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package jalview.gui; |
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import jalview.bin.Jalview; |
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import jalview.datamodel.Sequence; |
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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.io.SequenceAnnotationReport; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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import jalview.viewmodel.AlignmentViewport; |
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import jalview.viewmodel.ViewportRanges; |
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import java.awt.BorderLayout; |
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import java.awt.event.ActionEvent; |
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import java.awt.event.ActionListener; |
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import java.awt.event.MouseEvent; |
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import java.awt.event.MouseListener; |
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import java.awt.event.MouseMotionListener; |
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import java.awt.event.MouseWheelEvent; |
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import java.awt.event.MouseWheelListener; |
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import java.util.List; |
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import javax.swing.JPanel; |
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import javax.swing.SwingUtilities; |
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import javax.swing.Timer; |
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import javax.swing.ToolTipManager; |
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@author |
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@version |
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| 8% |
Uncovered Elements: 183 (199) |
Complexity: 60 |
Complexity Density: 0.49 |
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public class IdPanel extends JPanel |
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implements MouseListener, MouseMotionListener, MouseWheelListener |
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{ |
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private IdCanvas idCanvas; |
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protected AlignmentViewport av; |
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protected AlignmentPanel alignPanel; |
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ScrollThread scrollThread = null; |
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String linkImageURL; |
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int offy; |
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int lastid = -1; |
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boolean mouseDragging = false; |
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private final SequenceAnnotationReport seqAnnotReport; |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
|
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public IdPanel(AlignViewport av, AlignmentPanel parent)... |
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{ |
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this.av = av; |
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alignPanel = parent; |
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setIdCanvas(new IdCanvas(av)); |
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linkImageURL = getClass().getResource("/images/link.gif").toString(); |
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seqAnnotReport = new SequenceAnnotationReport(linkImageURL); |
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setLayout(new BorderLayout()); |
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add(getIdCanvas(), BorderLayout.CENTER); |
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addMouseListener(this); |
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addMouseMotionListener(this); |
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addMouseWheelListener(this); |
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ToolTipManager.sharedInstance().registerComponent(this); |
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} |
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@param |
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| 0% |
Uncovered Elements: 9 (9) |
Complexity: 3 |
Complexity Density: 0.43 |
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@Override... |
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public void mouseMoved(MouseEvent e) |
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{ |
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SeqPanel sp = alignPanel.getSeqPanel(); |
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int seq = Math.max(0, sp.findSeq(e)); |
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if (seq > -1 && seq < av.getAlignment().getHeight()) |
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{ |
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SequenceI sequence = av.getAlignment().getSequenceAt(seq); |
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StringBuilder tip = new StringBuilder(64); |
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seqAnnotReport.createTooltipAnnotationReport(tip, sequence, |
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av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr); |
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setToolTipText(JvSwingUtils.wrapTooltip(true, |
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sequence.getDisplayId(true) + " " + tip.toString())); |
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} |
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} |
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@param |
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| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
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@Override... |
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public void mouseDragged(MouseEvent e) |
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{ |
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mouseDragging = true; |
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int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e)); |
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if (seq < lastid) |
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{ |
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selectSeqs(lastid - 1, seq); |
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} |
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else if (seq > lastid) |
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{ |
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selectSeqs(lastid + 1, seq); |
