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package jalview.gui; |
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import java.awt.BorderLayout; |
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import java.awt.Color; |
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import java.awt.event.ActionEvent; |
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import java.awt.event.ActionListener; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.BitSet; |
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import java.util.Collection; |
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import java.util.Collections; |
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import java.util.Hashtable; |
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import java.util.LinkedHashMap; |
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import java.util.List; |
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import java.util.Locale; |
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import java.util.Map; |
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import java.util.Objects; |
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import java.util.SortedMap; |
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import java.util.TreeMap; |
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import java.util.Vector; |
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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.JMenuItem; |
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import javax.swing.JPanel; |
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import javax.swing.JPopupMenu; |
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import javax.swing.JRadioButtonMenuItem; |
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import javax.swing.JScrollPane; |
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import jalview.analysis.AAFrequency; |
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import jalview.analysis.AlignmentAnnotationUtils; |
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import jalview.analysis.AlignmentUtils; |
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import jalview.analysis.Conservation; |
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import jalview.api.AlignCalcWorkerI; |
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import jalview.api.AlignViewportI; |
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import jalview.bin.Console; |
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import jalview.commands.ChangeCaseCommand; |
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import jalview.commands.EditCommand; |
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import jalview.commands.EditCommand.Action; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.MappedFeatures; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.ColourMenuHelper.ColourChangeListener; |
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import jalview.gui.JalviewColourChooser.ColourChooserListener; |
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import jalview.io.FileFormatI; |
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import jalview.io.FileFormats; |
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import jalview.io.FormatAdapter; |
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import jalview.io.SequenceAnnotationReport; |
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import jalview.schemes.Blosum62ColourScheme; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.schemes.ColourSchemes; |
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import jalview.schemes.PIDColourScheme; |
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import jalview.schemes.ResidueColourScheme; |
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import jalview.util.Comparison; |
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import jalview.util.GroupUrlLink; |
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import jalview.util.GroupUrlLink.UrlStringTooLongException; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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import jalview.util.StringUtils; |
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import jalview.util.UrlLink; |
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import jalview.viewmodel.seqfeatures.FeatureRendererModel; |
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import jalview.workers.SecondaryStructureConsensusThread; |
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| 43.6% |
Uncovered Elements: 620 (1,100) |
Complexity: 232 |
Complexity Density: 0.3 |
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public class PopupMenu extends JPopupMenu implements ColourChangeListener |
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{ |
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private static final int FEATURE_DESC_MAX = 40; |
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private final boolean forIdPanel; |
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private final AlignmentPanel ap; |
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private final SequenceI sequence; |
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JMenu groupMenu = new JMenu(); |
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JMenuItem groupName = new JMenuItem(); |
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protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); |
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protected JMenuItem modifyPID = new JMenuItem(); |
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protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); |
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protected JRadioButtonMenuItem annotationColour; |
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protected JMenuItem modifyConservation = new JMenuItem(); |
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protected JCheckBoxMenuItem byConsensusSecondaryStructureMenuItem = new JCheckBoxMenuItem(); |
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protected JMenuItem modifyConsensusSecondaryStructureThreshold = new JMenuItem(); |
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JMenu sequenceMenu = new JMenu(); |
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JMenuItem makeReferenceSeq = new JMenuItem(); |
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JMenuItem createGroupMenuItem = new JMenuItem(); |
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JMenuItem unGroupMenuItem = new JMenuItem(); |
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JMenu colourMenu = new JMenu(); |
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JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); |
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JCheckBoxMenuItem showText = new JCheckBoxMenuItem(); |
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JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem(); |
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JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem(); |
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JMenu editMenu = new JMenu(); |
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JMenuItem upperCase = new JMenuItem(); |
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JMenuItem lowerCase = new JMenuItem(); |
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JMenuItem toggle = new JMenuItem(); |
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JMenu outputMenu = new JMenu(); |
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JMenu seqShowAnnotationsMenu = new JMenu(); |
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JMenu seqHideAnnotationsMenu = new JMenu(); |
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JMenuItem seqAddReferenceAnnotations = new JMenuItem( |
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MessageManager.getString("label.add_reference_annotations")); |
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JMenu groupShowAnnotationsMenu = new JMenu(); |
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JMenu groupHideAnnotationsMenu = new JMenu(); |
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JMenuItem groupAddReferenceAnnotations = new JMenuItem( |
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MessageManager.getString("label.add_reference_annotations")); |
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JMenuItem textColour = new JMenuItem(); |
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JMenu editGroupMenu = new JMenu(); |
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JMenu groupShowAutoCalculatedAnnotations = new JMenu(); |
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JMenu groupHideAutoCalculatedAnnotations = new JMenu(); |
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JMenuItem chooseStructure = new JMenuItem(); |
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JMenu rnaStructureMenu = new JMenu(); |
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@param |
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@param |
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@return |
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| 81.2% |
Uncovered Elements: 6 (32) |
Complexity: 6 |
Complexity Density: 0.25 |
|
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protected static JMenu buildLinkMenu(final SequenceI seq,... |
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List<SequenceFeature> features) |
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{ |
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JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); |
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List<String> nlinks = null; |
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if (seq != null) |
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{ |
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nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); |
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UrlLink.sort(nlinks); |
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} |
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else |
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{ |
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nlinks = new ArrayList<>(); |
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} |
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if (features != null) |
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{ |
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for (SequenceFeature sf : features) |
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{ |
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if (sf.links != null) |
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{ |
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for (String link : sf.links) |
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{ |
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nlinks.add(link); |
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} |
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} |
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} |
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} |
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Map<String, List<String>> linkset = new LinkedHashMap<>(); |
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for (String link : nlinks) |
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{ |
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UrlLink urlLink = null; |
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try |
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urlLink = new UrlLink(link); |
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} catch (Exception foo) |
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{ |
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Console.error("Exception for URLLink '" + link + "'", foo); |
