{ |
2314 |
|
} |
2315 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2316 |
0 |
protected void overviewMenuItem_actionPerformed(ActionEvent e)... |
2317 |
|
{ |
2318 |
|
} |
2319 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2320 |
0 |
protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)... |
2321 |
|
{ |
2322 |
|
} |
2323 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2324 |
0 |
protected void sortIDMenuItem_actionPerformed(ActionEvent e)... |
2325 |
|
{ |
2326 |
|
} |
2327 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2328 |
0 |
protected void sortLengthMenuItem_actionPerformed(ActionEvent e)... |
2329 |
|
{ |
2330 |
|
} |
2331 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2332 |
0 |
protected void sortGroupMenuItem_actionPerformed(ActionEvent e)... |
2333 |
|
{ |
2334 |
|
} |
2335 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2336 |
0 |
protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)... |
2337 |
|
{ |
2338 |
|
} |
2339 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2340 |
0 |
protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)... |
2341 |
|
{ |
2342 |
|
} |
2343 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2344 |
0 |
protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)... |
2345 |
|
{ |
2346 |
|
} |
2347 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2348 |
0 |
protected void conservationMenuItem_actionPerformed(boolean selected)... |
2349 |
|
{ |
2350 |
|
} |
2351 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2352 |
0 |
protected void printMenuItem_actionPerformed(ActionEvent e)... |
2353 |
|
{ |
2354 |
|
} |
2355 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2356 |
0 |
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)... |
2357 |
|
{ |
2358 |
|
} |
2359 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2360 |
0 |
protected void findMenuItem_actionPerformed(ActionEvent e)... |
2361 |
|
{ |
2362 |
|
} |
2363 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2364 |
0 |
protected void abovePIDThreshold_actionPerformed(boolean selected)... |
2365 |
|
{ |
2366 |
|
} |
2367 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2368 |
0 |
public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)... |
2369 |
|
{ |
2370 |
|
} |
2371 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2372 |
0 |
protected void deleteGroups_actionPerformed(ActionEvent e)... |
2373 |
|
{ |
2374 |
|
} |
2375 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2376 |
0 |
protected void createGroup_actionPerformed(ActionEvent e)... |
2377 |
|
{ |
2378 |
|
} |
2379 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2380 |
0 |
protected void unGroup_actionPerformed(ActionEvent e)... |
2381 |
|
{ |
2382 |
|
} |
2383 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2384 |
0 |
protected void copy_actionPerformed()... |
2385 |
|
{ |
2386 |
|
} |
2387 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2388 |
0 |
protected void cut_actionPerformed()... |
2389 |
|
{ |
2390 |
|
} |
2391 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2392 |
0 |
protected void delete_actionPerformed()... |
2393 |
|
{ |
2394 |
|
} |
2395 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2396 |
0 |
protected void pasteNew_actionPerformed(ActionEvent e)... |
2397 |
|
{ |
2398 |
|
} |
2399 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2400 |
0 |
protected void pasteThis_actionPerformed(ActionEvent e)... |
2401 |
|
{ |
2402 |
|
} |
2403 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2404 |
0 |
protected void applyToAllGroups_actionPerformed(boolean selected)... |
2405 |
|
{ |
2406 |
|
} |
2407 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2408 |
0 |
public void createPNG(java.io.File f)... |
2409 |
|
{ |
2410 |
|
} |
2411 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2412 |
0 |
protected void font_actionPerformed(ActionEvent e)... |
2413 |
|
{ |
2414 |
|
} |
2415 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2416 |
0 |
protected void seqLimit_actionPerformed(ActionEvent e)... |
2417 |
|
{ |
2418 |
|
} |
2419 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2420 |
0 |
public void seqDBRef_actionPerformed(ActionEvent e)... |
2421 |
|
{ |
2422 |
|
|
2423 |
|
} |
2424 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2425 |
0 |
public void createEPS(java.io.File f)... |
2426 |
|
{ |
2427 |
|
} |
2428 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2429 |
0 |
public void createSVG(java.io.File f)... |
2430 |
|
{ |
2431 |
|
|
2432 |
|
} |
2433 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2434 |
0 |
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)... |
2435 |
|
{ |
2436 |
|
|