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} |
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lastid = seq; |
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alignPanel.paintAlignment(false, false); |
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} |
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| 0% |
Uncovered Elements: 18 (18) |
Complexity: 5 |
Complexity Density: 0.5 |
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@Override... |
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public void mouseWheelMoved(MouseWheelEvent e) |
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{ |
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e.consume(); |
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double wheelRotation = e.getPreciseWheelRotation(); |
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if (wheelRotation > 0) |
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{ |
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if (e.isShiftDown()) |
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{ |
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av.getRanges().scrollRight(true); |
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} |
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else |
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{ |
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av.getRanges().scrollUp(false); |
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} |
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} |
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else if (wheelRotation < 0) |
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{ |
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if (e.isShiftDown()) |
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{ |
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av.getRanges().scrollRight(false); |
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} |
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else |
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{ |
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av.getRanges().scrollUp(true); |
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} |
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} |
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} |
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@param |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 4 |
Complexity Density: 0.44 |
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@Override... |
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public void mouseClicked(MouseEvent e) |
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{ |
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if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e)) |
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{ |
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return; |
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} |
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int seq = alignPanel.getSeqPanel().findSeq(e); |
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String id = av.getAlignment().getSequenceAt(seq).getName(); |
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String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id); |
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try |
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{ |
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jalview.util.BrowserLauncher.openURL(url); |
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} catch (Exception ex) |
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{ |
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JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
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MessageManager.getString("label.web_browser_not_found_unix"), |
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MessageManager.getString("label.web_browser_not_found"), |
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JvOptionPane.WARNING_MESSAGE); |
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ex.printStackTrace(); |
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} |
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} |
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@param |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public void mouseEntered(MouseEvent e) |
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{ |
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stopScrolling(); |
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} |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
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void stopScrolling()... |
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{ |
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if (scrollThread != null) |
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{ |
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scrollThread.stopScrolling(); |
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} |
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} |
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@param |
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| 0% |
Uncovered Elements: 16 (16) |
Complexity: 7 |
Complexity Density: 0.88 |
|
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0 |
@Override... |
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public void mouseExited(MouseEvent e) |
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{ |
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if (av.getWrapAlignment()) |
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{ |
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return; |
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} |
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if (mouseDragging) |
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{ |
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ViewportRanges ranges = av.getRanges(); |
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if (e.getY() < 0 && ranges.getStartSeq() > 0) |
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{ |
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startScrolling(true); |
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} |
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else if (e.getY() >= getHeight() |
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&& ranges.getEndSeq() <= av.getAlignment().getHeight()) |
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{ |
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startScrolling(false); |
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} |
273 |
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} |
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} |
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@param |
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
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0 |