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continue; |
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} |
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if (!urlLink.isValid()) |
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{ |
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Console.error(urlLink.getInvalidMessage()); |
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continue; |
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} |
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urlLink.createLinksFromSeq(seq, linkset); |
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} |
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addUrlLinks(linkMenu, linkset.values()); |
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return linkMenu; |
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} |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
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static private void addUrlLinks(JMenu linkMenu,... |
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Collection<List<String>> linkset) |
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{ |
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for (List<String> linkstrset : linkset) |
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{ |
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final String url = linkstrset.get(3); |
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JMenuItem item = new JMenuItem(linkstrset.get(1)); |
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item.setToolTipText(MessageManager |
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.formatMessage("label.open_url_param", new Object[] |
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{ url })); |
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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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0 |
@Override... |
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public void actionPerformed(ActionEvent e) |
287 |
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{ |
288 |
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new Thread(new Runnable() |
289 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
290 |
0 |
@Override... |
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public void run() |
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{ |
293 |
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showLink(url); |
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} |
295 |
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}).start(); |
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} |
297 |
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}); |
298 |
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linkMenu.add(item); |
299 |
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} |
300 |
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} |
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303 |
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305 |
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306 |
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@param |
307 |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
308 |
0 |
static void showLink(String url)... |
309 |
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{ |
310 |
0 |
try |
311 |
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{ |
312 |
0 |
jalview.util.BrowserLauncher.openURL(url); |
313 |
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} catch (Exception ex) |
314 |
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{ |
315 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
316 |
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MessageManager.getString("label.web_browser_not_found_unix"), |
317 |
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MessageManager.getString("label.web_browser_not_found"), |
318 |
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JvOptionPane.WARNING_MESSAGE); |
319 |
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|
320 |
0 |
ex.printStackTrace(); |
321 |
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} |
322 |
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} |
323 |
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324 |
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325 |
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326 |
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|
327 |
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@param |
328 |
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@param |
329 |
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330 |
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@param |
331 |
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|
332 |
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@param |
333 |
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|
334 |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
335 |
0 |
static void addshowLink(JMenu linkMenu, String label,... |
336 |
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final GroupUrlLink urlgenerator, final Object[] urlstub) |
337 |
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{ |
338 |
0 |
JMenuItem item = new JMenuItem(label); |
339 |
0 |
item.setToolTipText(MessageManager |
340 |
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.formatMessage("label.open_url_seqs_param", new Object[] |
341 |
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{ urlgenerator.getUrl_prefix(), |
342 |
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urlgenerator.getNumberInvolved(urlstub) })); |
343 |
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|
344 |
0 |
item.addActionListener(new ActionListener() |
345 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
346 |
0 |
@Override... |
347 |
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public void actionPerformed(ActionEvent e) |
348 |
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{ |
349 |
0 |
new Thread(new Runnable() |
350 |
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{ |
351 |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 2 |
Complexity Density: 1 |
|
352 |
0 |
@Override... |
353 |
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public void run() |
354 |
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{ |
355 |
0 |
try |
356 |
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{ |
357 |
0 |
showLink(urlgenerator.constructFrom(urlstub)); |
358 |
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} catch (UrlStringTooLongException e2) |
359 |
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{ |
360 |
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} |
361 |
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} |
362 |
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|
363 |
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}).start(); |
364 |
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} |
365 |
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}); |
366 |
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|
367 |
0 |
linkMenu.add(item); |
368 |
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} |
369 |
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370 |
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371 |
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372 |
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|
373 |
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|
374 |
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@param |
375 |
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|
376 |
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@param |
377 |
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|
378 |
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@throws |
379 |
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|
380 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
381 |
0 |
public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)... |
382 |
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{ |
383 |
0 |
this(false, ap, seq, column, null); |
384 |
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} |
385 |
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|
386 |
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|
387 |
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388 |
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|
389 |
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@param |
390 |
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|
391 |
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@param |
392 |
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|
393 |
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@param |
394 |
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|
395 |
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@throws |
396 |
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|
397 |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
398 |
19 |
public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,... |
399 |
|
List<String> groupLinks) |
400 |
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{ |
401 |
19 |
this(true, alignPanel, seq, -1, groupLinks); |
402 |
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} |
403 |
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|
404 |
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|
405 |
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|
406 |
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|
407 |
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|
408 |
|
@param |
409 |
|
@param |
410 |
|
@param |
411 |
|
@param |
412 |
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|
413 |
|
@param |
414 |
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|
|
|
| 58.4% |
Uncovered Elements: 77 (185) |
Complexity: 39 |
Complexity Density: 0.31 |
|
415 |
19 |
private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel,... |
416 |
|
final SequenceI seq, final int column, List<String> groupLinks) |
417 |
|
{ |
418 |
19 |
Objects.requireNonNull(seq); |
419 |
19 |
this.forIdPanel = fromIdPanel; |
420 |
19 |
this.ap = alignPanel; |
421 |
19 |
sequence = seq; |
422 |
|
|
423 |
19 |
for (String ff : FileFormats.getInstance().getWritableFormats(true)) |
424 |
|
{ |
425 |
209 |
JMenuItem item = new JMenuItem(ff); |
426 |
|
|
427 |
209 |
item.addActionListener(new ActionListener() |
428 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
429 |
0 |
@Override... |
430 |
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public void actionPerformed(ActionEvent e) |
431 |
|
{ |
432 |
0 |
outputText_actionPerformed(e); |
433 |
|
} |
434 |
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}); |
435 |
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|
436 |
209 |
outputMenu.add(item); |
437 |
|
} |
438 |
|
|
439 |
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|
440 |
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|
441 |
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|
442 |
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|
443 |
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|
444 |
19 |
final List<SequenceI> selectedSequence = (forIdPanel && seq != null |
445 |
|
? Arrays.asList(seq) |
446 |
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: Collections.<SequenceI> emptyList()); |
447 |
19 |
buildAnnotationTypesMenus(seqShowAnnotationsMenu, |
448 |
|
seqHideAnnotationsMenu, selectedSequence); |
449 |
19 |
configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, |
450 |
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selectedSequence); |
451 |
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|
452 |
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|
453 |
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|
454 |
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|
455 |
19 |
final List<SequenceI> selectedGroup = (alignPanel.av |
456 |
|