2437 |
|
} |
2438 |
|
|
2439 |
|
|
2440 |
|
|
2441 |
|
|
2442 |
|
|
2443 |
|
|
2444 |
|
@param |
2445 |
|
|
2446 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2447 |
0 |
protected void loadScores_actionPerformed(ActionEvent event)... |
2448 |
|
{ |
2449 |
|
|
2450 |
|
} |
2451 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2452 |
0 |
protected void jpred_actionPerformed(ActionEvent e)... |
2453 |
|
{ |
2454 |
|
} |
2455 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2456 |
0 |
protected void scaleAbove_actionPerformed(ActionEvent e)... |
2457 |
|
{ |
2458 |
|
} |
2459 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2460 |
0 |
protected void scaleLeft_actionPerformed(ActionEvent e)... |
2461 |
|
{ |
2462 |
|
} |
2463 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2464 |
0 |
protected void scaleRight_actionPerformed(ActionEvent e)... |
2465 |
|
{ |
2466 |
|
} |
2467 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2468 |
0 |
protected void modifyPID_actionPerformed()... |
2469 |
|
{ |
2470 |
|
} |
2471 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2472 |
0 |
protected void modifyConservation_actionPerformed()... |
2473 |
|
{ |
2474 |
|
} |
2475 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2476 |
0 |
protected void saveAs_actionPerformed()... |
2477 |
|
{ |
2478 |
|
} |
2479 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2480 |
0 |
protected void padGapsMenuitem_actionPerformed(ActionEvent e)... |
2481 |
|
{ |
2482 |
|
} |
2483 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2484 |
0 |
public void vamsasStore_actionPerformed(ActionEvent e)... |
2485 |
|
{ |
2486 |
|
|
2487 |
|
} |
2488 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2489 |
0 |
public void vamsasLoad_actionPerformed(ActionEvent e)... |
2490 |
|
{ |
2491 |
|
|
2492 |
|
} |
2493 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2494 |
0 |
public void showTranslation_actionPerformed(GeneticCodeI codeTable)... |
2495 |
|
{ |
2496 |
|
|
2497 |
|
} |
2498 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2499 |
0 |
public void featureSettings_actionPerformed(ActionEvent e)... |
2500 |
|
{ |
2501 |
|
|
2502 |
|
} |
2503 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2504 |
0 |
public void fetchSequence_actionPerformed()... |
2505 |
|
{ |
2506 |
|
|
2507 |
|
} |
2508 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2509 |
0 |
public void smoothFont_actionPerformed(ActionEvent e)... |
2510 |
|
{ |
2511 |
|
|
2512 |
|
} |
2513 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2514 |
0 |
public void annotationColour_actionPerformed()... |
2515 |
|
{ |
2516 |
|
} |
2517 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2518 |
0 |
public void annotationColumn_actionPerformed(ActionEvent e)... |
2519 |
|
{ |
2520 |
|
} |
2521 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2522 |
0 |
public void associatedData_actionPerformed(ActionEvent e)... |
2523 |
|
{ |
2524 |
|
|
2525 |
|
} |
2526 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2527 |
0 |
public void autoCalculate_actionPerformed(ActionEvent e)... |
2528 |
|
{ |
2529 |
|
|
2530 |
|
} |
2531 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2532 |
0 |
public void sortByTreeOption_actionPerformed(ActionEvent e)... |
2533 |
|
{ |
2534 |
|
|
2535 |
|
} |
2536 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2537 |
0 |
public void showAllSeqs_actionPerformed(ActionEvent e)... |
2538 |
|
{ |
2539 |
|
|
2540 |
|
} |
2541 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2542 |
0 |
public void showAllColumns_actionPerformed(ActionEvent e)... |
2543 |
|
{ |
2544 |
|
|
2545 |
|
} |
2546 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2547 |
0 |
public void hideSelSequences_actionPerformed(ActionEvent e)... |
2548 |
|
{ |
2549 |
|
|
2550 |
|
} |
2551 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2552 |
0 |
public void hideSelColumns_actionPerformed(ActionEvent e)... |
2553 |
|
{ |
2554 |
|
|
2555 |
|
} |
2556 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2557 |
0 |
public void hiddenMarkers_actionPerformed(ActionEvent e)... |
2558 |
|
{ |
2559 |
|
|
2560 |
|
} |
2561 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2562 |
0 |
public void findPdbId_actionPerformed(ActionEvent e)... |
2563 |
|
{ |
2564 |
|
|
2565 |
|
} |
2566 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2567 |
0 |
public void enterPdbId_actionPerformed(ActionEvent e)... |
2568 |
|
{ |
2569 |
|
|
2570 |
|
} |
2571 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2572 |
0 |
public void pdbFile_actionPerformed(ActionEvent e)... |
2573 |
|
{ |
2574 |
|
|
2575 |
|
} |
2576 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2577 |