void startScrolling(boolean up)... |
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{ |
283 |
0 |
scrollThread = new ScrollThread(up); |
284 |
0 |
if (!Jalview.isJS()) |
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{ |
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288 |
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289 |
0 |
scrollThread.start(); |
290 |
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} |
291 |
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else |
292 |
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{ |
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295 |
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296 |
0 |
Timer t = new Timer(20, new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
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0 |
@Override... |
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public void actionPerformed(ActionEvent e) |
300 |
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{ |
301 |
0 |
if (scrollThread != null) |
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{ |
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304 |
0 |
scrollThread.scrollOnce(); |
305 |
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} |
306 |
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} |
307 |
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}); |
308 |
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t.addActionListener(new ActionListener() |
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{ |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
310 |
0 |
@Override... |
311 |
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public void actionPerformed(ActionEvent e) |
312 |
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{ |
313 |
0 |
if (scrollThread == null) |
314 |
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{ |
315 |
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316 |
0 |
t.stop(); |
317 |
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} |
318 |
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} |
319 |
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}); |
320 |
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t.start(); |
321 |
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} |
322 |
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} |
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@param |
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| 0% |
Uncovered Elements: 27 (27) |
Complexity: 12 |
Complexity Density: 0.71 |
|
337 |
0 |
@Override... |
338 |
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public void mousePressed(MouseEvent e) |
339 |
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{ |
340 |
0 |
if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e)) |
341 |
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{ |
342 |
0 |
return; |
343 |
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} |
344 |
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345 |
0 |
if (e.isPopupTrigger()) |
346 |
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{ |
347 |
0 |
showPopupMenu(e); |
348 |
0 |
return; |
349 |
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} |
350 |
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356 |
0 |
if (SwingUtilities.isRightMouseButton(e) && !Platform.isAMac()) |
357 |
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{ |
358 |
0 |
return; |
359 |
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} |
360 |
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361 |
0 |
if ((av.getSelectionGroup() == null) |
362 |
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|| (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() |
363 |
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&& av.getSelectionGroup() != null)) |
364 |
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{ |
365 |
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av.setSelectionGroup(new SequenceGroup()); |
366 |
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av.getSelectionGroup().setStartRes(0); |
367 |
0 |
av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1); |
368 |
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} |
369 |
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370 |
0 |
int seq = alignPanel.getSeqPanel().findSeq(e); |
371 |
0 |
if (e.isShiftDown() && (lastid != -1)) |
372 |
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{ |
373 |
0 |
selectSeqs(lastid, seq); |
374 |
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} |
375 |
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else |
376 |
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{ |
377 |
0 |
selectSeq(seq); |
378 |
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} |
379 |
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380 |
0 |
av.isSelectionGroupChanged(true); |
381 |
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382 |
0 |
alignPanel.paintAlignment(false, false); |
383 |
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} |
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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@param |
389 |
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| 0% |
Uncovered Elements: 12 (12) |
Complexity: 2 |
Complexity Density: 0.2 |
|
390 |
0 |
void showPopupMenu(MouseEvent e)... |
391 |
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{ |
392 |
0 |
int seq2 = alignPanel.getSeqPanel().findSeq(e); |
393 |
0 |
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2); |
394 |
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395 |
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396 |
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397 |
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398 |
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399 |
0 |
List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); |
400 |
0 |
List<SequenceFeature> features = sq.getFeatures().getNonPositionalFeatures(); |
401 |
0 |
for (SequenceFeature sf : features) |
402 |
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{ |
403 |
0 |
if (sf.links != null) |
404 |
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{ |
405 |
0 |
for (String link : sf.links) |
406 |
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{ |
407 |
0 |
nlinks.add(link); |
408 |
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} |
409 |
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} |
410 |
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} |
411 |
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|
412 |
0 |
PopupMenu pop = new PopupMenu(alignPanel, sq, features, |
413 |
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Preferences.getGroupURLLinks()); |
414 |
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pop.show(this, e.getX(), e.getY()); |
415 |
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} |
416 |