.getSelectionGroup() == null |
457 |
|
? Collections.<SequenceI> emptyList() |
458 |
|
: alignPanel.av.getSelectionGroup().getSequences()); |
459 |
19 |
buildAnnotationTypesMenus(groupShowAnnotationsMenu, |
460 |
|
groupHideAnnotationsMenu, selectedGroup); |
461 |
19 |
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, |
462 |
|
selectedGroup); |
463 |
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|
464 |
|
|
465 |
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|
466 |
19 |
SequenceGroup selectedSequenceGroup = alignPanel.av.getSelectionGroup(); |
467 |
19 |
if (selectedSequenceGroup != null) |
468 |
|
{ |
469 |
3 |
buildAutoCalculatedAnnotationsMenu(groupShowAutoCalculatedAnnotations, |
470 |
|
groupHideAutoCalculatedAnnotations, selectedSequenceGroup); |
471 |
|
} |
472 |
|
|
473 |
19 |
try |
474 |
|
{ |
475 |
19 |
jbInit(); |
476 |
|
} catch (Exception e) |
477 |
|
{ |
478 |
0 |
e.printStackTrace(); |
479 |
|
} |
480 |
|
|
481 |
19 |
if (forIdPanel) |
482 |
|
{ |
483 |
19 |
JMenuItem menuItem; |
484 |
19 |
sequenceMenu.setText(sequence.getName()); |
485 |
19 |
if (seq == alignPanel.av.getAlignment().getSeqrep()) |
486 |
|
{ |
487 |
0 |
makeReferenceSeq.setText( |
488 |
|
MessageManager.getString("action.unmark_as_reference")); |
489 |
|
} |
490 |
|
else |
491 |
|
{ |
492 |
19 |
makeReferenceSeq.setText( |
493 |
|
MessageManager.getString("action.set_as_reference")); |
494 |
|
} |
495 |
|
|
496 |
19 |
if (!alignPanel.av.getAlignment().isNucleotide()) |
497 |
|
{ |
498 |
18 |
remove(rnaStructureMenu); |
499 |
|
} |
500 |
|
else |
501 |
|
{ |
502 |
1 |
int origCount = rnaStructureMenu.getItemCount(); |
503 |
|
|
504 |
|
|
505 |
|
|
506 |
|
|
507 |
1 |
AlignmentAnnotation[] aas = alignPanel.av.getAlignment() |
508 |
|
.getAlignmentAnnotation(); |
509 |
1 |
if (aas != null) |
510 |
|
{ |
511 |
1 |
for (final AlignmentAnnotation aa : aas) |
512 |
|
{ |
513 |
2 |
if (aa.isValidStruc() && aa.sequenceRef == null) |
514 |
|
{ |
515 |
|
|
516 |
|
|
517 |
|
|
518 |
0 |
menuItem = new JMenuItem(); |
519 |
0 |
menuItem.setText(MessageManager.formatMessage( |
520 |
|
"label.2d_rna_structure_line", new Object[] |
521 |
|
{ aa.label })); |
522 |
0 |
menuItem.addActionListener(new ActionListener() |
523 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
524 |
0 |
@Override... |
525 |
|
public void actionPerformed(ActionEvent e) |
526 |
|
{ |
527 |
0 |
new AppVarna(seq, aa, alignPanel); |
528 |
|
} |
529 |
|
}); |
530 |
0 |
rnaStructureMenu.add(menuItem); |
531 |
|
} |
532 |
|
} |
533 |
|
} |
534 |
|
|
535 |
1 |
if (seq.getAnnotation() != null) |
536 |
|
{ |
537 |
0 |
AlignmentAnnotation seqAnns[] = seq.getAnnotation(); |
538 |
0 |
for (final AlignmentAnnotation aa : seqAnns) |
539 |
|
{ |
540 |
0 |
if (aa.isValidStruc()) |
541 |
|
{ |
542 |
|
|
543 |
|
|
544 |
|
|
545 |
|
|
546 |
0 |
menuItem = new JMenuItem(); |
547 |
0 |
menuItem.setText(MessageManager.formatMessage( |
548 |
|
"label.2d_rna_sequence_name", new Object[] |
549 |
|
{ seq.getName() })); |
550 |
0 |
menuItem.addActionListener(new ActionListener() |
551 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
552 |
0 |
@Override... |
553 |
|
public void actionPerformed(ActionEvent e) |
554 |
|
{ |
555 |
|
|
556 |
0 |
new AppVarna(seq, aa, alignPanel); |
557 |
|
} |
558 |
|
}); |
559 |
0 |
rnaStructureMenu.add(menuItem); |
560 |
|
} |
561 |
|
} |
562 |
|
} |
563 |
1 |
if (rnaStructureMenu.getItemCount() == origCount) |
564 |
|
{ |
565 |
1 |
remove(rnaStructureMenu); |
566 |
|
} |
567 |
|
} |
568 |
|
|
569 |
19 |
menuItem = new JMenuItem( |
570 |
|
MessageManager.getString("action.hide_sequences")); |
571 |
19 |
menuItem.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 |
hideSequences(false); |
577 |
|
} |
578 |
|
}); |
579 |
19 |
add(menuItem); |
580 |
|
|
581 |
19 |
if (alignPanel.av.getSelectionGroup() != null |
582 |
|
&& alignPanel.av.getSelectionGroup().getSize() > 1) |
583 |
|
{ |
584 |
1 |
menuItem = new JMenuItem(MessageManager |
585 |
|
.formatMessage("label.represent_group_with", new Object[] |
586 |
|
{ seq.getName() })); |
587 |
1 |
menuItem.addActionListener(new ActionListener() |
588 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
589 |
0 |
@Override... |
590 |
|
public void actionPerformed(ActionEvent e) |
591 |
|
{ |
592 |
0 |
hideSequences(true); |
593 |
|
} |
594 |
|
}); |
595 |
1 |
sequenceMenu.add(menuItem); |
596 |
|
} |
597 |
|
|
598 |
19 |
if (alignPanel.av.hasHiddenRows()) |
599 |
|
{ |
600 |
0 |
final int index = alignPanel.av.getAlignment().findIndex(seq); |
601 |
|
|
602 |
0 |
if (alignPanel.av.adjustForHiddenSeqs(index) |
603 |
|
- alignPanel.av.adjustForHiddenSeqs(index - 1) > 1) |
604 |
|
{ |
605 |
0 |
menuItem = new JMenuItem( |
606 |
|
MessageManager.getString("action.reveal_sequences")); |
607 |
0 |
menuItem.addActionListener(new ActionListener() |
608 |
|
{ |
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
609 |
0 |
@Override... |
610 |
|
public void actionPerformed(ActionEvent e) |
611 |
|
{ |
612 |
0 |
alignPanel.av.showSequence(index); |
613 |
0 |
if (alignPanel.overviewPanel != null) |
614 |
|
{ |
615 |
0 |
alignPanel.overviewPanel.updateOverviewImage(); |
616 |
|
} |
617 |
|
} |
618 |
|
}); |
619 |
0 |
add(menuItem); |
620 |
|
} |
621 |
|
} |
622 |
|
} |
623 |
|
|
624 |
|
|
625 |
|
|
626 |
|
|
627 |
|
|
628 |
|
|
629 |
19 |
if (alignPanel.av.hasHiddenRows()) |
630 |
|
{ |
631 |
0 |
boolean addOption = seq != null; |
632 |
0 |
if (!addOption && alignPanel.av.getAlignment().getHeight() == 0) |
633 |
|
{ |
634 |
0 |
addOption = true; |
635 |
|
} |
636 |
0 |
if (addOption) |
637 |
|
{ |
638 |
0 |
JMenuItem menuItem = new JMenuItem( |
639 |
|
MessageManager.getString("action.reveal_all")); |
640 |
0 |
menuItem.addActionListener(new ActionListener() |
641 |
|
{ |
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
642 |
0 |
@Override... |
643 |
|
public void actionPerformed(ActionEvent e) |
644 |
|
{ |
645 |
0 |
alignPanel.av.showAllHiddenSeqs(); |
646 |
0 |
if (alignPanel.overviewPanel != null) |
647 |
|
{ |
648 |
0 |
alignPanel.overviewPanel.updateOverviewImage(); |
649 |
|
} |
650 |
|
} |
651 |
|
}); |
652 |
0 |
add(menuItem); |
653 |
|
} |
654 |
|
} |
655 |
|
|
656 |
19 |
SequenceGroup sg = alignPanel.av.getSelectionGroup(); |
657 |
19 |
boolean isDefinedGroup = (sg != null) |
658 |
|
? alignPanel.av.getAlignment().getGroups().contains(sg) |
659 |
|
: false; |
660 |
|
|
661 |
19 |
if (sg != null && sg.getSize() > 0) |
662 |
|
{ |
663 |
3 |
groupName.setText(MessageManager |
664 |
|
.getString("label.edit_name_and_description_current_group")); |
665 |
|
|
666 |
3 |
ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme()); |
667 |
|
|
668 |
3 |
conservationMenuItem.setEnabled(!sg.isNucleotide()); |
669 |
|
|
670 |
3 |
byConsensusSecondaryStructureMenuItem.setEnabled(!sg.isNucleotide()); |
671 |
|
|
672 |
3 |
if (sg.cs != null) |
673 |
|
{ |
674 |
3 |
if (sg.cs.conservationApplied()) |
675 |
|
{ |
676 |
0 |
conservationMenuItem.setSelected(true); |
677 |
|
} |
678 |
3 |
if (sg.cs.getThreshold() > 0) |
679 |
|
{ |
680 |
0 |
abovePIDColour.setSelected(true); |
681 |
|
} |
682 |
3 |
if (sg.cs.isConsensusSecondaryStructureColouring()) |
683 |
|
{ |
684 |
0 |
byConsensusSecondaryStructureMenuItem.setSelected(true); |
685 |
|
} |
686 |
|
} |
687 |
3 |
modifyConservation.setEnabled(conservationMenuItem.isSelected()); |
688 |
3 |
modifyPID.setEnabled(abovePIDColour.isSelected()); |
689 |
3 |
modifyConsensusSecondaryStructureThreshold.setEnabled( |
690 |
|
byConsensusSecondaryStructureMenuItem.isSelected()); |
691 |
3 |
displayNonconserved.setSelected(sg.getShowNonconserved()); |
692 |
3 |
showText.setSelected(sg.getDisplayText()); |
693 |
3 |
showColourText.setSelected(sg.getColourText()); |
694 |
3 |
showBoxes.setSelected(sg.getDisplayBoxes()); |
695 |
|
|
696 |
3 |
if (groupLinks != null && groupLinks.size() > 0) |
697 |
|
{ |
698 |
0 |
buildGroupURLMenu(sg, groupLinks); |
699 |
|
} |
700 |
|
|
701 |
3 |
Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), |
702 |
|
reppdb = new Hashtable<>(); |
703 |
|
|
704 |
3 |
SequenceI sqass = null; |
705 |
3 |
for (SequenceI sq : alignPanel.av.getSequenceSelection()) |
706 |
|
{ |
707 |
4 |
Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries(); |
708 |
4 |
if (pes != null && pes.size() > 0) |
709 |
|
{ |
710 |
0 |
reppdb.put(pes.get(0).getId(), pes.get(0)); |
711 |
0 |
for (PDBEntry pe : pes) |
712 |
|
{ |
713 |
0 |
pdbe.put(pe.getId(), pe); |
714 |
0 |
if (sqass == null) |
715 |
|
{ |
716 |
0 |
sqass = sq; |
717 |
|
} |
718 |
|
} |
719 |
|
} |
720 |
|
} |
721 |
3 |
if (pdbe.size() > 0) |
722 |
|
{ |
723 |
0 |
final PDBEntry[] pe = pdbe.values() |
724 |
|
.toArray(new PDBEntry[pdbe.size()]), |
725 |
|
pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]); |
726 |
0 |
final JMenuItem gpdbview, rpdbview; |
727 |
|
} |
728 |
|
} |
729 |
|
else |
730 |
|
{ |
731 |
16 |
groupMenu.setVisible(false); |
732 |
16 |
editMenu.setVisible(false); |
733 |
|
} |
734 |
|
|
735 |
19 |
if (!isDefinedGroup) |
736 |
|
{ |
737 |
19 |
createGroupMenuItem.setVisible(true); |
738 |
19 |
unGroupMenuItem.setVisible(false); |
739 |
19 |
editGroupMenu |
740 |
|
.setText(MessageManager.getString("action.edit_new_group")); |
741 |
|
|
742 |
|
|
743 |
|
|
744 |
|
|
745 |
19 |
groupShowAutoCalculatedAnnotations.setVisible(false); |
746 |
19 |
groupHideAutoCalculatedAnnotations.setVisible(false); |
747 |
|
} |
748 |
|
else |
749 |
|
{ |
750 |
0 |
createGroupMenuItem.setVisible(false); |
751 |
0 |
unGroupMenuItem.setVisible(true); |
752 |
0 |
editGroupMenu.setText(MessageManager.getString("action.edit_group")); |
753 |
|
|
754 |
|
|
755 |
|
|
756 |
|
|
757 |
|
|
758 |
0 |
if (alignPanel.av.isShowGroupSSConsensus()) |
759 |
|
{ |
760 |
0 |
groupShowAutoCalculatedAnnotations.setVisible(true); |
761 |
0 |
groupHideAutoCalculatedAnnotations.setVisible(true); |
762 |
|
} |
763 |
|
else |
764 |
|
{ |
765 |
0 |
groupShowAutoCalculatedAnnotations.setVisible(false); |
766 |
0 |
groupHideAutoCalculatedAnnotations.setVisible(false); |
767 |
|
} |
768 |
|
} |
769 |
|
|
770 |
19 |
if (!forIdPanel) |
771 |
|
{ |
772 |
0 |
sequenceMenu.setVisible(false); |
773 |
0 |
chooseStructure.setVisible(false); |
774 |
0 |
rnaStructureMenu.setVisible(false); |
775 |
|
} |
776 |
|
|
777 |
19 |
addLinksAndFeatures(seq, column); |
778 |
|
} |
779 |
|
|
780 |
|
|
781 |
|
|
782 |
|
|
783 |
|
|
784 |
|
|
785 |
|
|
786 |
|
|
787 |
|
|
788 |
|
|
789 |
|
|
790 |
|
|
791 |
|
@param |
792 |
|
@param |
793 |
|
|
|
|
| 63.6% |
Uncovered Elements: 4 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
794 |
19 |
void addLinksAndFeatures(final SequenceI seq, final int column)... |
795 |
|
{ |
796 |
19 |
List<SequenceFeature> features = null; |
797 |
19 |
if (forIdPanel) |
798 |
|
{ |
799 |
19 |
features = sequence.getFeatures().getNonPositionalFeatures(); |
800 |
|
} |
801 |
|
else |
802 |
|
{ |
803 |
0 |
features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence, |
804 |
|
column + 1); |
805 |
|
} |
806 |
|
|
807 |
19 |
addLinks(seq, features); |
808 |
|
|
809 |
19 |
if (!forIdPanel) |
810 |
|
{ |
811 |
0 |
addFeatureDetails(features, seq, column); |
812 |
|
} |
813 |
|
} |
814 |
|
|
815 |
|
|
816 |
|
|
817 |
|
|
818 |
|
|
819 |
|
|
820 |
|
@param |
821 |
|
@param |
822 |
|
@param |
823 |
|
|
|
|
| 53.8% |
Uncovered Elements: 12 (26) |
Complexity: 6 |
Complexity Density: 0.33 |
|
824 |
3 |
protected void addFeatureDetails(List<SequenceFeature> features,... |
825 |
|
final SequenceI seq, final int column) |
826 |
|
{ |
827 |
|
|
828 |
|
|
829 |
|
|
830 |
|
|
831 |
3 |
MappedFeatures mf = null; |
832 |
3 |
if (ap.av.isShowComplementFeatures()) |
833 |
|
{ |
834 |
0 |
if (!Comparison.isGap(sequence.getCharAt(column))) |
835 |
|
{ |
836 |
0 |
AlignViewportI complement = ap.getAlignViewport() |
837 |
|
.getCodingComplement(); |
838 |
0 |
AlignFrame af = Desktop.getAlignFrameFor(complement); |
839 |
0 |
FeatureRendererModel fr2 = af.getFeatureRenderer(); |
840 |
0 |
int seqPos = sequence.findPosition(column); |
841 |
0 |
mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos); |
842 |
|
} |
843 |
|
} |
844 |
|
|
845 |
3 |
if (features.isEmpty() && mf == null) |
846 |
|
{ |
847 |
|
|
848 |
|
|
849 |
|
|
850 |
1 |
return; |
851 |
|
} |
852 |
|
|
853 |
2 |
JMenu details = new JMenu( |
854 |
|
MessageManager.getString("label.feature_details")); |
855 |
2 |
add(details); |
856 |
|
|
857 |
2 |
String name = seq.getName(); |
858 |
2 |
for (final SequenceFeature sf : features) |
859 |
|
{ |
860 |
4 |
addFeatureDetailsMenuItem(details, name, sf, null); |
861 |
|
} |
862 |
|
|
863 |
2 |
if (mf != null) |
864 |
|
{ |
865 |
0 |
for (final SequenceFeature sf : mf.features) |
866 |
|
{ |
867 |
0 |
addFeatureDetailsMenuItem(details, name, sf, mf); |
868 |
|
} |
869 |
|
} |
870 |
|
} |
871 |
|
|
872 |
|
|
873 |
|
|
874 |
|
|
875 |
|
|
876 |
|
|
877 |
|
@param |
878 |
|
@param |
879 |
|
@param |
880 |
|
@param |
881 |
|
|
|
|
| 76.2% |
Uncovered Elements: 10 (42) |
Complexity: 9 |
Complexity Density: 0.32 |
|
882 |
4 |
void addFeatureDetailsMenuItem(JMenu details, final String seqName,... |
883 |
|
final SequenceFeature sf, MappedFeatures mf) |
884 |
|
{ |
885 |
4 |
int start = sf.getBegin(); |
886 |
4 |
int end = sf.getEnd(); |
887 |
4 |
if (mf != null) |
888 |
|
{ |
889 |
|
|
890 |
|
|
891 |
|
|
892 |
0 |
int[] localRange = mf.getMappedPositions(start, end); |
893 |
0 |
if (localRange == null) |
894 |
|
{ |
895 |
|
|
896 |
0 |
return; |
897 |
|
} |
898 |
0 |
start = localRange[0]; |
899 |
0 |
end = localRange[localRange.length - 1]; |
900 |
|
} |
901 |
4 |
StringBuilder desc = new StringBuilder(); |
902 |
4 |
desc.append(sf.getType()).append(" ").append(String.valueOf(start)); |
903 |
4 |
if (start != end) |
904 |
|
{ |
905 |
2 |
desc.append(sf.isContactFeature() ? ":" : "-"); |
906 |
2 |
desc.append(String.valueOf(end)); |
907 |
|
} |
908 |
4 |
String description = sf.getDescription(); |
909 |
4 |
if (description != null) |
910 |
|
{ |
911 |
4 |
desc.append(" "); |
912 |
4 |
description = StringUtils.stripHtmlTags(description); |
913 |
|
|
914 |
|
|
915 |
|
|
916 |
|
|
917 |
|
|
918 |
4 |
boolean hasLink = description.indexOf("a href") > -1; |
919 |
4 |
if (description.length() > FEATURE_DESC_MAX && !hasLink) |
920 |
|
{ |
921 |
1 |
description = description.substring(0, FEATURE_DESC_MAX) + "..."; |
922 |
|
} |
923 |
4 |
desc.append(description); |
924 |
|
} |
925 |
4 |
String featureGroup = sf.getFeatureGroup(); |
926 |
4 |
if (featureGroup != null) |
927 |
|
{ |
928 |
2 |
desc.append(" (").append(featureGroup).append(")"); |
929 |
|
} |
930 |
4 |
String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString()); |
931 |
4 |
JMenuItem item = new JMenuItem(htmlText); |
932 |
4 |
item.addActionListener(new ActionListener() |
933 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
934 |
0 |
@Override... |
935 |
|
public void actionPerformed(ActionEvent e) |
936 |
|
{ |
937 |
0 |
showFeatureDetails(sf, seqName, mf); |
938 |
|
} |
939 |
|
}); |
940 |
4 |
details.add(item); |
941 |
|
} |
942 |
|
|
943 |
|
|
944 |
|
|
945 |
|
|
946 |
|
@param |
947 |
|
@param |
948 |
|
@param |
949 |
|
|
|
|
| 0% |
Uncovered Elements: 21 (21) |
Complexity: 2 |
Complexity Density: 0.11 |
|
950 |
0 |
protected void showFeatureDetails(SequenceFeature sf, String seqName,... |
951 |
|
MappedFeatures mf) |
952 |
|
{ |
953 |
0 |
JInternalFrame details; |
954 |
0 |
if (Platform.isJS()) |
955 |
|
{ |
956 |
0 |
details = new JInternalFrame(); |
957 |
0 |
details.setFrameIcon(null); |
958 |
0 |
JPanel panel = new JPanel(new BorderLayout()); |
959 |
0 |
panel.setOpaque(true); |
960 |
0 |
panel.setBackground(Color.white); |
961 |
|
|
962 |
0 |
JLabel reprt = new JLabel(MessageManager |
963 |
|
.formatMessage("label.html_content", new Object[] |
964 |
|
{ sf.getDetailsReport(seqName, mf) })); |
965 |
0 |
reprt.setBackground(Color.WHITE); |
966 |
0 |
reprt.setOpaque(true); |
967 |
0 |
panel.add(reprt, BorderLayout.CENTER); |
968 |
0 |
details.setContentPane(panel); |
969 |
0 |
details.pack(); |
970 |
|
} |
971 |
|
else |
972 |
|
|
973 |
|
|
974 |
|
|
975 |
|
|
976 |
|
|
977 |
|
{ |
978 |
0 |
CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); |
979 |
|
|
980 |
0 |
cap.addStylesheetRule("table { border-collapse: collapse;}"); |
981 |
0 |
cap.addStylesheetRule("table, td, th {border: 1px solid black;}"); |
982 |
0 |
cap.setText(sf.getDetailsReport(seqName, mf)); |
983 |
0 |
details = cap; |
984 |
|
} |
985 |
0 |
Desktop.addInternalFrame(details, |
986 |
|
MessageManager.getString("label.feature_details"), 500, 500); |
987 |
|
} |
988 |
|
|
989 |
|
|
990 |
|
|
991 |
|
|
992 |
|
|
993 |
|
|
994 |
|
|
995 |
|
|
996 |
|
@param |
997 |
|
@param |
998 |
|
|
|
|
| 63.6% |
Uncovered Elements: 4 (11) |
Complexity: 4 |
Complexity Density: 0.8 |
|
999 |
19 |
void addLinks(final SequenceI seq, List<SequenceFeature> features)... |
1000 |
|
{ |
1001 |
19 |
JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features); |
1002 |
|
|
1003 |
|
|
1004 |
19 |
if (linkMenu.getItemCount() > 0) |
1005 |
|
{ |
1006 |
19 |
if (forIdPanel) |
1007 |
|
{ |
1008 |
19 |
sequenceMenu.add(linkMenu); |
1009 |
|
} |
1010 |
|
else |
1011 |
|
{ |
1012 |
0 |
add(linkMenu); |
1013 |
|
} |
1014 |
|
} |
1015 |
|
} |
1016 |
|
|
1017 |
|
|
1018 |
|
|
1019 |
|
|
1020 |
|
|
1021 |
|
|
1022 |
|
|
1023 |
|
|
1024 |
|
|
1025 |
|
|
1026 |
|
|
1027 |
|
|
1028 |
|
|
1029 |
|
|
1030 |
|
@param |
1031 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
|
1032 |
41 |
protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,... |
1033 |
|
List<SequenceI> forSequences) |
1034 |
|
{ |
1035 |
41 |
showMenu.removeAll(); |
1036 |
41 |
hideMenu.removeAll(); |
1037 |
|
|
1038 |
41 |
final List<String> all = Arrays |
1039 |
|
.asList(new String[] |
1040 |
|
{ MessageManager.getString("label.all") }); |
1041 |
41 |
addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, |
1042 |
|
true); |
1043 |
41 |
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, |
1044 |
|
false); |
1045 |
41 |
showMenu.addSeparator(); |
1046 |
41 |
hideMenu.addSeparator(); |
1047 |
|
|
1048 |
41 |
final AlignmentAnnotation[] annotations = ap.getAlignment() |
1049 |
|
.getAlignmentAnnotation(); |
1050 |
|
|
1051 |
|
|
1052 |
|
|
1053 |
|
|
1054 |
|
|
1055 |
|
|
1056 |
|
|
1057 |
41 |
Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>(); |
1058 |
41 |
Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>(); |
1059 |
41 |
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, |
1060 |
|
AlignmentAnnotationUtils.asList(annotations), forSequences); |
1061 |
|
|
1062 |
41 |
for (String calcId : hiddenTypes.keySet()) |
1063 |
|
{ |
1064 |
4 |
for (List<String> type : hiddenTypes.get(calcId)) |
1065 |
|
{ |
1066 |
4 |
addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type, |
1067 |
|
false, true); |
1068 |
|
} |
1069 |
|
} |
1070 |
|
|
1071 |
41 |
showMenu.setEnabled(!hiddenTypes.isEmpty()); |
1072 |
|
|
1073 |
41 |
for (String calcId : shownTypes.keySet()) |
1074 |
|
{ |
1075 |
2 |
for (List<String> type : shownTypes.get(calcId)) |
1076 |
|
{ |
1077 |
4 |
addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type, |
1078 |
|
false, false); |
1079 |
|
} |
1080 |
|
} |
1081 |
|
|
1082 |
41 |
hideMenu.setEnabled(!shownTypes.isEmpty()); |
1083 |
|
} |
1084 |
|
|
1085 |
|
|
1086 |
|
|
1087 |
|
|
1088 |
|
|
1089 |
|
|
1090 |
|
|
1091 |
|
@param |
1092 |
|
|
1093 |
|
@param |
1094 |
|
|
1095 |
|
@param |
1096 |
|
|
1097 |
|
|
|
|
| 88.2% |
Uncovered Elements: 2 (17) |
Complexity: 1 |
Complexity Density: 0.06 |
|
1098 |
3 |
protected void buildAutoCalculatedAnnotationsMenu(... |
1099 |
|
JMenu groupShowAutoCalculatedAnnotations, |
1100 |
|
JMenu groupHideAutoCalculatedAnnotations, |
1101 |
|
SequenceGroup selectedSequenceGroup) |
1102 |
|
{ |
1103 |
|
|
1104 |
|
|
1105 |
3 |
groupShowAutoCalculatedAnnotations.removeAll(); |
1106 |
3 |
groupHideAutoCalculatedAnnotations.removeAll(); |
1107 |
|
|
1108 |
|
|
1109 |
3 |
final String all = MessageManager.getString("label.all"); |
1110 |
3 |
addAutoCalculatedAnnotationTypeToShowHide( |
1111 |
|
groupShowAutoCalculatedAnnotations, selectedSequenceGroup, all, |
1112 |
|
true, true); |
1113 |
3 |
addAutoCalculatedAnnotationTypeToShowHide( |
1114 |
|
groupHideAutoCalculatedAnnotations, selectedSequenceGroup, all, |
1115 |
|
true, false); |
1116 |
|
|
1117 |
|
|
1118 |
3 |
groupShowAutoCalculatedAnnotations.addSeparator(); |
1119 |
3 |
groupHideAutoCalculatedAnnotations.addSeparator(); |
1120 |
|
|
1121 |
|
|
1122 |
3 |
final AlignmentAnnotation[] annotations = ap.getAlignment() |
1123 |
|
.getAlignmentAnnotation(); |
1124 |
|
|
1125 |
|
|
1126 |
3 |
List<String> shownTypes = new ArrayList<>(); |
1127 |
3 |
List<String> hiddenTypes = new ArrayList<>(); |
1128 |
|
|
1129 |
|
|
1130 |
|
|
1131 |
3 |
AlignmentAnnotationUtils |
1132 |
|
.getShownHiddenSecondaryStructureProvidersForGroup(shownTypes, |
1133 |
|
hiddenTypes, |
1134 |
|
AlignmentAnnotationUtils.asList(annotations), |
1135 |
|
selectedSequenceGroup); |
1136 |
|
|
1137 |
|
|
1138 |
|
|
1139 |
|
|
1140 |
|
|
1141 |
|
|
1142 |
3 |
for (String shownType : shownTypes) |
1143 |
|
{ |
1144 |
0 |
addAutoCalculatedAnnotationTypeToShowHide( |
1145 |
|
groupHideAutoCalculatedAnnotations, selectedSequenceGroup, |
1146 |
|
shownType, false, false); |
1147 |
|
} |
1148 |
|
|
1149 |
|
|
1150 |
3 |
for (String hiddenType : hiddenTypes) |
1151 |
|
{ |
1152 |
0 |
addAutoCalculatedAnnotationTypeToShowHide( |
1153 |
|
groupShowAutoCalculatedAnnotations, selectedSequenceGroup, |
1154 |
|
hiddenType, false, true); |
1155 |
|
} |
1156 |
|
|
1157 |
|
|
1158 |
|
|
1159 |
3 |
groupShowAutoCalculatedAnnotations.setEnabled(!hiddenTypes.isEmpty()); |
1160 |
3 |
groupHideAutoCalculatedAnnotations.setEnabled(!shownTypes.isEmpty()); |
1161 |
|
} |
1162 |
|
|
1163 |
|
|
1164 |
|
|
1165 |
|
|
1166 |
|
|
1167 |
|
@param |
1168 |
|
|
1169 |
|
@param |
1170 |
|
|
1171 |
|
|
1172 |
|
@param |
1173 |
|
|
1174 |
|
@param |
1175 |
|
|
1176 |
|
|
1177 |
|
@param |
1178 |
|
|
1179 |
|
|
1180 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
1181 |
6 |
protected void addAutoCalculatedAnnotationTypeToShowHide(... |
1182 |
|
JMenu showOrHideAutoCalculatedAnnotationsMenu, |
1183 |
|
final SequenceGroup selectedSequenceGroup, final String type, |
1184 |
|
final boolean allTypes, final boolean actionIsShow) |
1185 |
|
{ |
1186 |
|
|
1187 |
|
|
1188 |
6 |
final JMenuItem item = new JMenuItem(type); |
1189 |
|
|
1190 |
|
|
1191 |
6 |
item.addActionListener(new ActionListener() |
1192 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1193 |
0 |
@Override... |
1194 |
|
public void actionPerformed(ActionEvent e) |
1195 |
|
{ |
1196 |
|
|
1197 |
0 |
AlignmentUtils.showOrHideAutoCalculatedAnnotationsForGroup( |
1198 |
|
ap.getAlignment(), type, selectedSequenceGroup, allTypes, |
1199 |
|
actionIsShow); |
1200 |
|
|
1201 |
0 |
refresh(); |
1202 |
|
} |
1203 |
|
}); |
1204 |
|
|
1205 |
|
|
1206 |
6 |
showOrHideAutoCalculatedAnnotationsMenu.add(item); |
1207 |
|
} |
1208 |
|
|
1209 |
|
|
1210 |
|
|
1211 |
|
|
1212 |
|
|
1213 |
|
@param |
1214 |
|
@return |
1215 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 4 |
Complexity Density: 0.67 |
|
1216 |
0 |
protected List<SequenceI> getSequenceScope(SequenceI seq)... |
1217 |
|
{ |
1218 |
0 |
List<SequenceI> forSequences = null; |
1219 |
0 |
final SequenceGroup selectionGroup = ap.av.getSelectionGroup(); |
1220 |
0 |
if (selectionGroup != null && selectionGroup.getSize() > 0) |
1221 |
|
{ |
1222 |
0 |
forSequences = selectionGroup.getSequences(); |
1223 |
|
} |
1224 |
|
else |
1225 |
|
{ |
1226 |
0 |
forSequences = seq == null ? Collections.<SequenceI> emptyList() |
1227 |
|
: Arrays.asList(seq); |
1228 |
|
} |
1229 |
0 |
return forSequences; |
1230 |
|
} |
1231 |
|
|
1232 |
|
|
1233 |
|
|
1234 |
|
|
1235 |
|
|
1236 |
|
@param |
1237 |
|
|
1238 |
|
@param |
1239 |
|
|
1240 |
|
@param |
1241 |
|
@param |
1242 |
|
|
1243 |
|
@param |
1244 |
|
|
1245 |
|
@param |
1246 |
|
|
1247 |
|
|
1248 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
1249 |
90 |
protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,... |