0 |
public void invertColSel_actionPerformed(ActionEvent e)... |
2578 |
|
{ |
2579 |
|
|
2580 |
|
} |
2581 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2582 |
0 |
public void tabSelectionChanged(int sel)... |
2583 |
|
{ |
2584 |
|
|
2585 |
|
} |
2586 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2587 |
0 |
public void tabbedPane_mousePressed(MouseEvent e)... |
2588 |
|
{ |
2589 |
|
|
2590 |
|
} |
2591 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2592 |
59 |
public void tabbedPane_focusGained(FocusEvent e)... |
2593 |
|
{ |
2594 |
59 |
requestFocus(); |
2595 |
|
} |
2596 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2597 |
0 |
public void save_actionPerformed(ActionEvent e)... |
2598 |
|
{ |
2599 |
|
|
2600 |
|
} |
2601 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2602 |
0 |
public void reload_actionPerformed(ActionEvent e)... |
2603 |
|
{ |
2604 |
|
|
2605 |
|
} |
2606 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2607 |
0 |
public void newView_actionPerformed(ActionEvent e)... |
2608 |
|
{ |
2609 |
|
|
2610 |
|
} |
2611 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2612 |
0 |
public void textColour_actionPerformed()... |
2613 |
|
{ |
2614 |
|
|
2615 |
|
} |
2616 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2617 |
0 |
public void idRightAlign_actionPerformed(ActionEvent e)... |
2618 |
|
{ |
2619 |
|
|
2620 |
|
} |
2621 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2622 |
0 |
public void expandViews_actionPerformed(ActionEvent e)... |
2623 |
|
{ |
2624 |
|
|
2625 |
|
} |
2626 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2627 |
0 |
public void gatherViews_actionPerformed(ActionEvent e)... |
2628 |
|
{ |
2629 |
|
|
2630 |
|
} |
2631 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2632 |
0 |
public void buildTreeSortMenu()... |
2633 |
|
{ |
2634 |
|
|
2635 |
|
} |
2636 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2637 |
0 |
public void pageSetup_actionPerformed(ActionEvent e)... |
2638 |
|
{ |
2639 |
|
|
2640 |
|
} |
2641 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2642 |
0 |
public void alignmentProperties()... |
2643 |
|
{ |
2644 |
|
|
2645 |
|
} |
2646 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2647 |
0 |
protected void expand_newalign(ActionEvent e)... |
2648 |
|
{ |
2649 |
|
|
2650 |
|
|
2651 |
|
} |
2652 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2653 |
241 |
protected boolean isShowAutoCalculatedAbove()... |
2654 |
|
{ |
2655 |
241 |
return showAutoCalculatedAbove; |
2656 |
|
} |
2657 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2658 |
241 |
protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)... |
2659 |
|
{ |
2660 |
241 |
this.showAutoCalculatedAbove = showAutoCalculatedAbove; |
2661 |
|
} |
2662 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2663 |
0 |
protected SequenceAnnotationOrder getAnnotationSortOrder()... |
2664 |
|
{ |
2665 |
0 |
return annotationSortOrder; |
2666 |
|
} |
2667 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2668 |
0 |
protected void setAnnotationSortOrder(... |
2669 |
|
SequenceAnnotationOrder annotationSortOrder) |
2670 |
|
{ |
2671 |
0 |
this.annotationSortOrder = annotationSortOrder; |
2672 |
|
} |
2673 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2674 |
33 |
public Map<KeyStroke, JMenuItem> getAccelerators()... |
2675 |
|
{ |
2676 |
33 |
return this.accelerators; |
2677 |
|
} |
2678 |
|
|
2679 |
|
|
2680 |
|
|
2681 |
|
|
2682 |
|
|
2683 |
|
@return |
2684 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2685 |
0 |
public int getTabIndex()... |
2686 |
|
{ |
2687 |
0 |
return tabbedPane.getSelectedIndex(); |
2688 |
|
} |
2689 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2690 |
0 |
public JPanel getStatusPanel()... |
2691 |
|
{ |
2692 |
0 |
return statusPanel; |
2693 |
|
} |
2694 |
|
|
2695 |
|
|
2696 |
|
|
2697 |
|
|
2698 |
|
|
2699 |
|
@param |
2700 |
|
|
|
|
| 83.3% |
Uncovered Elements: 1 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
2701 |
6 |
public void setSplitFrame(SplitContainerI sf)... |
2702 |
|
{ |
2703 |
6 |
this.splitFrame = sf; |
2704 |
6 |
if (sf != null) |
2705 |
|
{ |
2706 |
6 |
this.showComplementMenuItem.setVisible(true); |
2707 |
6 |
this.showComplementMenuItem.setState(true); |
2708 |
|
} |
2709 |
|
} |
2710 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2711 |
3 |
public SplitContainerI getSplitViewContainer()... |
2712 |
|
{ |
2713 |
3 |
return this.splitFrame; |
2714 |
|
} |
2715 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
2716 |
0 |
protected void showComplement_actionPerformed(boolean complement)... |
2717 |
|
{ |
2718 |
|
} |
2719 |
|
} |