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417 |
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418 |
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419 |
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420 |
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@param |
421 |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
422 |
0 |
void selectSeq(int seq)... |
423 |
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{ |
424 |
0 |
lastid = seq; |
425 |
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|
426 |
0 |
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); |
427 |
0 |
av.getSelectionGroup().addOrRemove(pickedSeq, true); |
428 |
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} |
429 |
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430 |
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431 |
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432 |
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|
433 |
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|
434 |
|
@param |
435 |
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@param |
436 |
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| 0% |
Uncovered Elements: 20 (20) |
Complexity: 5 |
Complexity Density: 0.42 |
|
437 |
0 |
void selectSeqs(int start, int end)... |
438 |
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{ |
439 |
0 |
if (av.getSelectionGroup() == null) |
440 |
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{ |
441 |
0 |
return; |
442 |
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} |
443 |
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|
444 |
0 |
if (end >= av.getAlignment().getHeight()) |
445 |
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{ |
446 |
0 |
end = av.getAlignment().getHeight() - 1; |
447 |
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} |
448 |
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|
449 |
0 |
lastid = start; |
450 |
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|
451 |
0 |
if (end < start) |
452 |
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{ |
453 |
0 |
int tmp = start; |
454 |
0 |
start = end; |
455 |
0 |
end = tmp; |
456 |
0 |
lastid = end; |
457 |
|
} |
458 |
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|
459 |
0 |
for (int i = start; i <= end; i++) |
460 |
|
{ |
461 |
0 |
av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), |
462 |
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i == end); |
463 |
|
} |
464 |
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} |
465 |
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|
466 |
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|
467 |
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|
468 |
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|
469 |
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|
470 |
|
@param |
471 |
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|
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
472 |
0 |
@Override... |
473 |
|
public void mouseReleased(MouseEvent e) |
474 |
|
{ |
475 |
0 |
stopScrolling(); |
476 |
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|
477 |
0 |
mouseDragging = false; |
478 |
0 |
PaintRefresher.Refresh(this, av.getSequenceSetId()); |
479 |
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|
480 |
0 |
av.sendSelection(); |
481 |
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|
482 |
0 |
if (e.isPopupTrigger()) |
483 |
|
{ |
484 |
0 |
showPopupMenu(e); |
485 |
|
} |
486 |
|
} |
487 |
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|
488 |
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|
489 |
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|
490 |
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|
491 |
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|
492 |
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@param |
493 |
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| 0% |
Uncovered Elements: 10 (10) |
Complexity: 4 |
Complexity Density: 0.67 |
|
494 |
0 |
public void highlightSearchResults(List<SequenceI> list)... |
495 |
|
{ |
496 |
0 |
getIdCanvas().setHighlighted(list); |
497 |
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|
498 |
0 |
if (list == null) |
499 |
|
{ |
500 |
0 |
return; |
501 |
|
} |
502 |
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|
503 |
0 |
int index = av.getAlignment().findIndex(list.get(0)); |
504 |
|
|
505 |
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|
506 |
0 |
if ((av.getRanges().getStartSeq() > index) |
507 |
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|| (av.getRanges().getEndSeq() < index)) |
508 |
|
{ |
509 |
0 |
av.getRanges().setStartSeq(index); |
510 |
|
} |
511 |
|
} |
512 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
513 |
2234 |
public IdCanvas getIdCanvas()... |
514 |
|
{ |
515 |
2234 |
return idCanvas; |
516 |
|
} |
517 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
518 |
217 |
public void setIdCanvas(IdCanvas idCanvas)... |
519 |
|
{ |
520 |
217 |
this.idCanvas = idCanvas; |
521 |
|
} |
522 |
|
|
523 |
|
|
524 |
|
|
525 |
|
|
526 |
|
|
|
|
| 0% |
Uncovered Elements: 31 (31) |
Complexity: 9 |
Complexity Density: 0.47 |
|
527 |
|
class ScrollThread extends Thread |
528 |
|
{ |
529 |
|
private boolean running = false; |
530 |
|
|
531 |
|
private boolean up; |
532 |
|
|
533 |
|
|
534 |
|
|
535 |
|
|
536 |
|
@param |
537 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
538 |
0 |
public ScrollThread(boolean up)... |
539 |
|
{ |
540 |
0 |
this.up = up; |
541 |
0 |
setName("IdPanel$ScrollThread$" + String.valueOf(up)); |
542 |
0 |
start(); |
543 |
|
} |
544 |
|
|
545 |
|
|
546 |
|
|
547 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
548 |
0 |
public void stopScrolling()... |
549 |
|
{ |
550 |
0 |
running = false; |
551 |
|
} |
552 |
|
|
553 |
|
|
554 |
|
|
555 |
|
|
556 |
|
|
557 |
|
|
558 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
559 |
0 |
@Override... |
560 |
|
public void run() |
561 |
|
{ |
562 |
0 |
running = true; |
563 |
|
|
564 |
0 |
while (running) |
565 |
|
{ |
566 |
0 |
running = scrollOnce(); |
567 |
0 |
try |
568 |
|
{ |
569 |
0 |
Thread.sleep(100); |
570 |
|
} catch (Exception ex) |
571 |
|
{ |
572 |
|
} |
573 |
|
} |
574 |
0 |
IdPanel.this.scrollThread = null; |
575 |
|
} |
576 |
|
|
577 |
|
|
578 |
|
|
579 |
|
|
580 |
|
|
|
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 4 |
Complexity Density: 0.44 |
|
581 |
0 |
boolean scrollOnce()... |
582 |
|
{ |
583 |
0 |
ViewportRanges ranges = IdPanel.this.av.getRanges(); |
584 |
0 |
if (ranges.scrollUp(up)) |
585 |
|
{ |
586 |
0 |
int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq(); |
587 |
0 |
int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1; |
588 |
0 |
IdPanel.this.selectSeqs(fromSeq, toSeq); |
589 |
0 |
lastid = toSeq; |
590 |
0 |
alignPanel.paintAlignment(false, false); |
591 |
0 |
return true; |
592 |
|
} |
593 |
|
|
594 |
0 |
return false; |
595 |
|
} |
596 |
|
} |
597 |
|
} |