1250 |
|
final List<SequenceI> forSequences, String calcId, |
1251 |
|
final List<String> types, final boolean allTypes, |
1252 |
|
final boolean actionIsShow) |
1253 |
|
{ |
1254 |
90 |
String label = types.toString(); |
1255 |
90 |
label = label.substring(1, label.length() - 1); |
1256 |
90 |
final JMenuItem item = new JMenuItem(label); |
1257 |
90 |
item.setToolTipText(calcId); |
1258 |
90 |
item.addActionListener(new ActionListener() |
1259 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1260 |
0 |
@Override... |
1261 |
|
public void actionPerformed(ActionEvent e) |
1262 |
|
{ |
1263 |
0 |
AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), |
1264 |
|
types, forSequences, allTypes, actionIsShow); |
1265 |
0 |
refresh(); |
1266 |
|
} |
1267 |
|
}); |
1268 |
90 |
showOrHideMenu.add(item); |
1269 |
|
} |
1270 |
|
|
|
|
| 0% |
Uncovered Elements: 100 (100) |
Complexity: 23 |
Complexity Density: 0.35 |
|
1271 |
0 |
private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)... |
1272 |
|
{ |
1273 |
|
|
1274 |
|
|
1275 |
|
|
1276 |
|
|
1277 |
|
|
1278 |
0 |
JMenu groupLinksMenu = new JMenu( |
1279 |
|
MessageManager.getString("action.group_link")); |
1280 |
|
|
1281 |
0 |
JMenu[] linkMenus = new JMenu[] { null, |
1282 |
|
new JMenu(MessageManager.getString("action.ids")), |
1283 |
|
new JMenu(MessageManager.getString("action.sequences")), |
1284 |
|
new JMenu(MessageManager.getString("action.ids_sequences")) }; |
1285 |
|
|
1286 |
0 |
SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); |
1287 |
0 |
String[][] idandseqs = GroupUrlLink.formStrings(seqs); |
1288 |
0 |
Hashtable<String, Object[]> commonDbrefs = new Hashtable<>(); |
1289 |
0 |
for (int sq = 0; sq < seqs.length; sq++) |
1290 |
|
{ |
1291 |
|
|
1292 |
0 |
int start = seqs[sq].findPosition(sg.getStartRes()), |
1293 |
|
end = seqs[sq].findPosition(sg.getEndRes()); |
1294 |
|
|
1295 |
|
|
1296 |
|
|
1297 |
0 |
SequenceI sqi = seqs[sq]; |
1298 |
0 |
while (sqi.getDatasetSequence() != null) |
1299 |
|
{ |
1300 |
0 |
sqi = sqi.getDatasetSequence(); |
1301 |
|
} |
1302 |
0 |
List<DBRefEntry> dbr = sqi.getDBRefs(); |
1303 |
0 |
int nd; |
1304 |
0 |
if (dbr != null && (nd = dbr.size()) > 0) |
1305 |
|
{ |
1306 |
0 |
for (int d = 0; d < nd; d++) |
1307 |
|
{ |
1308 |
0 |
DBRefEntry e = dbr.get(d); |
1309 |
0 |
String src = e.getSource(); |
1310 |
0 |
Object[] sarray = commonDbrefs.get(src); |
1311 |
0 |
if (sarray == null) |
1312 |
|
{ |
1313 |
0 |
sarray = new Object[2]; |
1314 |
0 |
sarray[0] = new int[] { 0 }; |
1315 |
0 |
sarray[1] = new String[seqs.length]; |
1316 |
|
|
1317 |
0 |
commonDbrefs.put(src, sarray); |
1318 |
|
} |
1319 |
|
|
1320 |
0 |
if (((String[]) sarray[1])[sq] == null) |
1321 |
|
{ |
1322 |
0 |
if (!e.hasMap() |
1323 |
|
|| (e.getMap().locateMappedRange(start, end) != null)) |
1324 |
|
{ |
1325 |
0 |
((String[]) sarray[1])[sq] = e.getAccessionId(); |
1326 |
0 |
((int[]) sarray[0])[0]++; |
1327 |
|
} |
1328 |
|
} |
1329 |
|
} |
1330 |
|
} |
1331 |
|
} |
1332 |
|
|
1333 |
0 |
boolean addMenu = false; |
1334 |
|
|
1335 |
0 |
for (String link : groupLinks) |
1336 |
|
{ |
1337 |
0 |
GroupUrlLink urlLink = null; |
1338 |
0 |
try |
1339 |
|
{ |
1340 |
0 |
urlLink = new GroupUrlLink(link); |
1341 |
|
} catch (Exception foo) |
1342 |
|
{ |
1343 |
0 |
Console.error("Exception for GroupURLLink '" + link + "'", foo); |
1344 |
0 |
continue; |
1345 |
|
} |
1346 |
0 |
if (!urlLink.isValid()) |
1347 |
|
{ |
1348 |
0 |
Console.error(urlLink.getInvalidMessage()); |
1349 |
0 |
continue; |
1350 |
|
} |
1351 |
0 |
final String label = urlLink.getLabel(); |
1352 |
0 |
boolean usingNames = false; |
1353 |
|
|
1354 |
0 |
String ltarget = urlLink.getTarget(); |
1355 |
0 |
Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT)); |
1356 |
0 |
String[] seqstr, ids; |
1357 |
0 |
if (idset != null) |
1358 |
|
{ |
1359 |
0 |
int numinput = ((int[]) idset[0])[0]; |
1360 |
0 |
String[] allids = ((String[]) idset[1]); |
1361 |
0 |
seqstr = new String[numinput]; |
1362 |
0 |
ids = new String[numinput]; |
1363 |
0 |
for (int sq = 0, idcount = 0; sq < seqs.length; sq++) |
1364 |
|
{ |
1365 |
0 |
if (allids[sq] != null) |
1366 |
|
{ |
1367 |
0 |
ids[idcount] = allids[sq]; |
1368 |
0 |
seqstr[idcount++] = idandseqs[1][sq]; |
1369 |
|
} |
1370 |
|
} |
1371 |
|
} |
1372 |
|
else |
1373 |
|
{ |
1374 |
|
|
1375 |
0 |
seqstr = idandseqs[1]; |
1376 |
0 |
ids = idandseqs[0]; |
1377 |
0 |
usingNames = true; |
1378 |
|
} |
1379 |
|
|
1380 |
|
|
1381 |
0 |
Object[] urlset = null; |
1382 |
0 |
try |
1383 |
|
{ |
1384 |
0 |
urlset = urlLink.makeUrlStubs(ids, seqstr, |
1385 |
|
"FromJalview" + System.currentTimeMillis(), false); |
1386 |
|
} catch (UrlStringTooLongException e) |
1387 |
|
{ |
1388 |
|
} |
1389 |
0 |
if (urlset != null) |
1390 |
|
{ |
1391 |
0 |
int type = urlLink.getGroupURLType() & 3; |
1392 |
|
|
1393 |
|
|
1394 |
0 |
addshowLink(linkMenus[type], |
1395 |
0 |
label + (((type & 1) == 1) |
1396 |
0 |
? ("(" + (usingNames ? "Names" : ltarget) + ")") |
1397 |
|
: ""), |
1398 |
|
urlLink, urlset); |
1399 |
0 |
addMenu = true; |
1400 |
|
} |
1401 |
|
} |
1402 |
0 |
if (addMenu) |
1403 |
|
{ |
1404 |
0 |
groupLinksMenu = new JMenu( |
1405 |
|
MessageManager.getString("action.group_link")); |
1406 |
0 |
for (int m = 0; m < linkMenus.length; m++) |
1407 |
|
{ |
1408 |
0 |
if (linkMenus[m] != null |
1409 |
|
&& linkMenus[m].getMenuComponentCount() > 0) |
1410 |
|
{ |
1411 |
0 |
groupLinksMenu.add(linkMenus[m]); |
1412 |
|
} |
1413 |
|
} |
1414 |
|
|
1415 |
0 |
groupMenu.add(groupLinksMenu); |
1416 |
|
} |
1417 |
|
} |
1418 |
|
|
1419 |
|
|
1420 |
|
|
1421 |
|
|
1422 |
|
@throws |
1423 |
|
|
1424 |
|
|
|
|
| 99.1% |
Uncovered Elements: 1 (106) |
Complexity: 2 |
Complexity Density: 0.02 |
|
1425 |
19 |
private void jbInit() throws Exception... |
1426 |
|
{ |
1427 |
19 |
groupMenu.setText(MessageManager.getString("label.selection")); |
1428 |
19 |
groupName.setText(MessageManager.getString("label.name")); |
1429 |
19 |
groupName.addActionListener(new ActionListener() |
1430 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1431 |
0 |
@Override... |
1432 |
|
public void actionPerformed(ActionEvent e) |
1433 |
|
{ |
1434 |
0 |
groupName_actionPerformed(); |
1435 |
|
} |
1436 |
|
}); |
1437 |
19 |
sequenceMenu.setText(MessageManager.getString("label.sequence")); |
1438 |
|
|
1439 |
19 |
JMenuItem sequenceName = new JMenuItem( |
1440 |
|
MessageManager.getString("label.edit_name_description")); |
1441 |
19 |
sequenceName.addActionListener(new ActionListener() |
1442 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1443 |
0 |
@Override... |
1444 |
|
public void actionPerformed(ActionEvent e) |
1445 |
|
{ |
1446 |
0 |
sequenceName_actionPerformed(); |
1447 |
|
} |
1448 |
|
}); |
1449 |
19 |
JMenuItem chooseAnnotations = new JMenuItem( |
1450 |
|
MessageManager.getString("action.choose_annotations")); |
1451 |
19 |
chooseAnnotations.addActionListener(new ActionListener() |
1452 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1453 |
0 |
@Override... |
1454 |
|
public void actionPerformed(ActionEvent e) |
1455 |
|
{ |
1456 |
0 |
chooseAnnotations_actionPerformed(e); |
1457 |
|
} |
1458 |
|
}); |
1459 |
19 |
JMenuItem sequenceDetails = new JMenuItem( |
1460 |
|
MessageManager.getString("label.sequence_details")); |
1461 |
19 |
sequenceDetails.addActionListener(new ActionListener() |
1462 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1463 |
0 |
@Override... |
1464 |
|
public void actionPerformed(ActionEvent e) |
1465 |
|
{ |
1466 |
0 |
createSequenceDetailsReport(new SequenceI[] { sequence }); |
1467 |
|
} |
1468 |
|
}); |
1469 |
19 |
JMenuItem sequenceSelDetails = new JMenuItem( |
1470 |
|
MessageManager.getString("label.sequence_details")); |
1471 |
19 |
sequenceSelDetails.addActionListener(new ActionListener() |
1472 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1473 |
0 |
@Override... |
1474 |
|
public void actionPerformed(ActionEvent e) |
1475 |
|
{ |
1476 |
0 |
createSequenceDetailsReport(ap.av.getSequenceSelection()); |
1477 |
|
} |
1478 |
|
}); |
1479 |
|
|
1480 |
19 |
unGroupMenuItem |
1481 |
|
.setText(MessageManager.getString("action.remove_group")); |
1482 |
19 |
unGroupMenuItem.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 |
unGroupMenuItem_actionPerformed(); |
1488 |
|
} |
1489 |
|
}); |
1490 |
19 |
createGroupMenuItem |
1491 |
|
.setText(MessageManager.getString("action.create_group")); |
1492 |
19 |
createGroupMenuItem.addActionListener(new ActionListener() |
1493 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1494 |
0 |
@Override... |
1495 |
|
public void actionPerformed(ActionEvent e) |
1496 |
|
{ |
1497 |
0 |
createGroupMenuItem_actionPerformed(); |
1498 |
|
} |
1499 |
|
}); |
1500 |
|
|
1501 |
19 |
JMenuItem outline = new JMenuItem( |
1502 |
|
MessageManager.getString("action.border_colour")); |
1503 |
19 |
outline.addActionListener(new ActionListener() |
1504 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1505 |
0 |
@Override... |
1506 |
|
public void actionPerformed(ActionEvent e) |
1507 |
|
{ |
1508 |
0 |
outline_actionPerformed(); |
1509 |
|
} |
1510 |
|
}); |
1511 |
19 |
showBoxes.setText(MessageManager.getString("action.boxes")); |
1512 |
19 |
showBoxes.setState(true); |
1513 |
19 |
showBoxes.addActionListener(new ActionListener() |
1514 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1515 |
0 |
@Override... |
1516 |
|
public void actionPerformed(ActionEvent e) |
1517 |
|
{ |
1518 |
0 |
showBoxes_actionPerformed(); |
1519 |
|
} |
1520 |
|
}); |
1521 |
19 |
showText.setText(MessageManager.getString("action.text")); |
1522 |
19 |
showText.setState(true); |
1523 |
19 |
showText.addActionListener(new ActionListener() |
1524 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1525 |
0 |
@Override... |
1526 |
|
public void actionPerformed(ActionEvent e) |
1527 |
|
{ |
1528 |
0 |
showText_actionPerformed(); |
1529 |
|
} |
1530 |
|
}); |
1531 |
19 |
showColourText.setText(MessageManager.getString("label.colour_text")); |
1532 |
19 |
showColourText.addActionListener(new ActionListener() |
1533 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1534 |
0 |
@Override... |
1535 |
|
public void actionPerformed(ActionEvent e) |
1536 |
|
{ |
1537 |
0 |
showColourText_actionPerformed(); |
1538 |
|
} |
1539 |
|
}); |
1540 |
19 |
displayNonconserved |
1541 |
|
.setText(MessageManager.getString("label.show_non_conserved")); |
1542 |
19 |
displayNonconserved.setState(true); |
1543 |
19 |
displayNonconserved.addActionListener(new ActionListener() |
1544 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1545 |
0 |
@Override... |
1546 |
|
public void actionPerformed(ActionEvent e) |
1547 |
|
{ |
1548 |
0 |
showNonconserved_actionPerformed(); |
1549 |
|
} |
1550 |
|
}); |
1551 |
19 |
editMenu.setText(MessageManager.getString("action.edit")); |
1552 |
19 |
JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut")); |
1553 |
19 |
cut.addActionListener(new ActionListener() |
1554 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1555 |
0 |
@Override... |
1556 |
|
public void actionPerformed(ActionEvent e) |
1557 |
|
{ |
1558 |
0 |
cut_actionPerformed(); |
1559 |
|
} |
1560 |
|
}); |
1561 |
19 |
JMenuItem justifyLeftMenuItem = new JMenuItem( |
1562 |
|
MessageManager.getString("action.left_justify")); |
1563 |
19 |
justifyLeftMenuItem.addActionListener(new ActionListener() |
1564 |
|
{ |
1565 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1566 |
0 |
@Override... |
1567 |
|
public void actionPerformed(ActionEvent e) |
1568 |
|
{ |
1569 |
0 |
ap.alignFrame.avc.justify_Region(true); |
1570 |
|
} |
1571 |
|
}); |
1572 |
19 |
JMenuItem justifyRightMenuItem = new JMenuItem( |
1573 |
|
MessageManager.getString("action.right_justify")); |
1574 |
19 |
justifyRightMenuItem.addActionListener(new ActionListener() |
1575 |
|
{ |
1576 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1577 |
0 |
@Override... |
1578 |
|
public void actionPerformed(ActionEvent e) |
1579 |
|
{ |
1580 |
0 |
ap.alignFrame.avc.justify_Region(false); |
1581 |
|
} |
1582 |
|
}); |
1583 |
|
|
1584 |
19 |
upperCase.setText(MessageManager.getString("label.to_upper_case")); |
1585 |
19 |
upperCase.addActionListener(new ActionListener() |
1586 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1587 |
0 |
@Override... |
1588 |
|
public void actionPerformed(ActionEvent e) |
1589 |
|
{ |
1590 |
0 |
changeCase(e); |
1591 |
|
} |
1592 |
|
}); |
1593 |
19 |
JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy")); |
1594 |
19 |
copy.addActionListener(new ActionListener() |
1595 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1596 |
0 |
@Override... |
1597 |
|
public void actionPerformed(ActionEvent e) |
1598 |
|
{ |
1599 |
0 |
copy_actionPerformed(); |
1600 |
|
} |
1601 |
|
}); |
1602 |
19 |
lowerCase.setText(MessageManager.getString("label.to_lower_case")); |
1603 |
19 |
lowerCase.addActionListener(new ActionListener() |
1604 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1605 |
0 |
@Override... |
1606 |
|
public void actionPerformed(ActionEvent e) |
1607 |
|
{ |
1608 |
0 |
changeCase(e); |
1609 |
|
} |
1610 |
|
}); |
1611 |
19 |
toggle.setText(MessageManager.getString("label.toggle_case")); |
1612 |
19 |
toggle.addActionListener(new ActionListener() |
1613 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1614 |
0 |
@Override... |
1615 |
|
public void actionPerformed(ActionEvent e) |
1616 |
|
{ |
1617 |
0 |
changeCase(e); |
1618 |
|
} |
1619 |
|
}); |
1620 |
19 |
outputMenu.setText( |
1621 |
|
MessageManager.getString("label.out_to_textbox") + "..."); |
1622 |
19 |
seqShowAnnotationsMenu |
1623 |
|
.setText(MessageManager.getString("label.show_annotations")); |
1624 |
19 |
seqHideAnnotationsMenu |
1625 |
|
.setText(MessageManager.getString("label.hide_annotations")); |
1626 |
19 |
groupShowAnnotationsMenu |
1627 |
|
.setText(MessageManager.getString("label.show_annotations")); |
1628 |
19 |
groupHideAnnotationsMenu |
1629 |
|
.setText(MessageManager.getString("label.hide_annotations")); |
1630 |
19 |
groupShowAutoCalculatedAnnotations.setText(MessageManager |
1631 |
|
.getString("label.group_show_auto_calculated_annotations")); |
1632 |
19 |
groupHideAutoCalculatedAnnotations.setText(MessageManager |
1633 |
|
.getString("label.group_hide_auto_calculated_annotations")); |
1634 |
19 |
JMenuItem sequenceFeature = new JMenuItem( |
1635 |
|
MessageManager.getString("label.create_sequence_feature")); |
1636 |
19 |
sequenceFeature.addActionListener(new ActionListener() |
1637 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1638 |
0 |
@Override... |
1639 |
|
public void actionPerformed(ActionEvent e) |
1640 |
|
{ |
1641 |
0 |
sequenceFeature_actionPerformed(); |
1642 |
|
} |
1643 |
|
}); |
1644 |
19 |
editGroupMenu.setText(MessageManager.getString("label.group")); |
1645 |
19 |
chooseStructure.setText( |
1646 |
|
MessageManager.getString("label.show_pdbstruct_dialog")); |
1647 |
19 |
chooseStructure.addActionListener(new ActionListener() |
1648 |
|
{ |
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1649 |
0 |
@Override... |
1650 |
|
public void actionPerformed(ActionEvent actionEvent) |
1651 |
|
{ |
1652 |
0 |
SequenceI[] selectedSeqs = new SequenceI[] { sequence }; |
1653 |
0 |
if (ap.av.getSelectionGroup() != null) |
1654 |
|
{ |
1655 |
0 |
selectedSeqs = ap.av.getSequenceSelection(); |
1656 |
|
} |
1657 |
0 |
new StructureChooser(selectedSeqs, sequence, ap); |
1658 |
|
} |
1659 |
|
}); |
1660 |
|
|
1661 |
19 |
rnaStructureMenu |
1662 |
|
.setText(MessageManager.getString("label.view_rna_structure")); |
1663 |
|
|
1664 |
|
|
1665 |
19 |
JMenuItem editSequence = new JMenuItem( |
1666 |
|
MessageManager.getString("label.edit_sequence") + "..."); |
1667 |
19 |
editSequence.addActionListener(new ActionListener() |
1668 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1669 |
0 |
@Override... |
1670 |
|
public void actionPerformed(ActionEvent actionEvent) |
1671 |
|
{ |
1672 |
0 |
editSequence_actionPerformed(); |
1673 |
|
} |
1674 |
|
}); |
1675 |
19 |
makeReferenceSeq.setText( |
1676 |
|
MessageManager.getString("label.mark_as_representative")); |
1677 |
19 |
makeReferenceSeq.addActionListener(new ActionListener() |
1678 |
|
{ |
1679 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1680 |
0 |
@Override... |
1681 |
|
public void actionPerformed(ActionEvent actionEvent) |
1682 |
|
{ |
1683 |
0 |
makeReferenceSeq_actionPerformed(actionEvent); |
1684 |
|
|
1685 |
|
} |
1686 |
|
}); |
1687 |
|
|
1688 |
19 |
groupMenu.add(sequenceSelDetails); |
1689 |
19 |
add(groupMenu); |
1690 |
19 |
add(sequenceMenu); |
1691 |
19 |
add(rnaStructureMenu); |
1692 |
19 |
add(chooseStructure); |
1693 |
19 |
if (forIdPanel) |
1694 |
|
{ |
1695 |
19 |
JMenuItem hideInsertions = new JMenuItem( |
1696 |
|
MessageManager.getString("label.hide_insertions")); |
1697 |
19 |
hideInsertions.addActionListener(new ActionListener() |
1698 |
|
{ |
1699 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1700 |
0 |
@Override... |
1701 |
|
public void actionPerformed(ActionEvent e) |
1702 |
|
{ |
1703 |
0 |
hideInsertions_actionPerformed(e); |
1704 |
|
} |
1705 |
|
}); |
1706 |
19 |
add(hideInsertions); |
1707 |
|
} |
1708 |
|
|
1709 |
|
|
1710 |
|
|
1711 |
|
|
1712 |
|
|
1713 |
|
|
1714 |
|
|
1715 |
19 |
sequenceMenu.add(seqShowAnnotationsMenu); |
1716 |
19 |
sequenceMenu.add(seqHideAnnotationsMenu); |
1717 |
19 |
sequenceMenu.add(seqAddReferenceAnnotations); |
1718 |
19 |
groupMenu.add(groupShowAnnotationsMenu); |
1719 |
19 |
groupMenu.add(groupHideAnnotationsMenu); |
1720 |
19 |
groupMenu.add(groupAddReferenceAnnotations); |
1721 |
19 |
groupMenu.add(groupShowAutoCalculatedAnnotations); |
1722 |
19 |
groupMenu.add(groupHideAutoCalculatedAnnotations); |
1723 |
19 |
groupMenu.add(editMenu); |
1724 |
19 |
groupMenu.add(outputMenu); |
1725 |
19 |
groupMenu.add(sequenceFeature); |
1726 |
19 |
groupMenu.add(createGroupMenuItem); |
1727 |
19 |
groupMenu.add(unGroupMenuItem); |
1728 |
19 |
groupMenu.add(editGroupMenu); |
1729 |
19 |
sequenceMenu.add(sequenceName); |
1730 |
19 |
sequenceMenu.add(sequenceDetails); |
1731 |
19 |
sequenceMenu.add(makeReferenceSeq); |
1732 |
|
|
1733 |
19 |
initColourMenu(); |
1734 |
19 |
buildColourMenu(); |
1735 |
|
|
1736 |
19 |
editMenu.add(copy); |
1737 |
19 |
editMenu.add(cut); |
1738 |
19 |
editMenu.add(justifyLeftMenuItem); |
1739 |
19 |
editMenu.add(justifyRightMenuItem); |
1740 |
19 |
editMenu.add(editSequence); |
1741 |
19 |
editMenu.add(upperCase); |
1742 |
19 |
editMenu.add(lowerCase); |
1743 |
19 |
editMenu.add(toggle); |
1744 |
19 |
editGroupMenu.add(groupName); |
1745 |
19 |
editGroupMenu.add(colourMenu); |
1746 |
19 |
editGroupMenu.add(showBoxes); |
1747 |
19 |
editGroupMenu.add(showText); |
1748 |
19 |
editGroupMenu.add(showColourText); |
1749 |
19 |
editGroupMenu.add(outline); |
1750 |
19 |
editGroupMenu.add(displayNonconserved); |
1751 |
|
} |
1752 |
|
|
1753 |
|
|
1754 |
|
|
1755 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
|
1756 |
19 |
protected void initColourMenu()... |
1757 |
|
{ |
1758 |
19 |
colourMenu.setText(MessageManager.getString("label.group_colour")); |
1759 |
19 |
textColour.setText(MessageManager.getString("label.text_colour")); |
1760 |
19 |
textColour.addActionListener(new ActionListener() |
1761 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1762 |
0 |
@Override... |
1763 |
|
public void actionPerformed(ActionEvent e) |
1764 |
|
{ |
1765 |
0 |
textColour_actionPerformed(); |
1766 |
|
} |
1767 |
|
}); |
1768 |
|
|
1769 |
19 |
abovePIDColour.setText( |
1770 |
|
MessageManager.getString("label.above_identity_threshold")); |
1771 |
19 |
abovePIDColour.addActionListener(new ActionListener() |
1772 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1773 |
0 |
@Override... |
1774 |
|
public void actionPerformed(ActionEvent e) |
1775 |
|
{ |
1776 |
0 |
abovePIDColour_actionPerformed(abovePIDColour.isSelected()); |
1777 |
|
} |
1778 |
|
}); |
1779 |
|
|
1780 |
19 |
modifyPID.setText( |
1781 |
|
MessageManager.getString("label.modify_identity_threshold")); |
1782 |
19 |
modifyPID.addActionListener(new ActionListener() |
1783 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1784 |
0 |
@Override... |
1785 |
|
public void actionPerformed(ActionEvent e) |
1786 |
|
{ |
1787 |
0 |
modifyPID_actionPerformed(); |
1788 |
|
} |
1789 |
|
}); |
1790 |
|
|
1791 |
19 |
conservationMenuItem |
1792 |
|
.setText(MessageManager.getString("action.by_conservation")); |
1793 |
19 |
conservationMenuItem.addActionListener(new ActionListener() |
1794 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1795 |
0 |
@Override... |
1796 |
|
public void actionPerformed(ActionEvent e) |
1797 |
|
{ |
1798 |
0 |
conservationMenuItem_actionPerformed( |
1799 |
|
conservationMenuItem.isSelected()); |
1800 |
|
} |
1801 |
|
}); |
1802 |
|
|
1803 |
19 |
byConsensusSecondaryStructureMenuItem.setText(MessageManager |
1804 |
|
.getString("action.by_secondary_structure_conservation")); |
1805 |
19 |
byConsensusSecondaryStructureMenuItem |
1806 |
|
.addActionListener(new ActionListener() |
1807 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1808 |
0 |
@Override... |
1809 |
|
public void actionPerformed(ActionEvent e) |
1810 |
|
{ |
1811 |
0 |
colourByConsensusSecondaryStructureMenuItem_actionPerformed( |
1812 |
|
byConsensusSecondaryStructureMenuItem.isSelected()); |
1813 |
|
} |
1814 |
|
}); |
1815 |
|
|
1816 |
19 |
annotationColour = new JRadioButtonMenuItem( |
1817 |
|
MessageManager.getString("action.by_annotation")); |
1818 |
19 |
annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR); |
1819 |
19 |
annotationColour.setEnabled(false); |
1820 |
19 |
annotationColour.setToolTipText( |
1821 |
|
MessageManager.getString("label.by_annotation_tooltip")); |
1822 |
|
|
1823 |
19 |
modifyConservation.setText(MessageManager |
1824 |
|
.getString("label.modify_conservation_threshold")); |
1825 |
19 |
modifyConservation.addActionListener(new ActionListener() |
1826 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1827 |
0 |
@Override... |
1828 |
|
public void actionPerformed(ActionEvent e) |
1829 |
|
{ |
1830 |
0 |
modifyConservation_actionPerformed(); |
1831 |
|
} |
1832 |
|
}); |
1833 |
|
|
1834 |
19 |
modifyConsensusSecondaryStructureThreshold |
1835 |
|
.setText(MessageManager.getString( |
1836 |
|
"label.modify_secondary_structure_conservation_threshold")); |
1837 |
19 |
modifyConsensusSecondaryStructureThreshold |
1838 |
|
.addActionListener(new ActionListener() |
1839 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1840 |
0 |
@Override... |
1841 |
|
public void actionPerformed(ActionEvent e) |
1842 |
|
{ |
1843 |
0 |
modifyConsensusSecondaryStructureThreshold_actionPerformed(); |
1844 |
|
} |
1845 |
|
}); |
1846 |
|
} |
1847 |
|
|
1848 |
|
|
1849 |
|
|
1850 |
|
|
1851 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (18) |
Complexity: 2 |
Complexity Density: 0.12 |
|
1852 |
19 |
protected void buildColourMenu()... |
1853 |
|
{ |
1854 |
19 |
SequenceGroup sg = ap.av.getSelectionGroup(); |
1855 |
19 |
if (sg == null) |
1856 |
|
{ |
1857 |
|
|
1858 |
|
|
1859 |
|
|
1860 |
16 |
return; |
1861 |
|
} |
1862 |
3 |
colourMenu.removeAll(); |
1863 |
3 |
colourMenu.add(textColour); |
1864 |
3 |
colourMenu.addSeparator(); |
1865 |
|
|
1866 |
3 |
ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg, |
1867 |
|
false); |
1868 |
3 |
bg.add(annotationColour); |
1869 |
3 |
colourMenu.add(annotationColour); |
1870 |
|
|
1871 |
3 |
colourMenu.addSeparator(); |
1872 |
3 |
colourMenu.add(conservationMenuItem); |
1873 |
3 |
colourMenu.add(modifyConservation); |
1874 |
3 |
colourMenu.add(byConsensusSecondaryStructureMenuItem); |
1875 |
3 |
colourMenu.add(modifyConsensusSecondaryStructureThreshold); |
1876 |
3 |
colourMenu.add(abovePIDColour); |
1877 |
3 |
colourMenu.add(modifyPID); |
1878 |
|
} |
1879 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1880 |
0 |
protected void modifyConservation_actionPerformed()... |
1881 |
|
{ |
1882 |
0 |
SequenceGroup sg = getGroup(); |
1883 |
0 |
if (sg.cs != null) |
1884 |
|
{ |
1885 |
0 |
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); |
1886 |
0 |
SliderPanel.showConservationSlider(); |
1887 |
|
} |
1888 |
|
} |
1889 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1890 |
0 |
protected void modifyConsensusSecondaryStructureThreshold_actionPerformed()... |
1891 |
|
{ |
1892 |
0 |
SequenceGroup sg = getGroup(); |
1893 |
0 |
if (sg.cs != null) |
1894 |
|
{ |
1895 |
0 |
SliderPanel.setConsensusSecondaryStructureSlider(ap, sg.cs, |
1896 |
|
sg.getName()); |
1897 |
0 |
SliderPanel.showConsensusSecondaryStructureSlider(); |
1898 |
|
} |
1899 |
|
} |
1900 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1901 |
0 |
protected void modifyPID_actionPerformed()... |
1902 |
|
{ |
1903 |
0 |
SequenceGroup sg = getGroup(); |
1904 |
0 |
if (sg.cs != null) |
1905 |
|
{ |
1906 |
|
|
1907 |
|
|
1908 |
|
|
1909 |
0 |
SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); |
1910 |
0 |
SliderPanel.showPIDSlider(); |
1911 |
|
} |
1912 |
|
} |
1913 |
|
|
1914 |
|
|
1915 |
|
|
1916 |
|
|
1917 |
|
|
1918 |
|
|
1919 |
|
|
1920 |
|
|
1921 |
|
|
1922 |
|
|
1923 |
|
|
1924 |
|
@param |
1925 |
|
@param |
1926 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (16) |
Complexity: 2 |
Complexity Density: 0.14 |
|
1927 |
44 |
protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,... |
1928 |
|
List<SequenceI> forSequences) |
1929 |
|
{ |
1930 |
44 |
menuItem.setEnabled(false); |
1931 |
|
|
1932 |
|
|
1933 |
|
|
1934 |
|
|
1935 |
|
|
1936 |
44 |
SortedMap<String, String> tipEntries = new TreeMap<>(); |
1937 |
44 |
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>(); |
1938 |
44 |
AlignmentI al = this.ap.av.getAlignment(); |
1939 |
44 |
AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries, |
1940 |
|
candidates, al); |
1941 |
44 |
if (!candidates.isEmpty()) |
1942 |
|
{ |
1943 |
2 |
StringBuilder tooltip = new StringBuilder(64); |
1944 |
2 |
tooltip.append(MessageManager.getString("label.add_annotations_for")); |
1945 |
|
|
1946 |
|
|
1947 |
|
|
1948 |
|
|
1949 |
|
|
1950 |
2 |
menuItem.setEnabled(true); |
1951 |
2 |
for (String calcId : tipEntries.keySet()) |
1952 |
|
{ |
1953 |
4 |
tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId)); |
1954 |
|
} |
1955 |
2 |
String tooltipText = JvSwingUtils.wrapTooltip(true, |
1956 |
|
tooltip.toString()); |
1957 |
2 |
menuItem.setToolTipText(tooltipText); |
1958 |
|
|
1959 |
2 |
menuItem.addActionListener(new ActionListener() |
1960 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1961 |
0 |
@Override... |
1962 |
|
public void actionPerformed(ActionEvent e) |
1963 |
|
{ |
1964 |
0 |
addReferenceAnnotations_actionPerformed(candidates); |
1965 |
|
} |
1966 |
|
}); |
1967 |
|
} |
1968 |
|
} |
1969 |
|
|
1970 |
|
|
1971 |
|
|
1972 |
|
|
1973 |
|
@param |
1974 |
|
|
1975 |
|
|
1976 |
|
|
|
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 2 |
Complexity Density: 0.22 |
|
1977 |
0 |
protected void addReferenceAnnotations_actionPerformed(... |
1978 |
|
Map<SequenceI, List<AlignmentAnnotation>> candidates) |
1979 |
|
{ |
1980 |
0 |
final AlignmentI alignment = this.ap.getAlignment(); |
1981 |
0 |
AlignmentUtils.addReferenceAnnotations(candidates, alignment, null); |
1982 |
|
|
1983 |
0 |
if (AlignmentUtils.isSSAnnotationPresent(candidates)) |
1984 |
|
{ |
1985 |
|
|
1986 |
0 |
restartSSConsensusWorker(); |
1987 |
0 |
ap.validateAnnotationDimensions(true); |
1988 |
0 |
ap.fontChanged(); |
1989 |
0 |
ap.av.alignmentChanged(ap); |
1990 |
0 |
ap.adjustAnnotationHeight(); |
1991 |
0 |
restartSSConsensusWorker(); |
1992 |
|
|
1993 |
|
} |
1994 |
|
} |
1995 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
1996 |
0 |
private void restartSSConsensusWorker()... |
1997 |
|
{ |
1998 |
|
|
1999 |
0 |
List<AlignCalcWorkerI> workers = ap.alignFrame.getViewport() |
2000 |
|
.getCalcManager().getRegisteredWorkersOfClass( |
2001 |
|
SecondaryStructureConsensusThread.class); |
2002 |
0 |
if (workers!=null && !workers.isEmpty()) |
2003 |
|
{ |
2004 |
|
|
2005 |
0 |
ap.alignFrame.getViewport().getCalcManager() |
2006 |
|
.startWorker(workers.remove(0)); |
2007 |
|
|
2008 |
|
} |
2009 |
|
|
2010 |
|
} |
2011 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
2012 |
0 |
protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)... |
2013 |
|
{ |
2014 |
0 |
if (!ap.av.getAlignment().hasSeqrep()) |
2015 |
|
{ |
2016 |
|
|
2017 |
0 |
ap.av.setDisplayReferenceSeq(true); |
2018 |
0 |
ap.av.setColourByReferenceSeq(true); |
2019 |
0 |
ap.av.getAlignment().setSeqrep(sequence); |
2020 |
|
} |
2021 |
|
else |
2022 |
|
{ |
2023 |
0 |
if (ap.av.getAlignment().getSeqrep() == sequence) |
2024 |
|
{ |
2025 |
0 |
ap.av.getAlignment().setSeqrep(null); |
2026 |
|
} |
2027 |
|
else |
2028 |
|
{ |
2029 |
0 |
ap.av.getAlignment().setSeqrep(sequence); |
2030 |
|
} |
2031 |
|
} |
2032 |
0 |
refresh(); |
2033 |
|
} |
2034 |
|
|
|
|
| 95% |
Uncovered Elements: 1 (20) |
Complexity: 5 |
Complexity Density: 0.36 |
|
2035 |
3 |
protected void hideInsertions_actionPerformed(ActionEvent actionEvent)... |
2036 |
|
{ |
2037 |
3 |
HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns(); |
2038 |
3 |
BitSet inserts = new BitSet(); |
2039 |
|
|
2040 |
3 |
boolean markedPopup = false; |
2041 |
|
|
2042 |
3 |
if (ap.av.getSelectionGroup() != null) |
2043 |
|
{ |
2044 |
|
|
2045 |
1 |
inserts.set(ap.av.getSelectionGroup().getStartRes(), |
2046 |
|
ap.av.getSelectionGroup().getEndRes() + 1); |
2047 |
|
|
2048 |
|
|
2049 |
1 |
for (SequenceI sq : ap.av.getSelectionGroup().getSequences()) |
2050 |
|
{ |
2051 |
2 |
if (sq == sequence) |
2052 |
|
{ |
2053 |
1 |
markedPopup = true; |
2054 |
|
} |
2055 |
2 |
inserts.and(sq.getInsertionsAsBits()); |
2056 |
|
} |
2057 |
1 |
hidden.clearAndHideColumns(inserts, |
2058 |
|
ap.av.getSelectionGroup().getStartRes(), |
2059 |
|
ap.av.getSelectionGroup().getEndRes()); |
2060 |
|
} |
2061 |
|
|
2062 |
|
|
2063 |
2 |
else if (!markedPopup && sequence != null) |
2064 |
|
{ |
2065 |
2 |
inserts.or(sequence.getInsertionsAsBits()); |
2066 |
|
|
2067 |
|
|
2068 |
2 |
hidden.hideColumns(inserts); |
2069 |
|
} |
2070 |
3 |
refresh(); |
2071 |
|
} |
2072 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2073 |
0 |
protected void sequenceSelectionDetails_actionPerformed()... |
2074 |
|
{ |
2075 |
0 |
createSequenceDetailsReport(ap.av.getSequenceSelection()); |
2076 |
|
} |
2077 |
|
|
|
|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 3 |
Complexity Density: 0.12 |
|
2078 |
0 |
public void createSequenceDetailsReport(SequenceI[] sequences)... |
2079 |
|
{ |
2080 |
0 |
StringBuilder contents = new StringBuilder(128); |
2081 |
0 |
contents.append("<html><body>"); |
2082 |
0 |
for (SequenceI seq : sequences) |
2083 |
|
{ |
2084 |
0 |
contents.append("<p><h2>" + MessageManager.formatMessage( |
2085 |
|
"label.create_sequence_details_report_annotation_for", |
2086 |
|
new Object[] |
2087 |
|
{ seq.getDisplayId(true) }) + "</h2></p>\n<p>"); |
2088 |
0 |
new SequenceAnnotationReport(false).createSequenceAnnotationReport( |
2089 |
|
contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr); |
2090 |
0 |
contents.append("</p>"); |
2091 |
|
} |
2092 |
0 |
contents.append("</body></html>"); |
2093 |
0 |
String report = contents.toString(); |
2094 |
|
|
2095 |
0 |
JInternalFrame frame; |
2096 |
0 |
if (Platform.isJS()) |
2097 |
|
{ |
2098 |
0 |
JLabel textLabel = new JLabel(); |
2099 |
0 |
textLabel.setText(report); |
2100 |
0 |
textLabel.setBackground(Color.WHITE); |
2101 |
0 |
JPanel pane = new JPanel(new BorderLayout()); |
2102 |
0 |
pane.setOpaque(true); |
2103 |
0 |
pane.setBackground(Color.WHITE); |
2104 |
0 |
pane.add(textLabel, BorderLayout.NORTH); |
2105 |
0 |
frame = new JInternalFrame(); |
2106 |
0 |
frame.setFrameIcon(null); |
2107 |
0 |
frame.getContentPane().add(new JScrollPane(pane)); |
2108 |
|
} |
2109 |
|
else |
2110 |
|
|
2111 |
|
|
2112 |
|
|
2113 |
|
|
2114 |
|
|
2115 |
|
{ |
2116 |
0 |
CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); |
2117 |
0 |
cap.setText(report); |
2118 |
0 |
frame = cap; |
2119 |
|
} |
2120 |
|
|
2121 |
0 |
Desktop.addInternalFrame(frame, |
2122 |
|
MessageManager.formatMessage("label.sequence_details_for", |
2123 |
0 |
(sequences.length == 1 ? new Object[] |
2124 |
|
{ sequences[0].getDisplayId(true) } |
2125 |
|
: new Object[] |
2126 |
|
{ MessageManager |
2127 |
|
.getString("label.selection") })), |
2128 |
|
500, 400); |
2129 |
|
} |
2130 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2131 |
0 |
protected void showNonconserved_actionPerformed()... |
2132 |
|
{ |
2133 |
0 |
getGroup().setShowNonconserved(displayNonconserved.isSelected()); |
2134 |
0 |
refresh(); |
2135 |
|
} |
2136 |
|
|
2137 |
|
|
2138 |
|
|
2139 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2140 |
9 |
void refresh()... |
2141 |
|
{ |
2142 |
9 |
ap.updateAnnotation(); |
2143 |
|
|
2144 |
|
|
2145 |
|
|
2146 |
|
|
2147 |
9 |
PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); |
2148 |
|
} |
2149 |
|
|
2150 |
|
|
2151 |
|
|
2152 |
|
|
2153 |
|
|
2154 |
|
|
2155 |
|
|
2156 |
|
|
2157 |
|
@param |
2158 |
|
|
2159 |
|
@param |
2160 |
|
|
2161 |
|
|
|
|
| 68.8% |
Uncovered Elements: 5 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
|
2162 |
2 |
public void abovePIDColour_actionPerformed(boolean selected)... |
2163 |
|
{ |
2164 |
2 |
SequenceGroup sg = getGroup(); |
2165 |
2 |
if (sg.cs == null) |
2166 |
|
{ |
2167 |
0 |
return; |
2168 |
|
} |
2169 |
|
|
2170 |
2 |
if (selected) |
2171 |
|
{ |
2172 |
2 |
sg.cs.setConsensus(AAFrequency.calculate( |
2173 |
|
sg.getSequences(ap.av.getHiddenRepSequences()), |
2174 |
|
sg.getStartRes(), sg.getEndRes() + 1)); |
2175 |
|
|
2176 |
2 |
int threshold = SliderPanel.setPIDSliderSource(ap, |
2177 |
|
sg.getGroupColourScheme(), getGroup().getName()); |
2178 |
|
|
2179 |
2 |
sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); |
2180 |
|
|
2181 |
2 |
SliderPanel.showPIDSlider(); |
2182 |
|
} |
2183 |
|
else |
2184 |
|
|
2185 |
|
{ |
2186 |
0 |
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); |
2187 |
0 |
SliderPanel.hidePIDSlider(); |
2188 |
|
} |
2189 |
2 |
modifyPID.setEnabled(selected); |
2190 |
|
|
2191 |
2 |
refresh(); |
2192 |
|
} |
2193 |
|
|
2194 |
|
|
2195 |
|
|
2196 |
|
|
2197 |
|
|
2198 |
|
@param |
2199 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2200 |
0 |
protected void chooseAnnotations_actionPerformed(ActionEvent e)... |
2201 |
|
{ |
2202 |
|
|
2203 |
0 |
new AnnotationChooser(ap); |
2204 |
|
} |
2205 |
|
|
2206 |
|
|
2207 |
|
|
2208 |
|
|
2209 |
|
@param |
2210 |
|
|
2211 |
|
|
|
|
| 72.2% |
Uncovered Elements: 5 (18) |
Complexity: 3 |
Complexity Density: 0.21 |
|
2212 |
2 |
public void conservationMenuItem_actionPerformed(boolean selected)... |
2213 |
|
{ |
2214 |
2 |
SequenceGroup sg = getGroup(); |
2215 |
2 |
if (sg.cs == null) |
2216 |
|
{ |
2217 |
0 |
return; |
2218 |
|
} |
2219 |
|
|
2220 |
2 |
if (selected) |
2221 |
|
{ |
2222 |
|
|
2223 |
2 |
Conservation c = new Conservation("Group", |
2224 |
|
sg.getSequences(ap.av.getHiddenRepSequences()), |
2225 |
|
sg.getStartRes(), sg.getEndRes() + 1); |
2226 |
|
|
2227 |
2 |
c.calculate(); |
2228 |
2 |
c.verdict(false, ap.av.getConsPercGaps()); |
2229 |
2 |
sg.cs.setConservation(c); |
2230 |
|
|
2231 |
2 |
SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(), |
2232 |
|
sg.getName()); |
2233 |
2 |
SliderPanel.showConservationSlider(); |
2234 |
|
} |
2235 |
|
else |
2236 |
|
|
2237 |
|
{ |
2238 |
0 |
sg.cs.setConservation(null); |
2239 |
0 |
SliderPanel.hideConservationSlider(); |
2240 |
|
} |
2241 |
2 |
modifyConservation.setEnabled(selected); |
2242 |
|
|
2243 |
2 |
refresh(); |
2244 |
|
} |
2245 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
2246 |
0 |
public void colourByConsensusSecondaryStructureMenuItem_actionPerformed(... |
2247 |
|
boolean selected) |
2248 |
|
{ |
2249 |
0 |
SequenceGroup sg = getGroup(); |
2250 |
0 |
if (sg.cs == null) |
2251 |
|
{ |
2252 |
0 |
return; |
2253 |
|
} |
2254 |
|
|
2255 |
0 |
if (selected) |
2256 |
|
{ |
2257 |
|
|
2258 |
0 |
sg.cs.setConsensusSecondaryStructureColouring(selected); |
2259 |
|
|
2260 |
0 |
SliderPanel.setConsensusSecondaryStructureSlider(ap, |
2261 |
|
sg.getGroupColourScheme(), sg.getName()); |
2262 |
0 |
SliderPanel.showConsensusSecondaryStructureSlider(); |
2263 |
|
} |
2264 |
|
else |
2265 |
|
|
2266 |
|
{ |
2267 |
0 |
sg.cs.setConsensusSecondaryStructureColouring(selected); |
2268 |
0 |
SliderPanel.hideConsensusSecondaryStructureSlider(); |
2269 |
|
} |
2270 |
0 |
modifyConsensusSecondaryStructureThreshold.setEnabled(selected); |
2271 |
|
|
2272 |
0 |
refresh(); |
2273 |
|
} |
2274 |
|
|
2275 |
|
|
2276 |
|
|
2277 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
2278 |
0 |
protected void groupName_actionPerformed()... |
2279 |
|
{ |
2280 |
0 |
SequenceGroup sg = getGroup(); |
2281 |
0 |
EditNameDialog dialog = new EditNameDialog(sg.getName(), |
2282 |
|
sg.getDescription(), |
2283 |
|
MessageManager.getString("label.group_name"), |
2284 |
|
MessageManager.getString("label.group_description")); |
2285 |
0 |
dialog.showDialog(ap.alignFrame, |
2286 |
|
MessageManager.getString("label.edit_group_name_description"), |
2287 |
|
() -> { |
2288 |
0 |
sg.setName(dialog.getName()); |
2289 |
0 |
sg.setDescription(dialog.getDescription()); |
2290 |
0 |
refresh(); |
2291 |
|
}); |
2292 |
|
} |
2293 |
|
|
2294 |
|
|
2295 |
|
|
2296 |
|
|
2297 |
|
@return |
2298 |
|
|
|
|
| 83.3% |
Uncovered Elements: 1 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
2299 |
8 |
SequenceGroup getGroup()... |
2300 |
|
{ |
2301 |
8 |
SequenceGroup sg = ap.av.getSelectionGroup(); |
2302 |
|
|
2303 |
8 |
if (sg != null) |
2304 |
|
{ |
2305 |
8 |
ap.av.getAlignment().addGroup(sg); |
2306 |
|
} |
2307 |
|
|
2308 |
8 |
return sg; |
2309 |
|
} |
2310 |
|
|
2311 |
|
|
2312 |
|
|
2313 |
|
|
2314 |
|
|
2315 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 3 |
Complexity Density: 0.21 |
|
2316 |
0 |
void sequenceName_actionPerformed()... |
2317 |
|
{ |
2318 |
0 |
EditNameDialog dialog = new EditNameDialog(sequence.getName(), |
2319 |
|
sequence.getDescription(), |
2320 |
|
MessageManager.getString("label.sequence_name"), |
2321 |
|
MessageManager.getString("label.sequence_description")); |
2322 |
0 |
dialog.showDialog(ap.alignFrame, MessageManager |
2323 |
|
.getString("label.edit_sequence_name_description"), () -> { |
2324 |
0 |
if (dialog.getName() != null) |
2325 |
|
{ |
2326 |
0 |
if (dialog.getName().indexOf(" ") > -1) |
2327 |
|
{ |
2328 |
0 |
String ok = MessageManager.getString("action.ok"); |
2329 |
0 |
String cancel = MessageManager.getString("action.cancel"); |
2330 |
0 |
String message = MessageManager.getString( |
2331 |
|
"label.spaces_converted_to_underscores"); |
2332 |
0 |
String title = MessageManager.getString( |
2333 |
|
"label.no_spaces_allowed_sequence_name"); |
2334 |
0 |
Object[] options = new Object[] { ok, cancel }; |
2335 |
|
|
2336 |
0 |
JvOptionPane.frameDialog(message, title, |
2337 |
|
JvOptionPane.WARNING_MESSAGE, null, null, null, |
2338 |
|
false); |
2339 |
|
} |
2340 |
0 |
sequence.setName(dialog.getName().replace(' ', '_')); |
2341 |
0 |
ap.paintAlignment(false, false); |
2342 |
|
} |
2343 |
0 |
sequence.setDescription(dialog.getDescription()); |
2344 |
0 |
ap.av.firePropertyChange("alignment", null, |
2345 |
|
ap.av.getAlignment().getSequences()); |
2346 |
|
}); |
2347 |
|
} |
2348 |
|
|
2349 |
|
|
2350 |
|
|
2351 |
|
|
2352 |
|
@param |
2353 |
|
|
2354 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
2355 |
0 |
void unGroupMenuItem_actionPerformed()... |
2356 |
|
{ |
2357 |
0 |
SequenceGroup sg = ap.av.getSelectionGroup(); |
2358 |
0 |
ap.av.getAlignment().deleteGroup(sg); |
2359 |
0 |
ap.av.setSelectionGroup(null); |
2360 |
0 |
refresh(); |
2361 |
|
} |
2362 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2363 |
0 |
void createGroupMenuItem_actionPerformed()... |
2364 |
|
{ |
2365 |
0 |
getGroup(); |
2366 |
|
|
2367 |
0 |
refresh(); |
2368 |
|
} |
2369 |
|
|
2370 |
|
|
2371 |
|
|
2372 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
2373 |
0 |
protected void outline_actionPerformed()... |
2374 |
|
{ |
2375 |
0 |
String title = MessageManager.getString("label.select_outline_colour"); |
2376 |
0 |
ColourChooserListener listener = new ColourChooserListener() |
2377 |
|
{ |
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2378 |
0 |
@Override... |
2379 |
|
public void colourSelected(Color c) |
2380 |
|
{ |
2381 |
0 |
getGroup().setOutlineColour(c); |
2382 |
0 |
refresh(); |
2383 |
|
} |
2384 |
|
}; |
2385 |
0 |
JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title, |
2386 |
|
Color.BLUE, listener); |
2387 |
|
} |
2388 |
|
|
2389 |
|
|
2390 |
|
|
2391 |
|
|
2392 |
|
@param |
2393 |
|
|
2394 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2395 |
0 |
public void showBoxes_actionPerformed()... |
2396 |
|
{ |
2397 |
0 |
getGroup().setDisplayBoxes(showBoxes.isSelected()); |
2398 |
0 |
refresh(); |
2399 |
|
} |
2400 |
|
|
2401 |
|
|
2402 |
|
|
2403 |
|
|
2404 |
|
@param |
2405 |
|
|
2406 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2407 |
0 |
public void showText_actionPerformed()... |
2408 |
|
{ |
2409 |
0 |
getGroup().setDisplayText(showText.isSelected()); |
2410 |
0 |
refresh(); |
2411 |
|
} |
2412 |
|
|
2413 |
|
|
2414 |
|
|
2415 |
|
|
2416 |
|
@param |
2417 |
|
|
2418 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
2419 |
0 |
public void showColourText_actionPerformed()... |
2420 |
|
{ |
2421 |
0 |
getGroup().setColourText(showColourText.isSelected()); |
2422 |
0 |
refresh(); |
2423 |
|
} |
2424 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2425 |
0 |
void hideSequences(boolean representGroup)... |
2426 |
|
{ |
2427 |
0 |
ap.av.hideSequences(sequence, representGroup); |
2428 |
|
} |
2429 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2430 |
0 |
public void copy_actionPerformed()... |
2431 |
|
{ |
2432 |
0 |
ap.alignFrame.copy_actionPerformed(); |
2433 |
|
} |
2434 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
2435 |
0 |
public void cut_actionPerformed()... |
2436 |
|
{ |
2437 |
0 |
ap.alignFrame.cut_actionPerformed(); |
2438 |
|
} |
2439 |
|
|
|
|
| 0% |
Uncovered Elements: 23 (23) |
Complexity: 4 |
Complexity Density: 0.24 |
|
2440 |
0 |
void changeCase(ActionEvent e)... |
2441 |
|
{ |
2442 |
0 |
Object source = e.getSource(); |
2443 |
0 |
SequenceGroup sg = ap.av.getSelectionGroup(); |
2444 |
|
|
2445 |
0 |
if (sg != null) |
2446 |
|
{ |
2447 |
0 |
List<int[]> startEnd = ap.av.getVisibleRegionBoundaries( |
2448 |
|
sg.getStartRes(), sg.getEndRes() + 1); |
2449 |
|
|
2450 |
0 |
String description; |
2451 |
0 |
int caseChange; |
2452 |
|
|
2453 |
0 |
if (source == toggle) |
2454 |
|
{ |
2455 |
0 |
description = MessageManager.getString("label.toggle_case"); |
2456 |
0 |
caseChange = ChangeCaseCommand.TOGGLE_CASE; |
2457 |
|
} |
2458 |
0 |
else if (source == upperCase) |
2459 |
|
{ |
2460 |
0 |
description = MessageManager.getString("label.to_upper_case"); |
2461 |
0 |
caseChange = ChangeCaseCommand.TO_UPPER; |
2462 |
|
} |
2463 |
|
else |
2464 |
|
{ |
2465 |
0 |
description = MessageManager.getString("label.to_lower_case"); |
2466 |
0 |
caseChange = ChangeCaseCommand.TO_LOWER; |
2467 |
|
} |
2468 |
|
|
2469 |
0 |
ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, |
2470 |
|
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), |
2471 |
|
startEnd, caseChange); |
2472 |
|
|
2473 |
0 |
ap.alignFrame.addHistoryItem(caseCommand); |
2474 |
|
|
2475 |
0 |
ap.av.firePropertyChange("alignment", null, |
2476 |
|
ap.av.getAlignment().getSequences()); |
2477 |
|
|
2478 |
|
} |
2479 |
|
} |
2480 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
|
2481 |
0 |
public void outputText_actionPerformed(ActionEvent e)... |
2482 |
|
{ |
2483 |
0 |
CutAndPasteTransfer cap = new CutAndPasteTransfer(); |
2484 |
0 |
cap.setForInput(null); |
2485 |
0 |
Desktop.addInternalFrame(cap, MessageManager |
2486 |
|
.formatMessage("label.alignment_output_command", new Object[] |
2487 |
|
{ e.getActionCommand() }), 600, 500); |
2488 |
|
|
2489 |
0 |
String[] omitHidden = null; |
2490 |
|
|
2491 |
0 |
jalview.bin.Console.outPrintln("PROMPT USER HERE"); |
2492 |
|
|
2493 |
|
|
2494 |
|
|
2495 |
|
|
2496 |
0 |
FileFormatI fileFormat = FileFormats.getInstance() |
2497 |
|
.forName(e.getActionCommand()); |
2498 |
0 |
cap.setText( |
2499 |
|
new FormatAdapter(ap).formatSequences(fileFormat, ap, true)); |
2500 |
|
} |
2501 |
|
|
|
|
| 0% |
Uncovered Elements: 22 (22) |
Complexity: 5 |
Complexity Density: 0.36 |
|
2502 |
0 |
public void sequenceFeature_actionPerformed()... |
2503 |
|
{ |
2504 |
0 |
SequenceGroup sg = ap.av.getSelectionGroup(); |
2505 |
0 |
if (sg == null) |
2506 |
|
{ |
2507 |
0 |
return; |
2508 |
|
} |
2509 |
|
|
2510 |
0 |
List<SequenceI> seqs = new ArrayList<>(); |
2511 |
0 |
List<SequenceFeature> features = new ArrayList<>(); |
2512 |
|
|
2513 |
|
|
2514 |
|
|
2515 |
|
|
2516 |
|
|
2517 |
0 |
int gSize = sg.getSize(); |
2518 |
0 |
for (int i = 0; i < gSize; i++) |
2519 |
|
{ |
2520 |
0 |
int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); |
2521 |
0 |
int end = sg.findEndRes(sg.getSequenceAt(i)); |
2522 |
0 |
if (start <= end) |
2523 |
|
{ |
2524 |
0 |
seqs.add(sg.getSequenceAt(i).getDatasetSequence()); |
2525 |
0 |
features.add(new SequenceFeature(null, null, start, end, null)); |
2526 |
|
} |
2527 |
|
} |
2528 |
|
|
2529 |
|
|
2530 |
|
|
2531 |
|
|
2532 |
0 |
if (!seqs.isEmpty()) |
2533 |
|
{ |
2534 |
0 |
new FeatureEditor(ap, seqs, features, true).showDialog(); |
2535 |
|
} |
2536 |
|
} |
2537 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
2538 |
0 |
public void textColour_actionPerformed()... |
2539 |
|
{ |
2540 |
0 |
SequenceGroup sg = getGroup(); |
2541 |
0 |
if (sg != null) |
2542 |
|
{ |
2543 |
0 |
new TextColourChooser().chooseColour(ap, sg); |
2544 |
|
} |
2545 |
|
} |
2546 |
|
|
2547 |
|
|
2548 |
|
|
2549 |
|
|
2550 |
|
|
2551 |
|
|
|
|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 3 |
Complexity Density: 0.3 |
|
2552 |
0 |
public void editSequence_actionPerformed()... |
2553 |
|
{ |
2554 |
0 |
SequenceGroup sg = ap.av.getSelectionGroup(); |
2555 |
|
|
2556 |
0 |
SequenceI seq = sequence; |
2557 |
0 |
if (sg != null) |
2558 |
|
{ |
2559 |
0 |
if (seq == null) |
2560 |
|
{ |
2561 |
0 |
seq = sg.getSequenceAt(0); |
2562 |
|
} |
2563 |
|
|
2564 |
0 |
EditNameDialog dialog = new EditNameDialog( |
2565 |
|
seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), |
2566 |
|
null, MessageManager.getString("label.edit_sequence"), null); |
2567 |
0 |
dialog.showDialog(ap.alignFrame, |
2568 |
|
MessageManager.getString("label.edit_sequence"), () -> { |
2569 |
0 |
EditCommand editCommand = new EditCommand( |
2570 |
|
MessageManager.getString("label.edit_sequences"), |
2571 |
|
Action.REPLACE, |
2572 |
|
dialog.getName().replace(' ', |
2573 |
|
ap.av.getGapCharacter()), |
2574 |
|
sg.getSequencesAsArray( |
2575 |
|
ap.av.getHiddenRepSequences()), |
2576 |
|
sg.getStartRes(), sg.getEndRes() + 1, |
2577 |
|
ap.av.getAlignment()); |
2578 |
0 |
ap.alignFrame.addHistoryItem(editCommand); |
2579 |
0 |
ap.av.firePropertyChange("alignment", null, |
2580 |
|
ap.av.getAlignment().getSequences()); |
2581 |
|
}); |
2582 |
|
} |
2583 |
|
} |
2584 |
|
|
2585 |
|
|
2586 |
|
|
2587 |
|
|
2588 |
|
|
2589 |
|
@return |
2590 |
|
|
|
|
| 75% |
Uncovered Elements: 2 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
2591 |
2 |
@Override... |
2592 |
|
public void changeColour_actionPerformed(String colourSchemeName) |
2593 |
|
{ |
2594 |
2 |
SequenceGroup sg = getGroup(); |
2595 |
|
|
2596 |
|
|
2597 |
|
|
2598 |
2 |
ColourSchemeI colourScheme = ColourSchemes.getInstance() |
2599 |
|
.getColourScheme(colourSchemeName, ap.av, sg, |
2600 |
|
ap.av.getHiddenRepSequences()); |
2601 |
2 |
sg.setColourScheme(colourScheme); |
2602 |
2 |
if (colourScheme instanceof Blosum62ColourScheme |
2603 |
|
|| colourScheme instanceof PIDColourScheme) |
2604 |
|
{ |
2605 |
0 |
sg.cs.setConsensus(AAFrequency.calculate( |
2606 |
|
sg.getSequences(ap.av.getHiddenRepSequences()), |
2607 |
|
sg.getStartRes(), sg.getEndRes() + 1)); |
2608 |
|
} |
2609 |
|
|
2610 |
2 |
refresh(); |
2611 |
|
} |
2612 |
|
|
2613 |
|
} |