import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.SeqPanel.MousePos;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
+import javax.swing.Timer;
import javax.swing.ToolTipManager;
/**
}
/**
- * Respond to mouse movement by constructing tooltip text for the sequence id
- * under the mouse.
+ * Responds to mouse movement by setting tooltip text for the sequence id
+ * under the mouse (or possibly annotation label, when in wrapped mode)
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseMoved(MouseEvent e)
/*
* mouse is over an annotation label in wrapped mode
*/
- AlignmentAnnotation annotation = av.getAlignment()
- .getAlignmentAnnotation()[pos.annotationIndex];
+ AlignmentAnnotation[] anns = av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation annotation = anns[pos.annotationIndex];
setToolTipText(AnnotationLabels.getTooltip(annotation));
+ alignPanel.alignFrame.setStatus(
+ AnnotationLabels.getStatusMessage(annotation, anns));
}
else
{
{
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
StringBuilder tip = new StringBuilder(64);
+ tip.append(sequence.getDisplayId(true)).append(" ");
seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
- setToolTipText(JvSwingUtils.wrapTooltip(true,
- sequence.getDisplayId(true) + " " + tip.toString()));
+ setToolTipText(JvSwingUtils.wrapTooltip(true, tip.toString()));
+
+ StringBuilder text = new StringBuilder();
+ text.append("Sequence ").append(String.valueOf(seq + 1))
+ .append(" ID: ")
+ .append(sequence.getName());
+ alignPanel.alignFrame.setStatus(text.toString());
}
}
}
}
MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
- if (pos.isOverAnnotation())
+ int seq = pos.seqIndex;
+ if (pos.isOverAnnotation() || seq < 0)
{
- // mouse is over annotation label in wrapped mode
return;
}
- int seq = pos.seqIndex;
String id = av.getAlignment().getSequenceAt(seq).getName();
String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
JvOptionPane.WARNING_MESSAGE);
}
/**
- * DOCUMENT ME!
+ * On (re-)entering the panel, stop any scrolling
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseEntered(MouseEvent e)
{
+ stopScrolling();
+ }
+
+ /**
+ * Interrupts the scroll thread if one is running
+ */
+ void stopScrolling()
+ {
if (scrollThread != null)
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
+ scrollThread = null;
}
}
return;
}
- if (mouseDragging && (e.getY() < 0)
- && (av.getRanges().getStartSeq() > 0))
+ if (mouseDragging)
{
- scrollThread = new ScrollThread(true);
+ /*
+ * on mouse drag above or below the panel, start
+ * scrolling if there are more sequences to show
+ */
+ ViewportRanges ranges = av.getRanges();
+ if (e.getY() < 0 && ranges.getStartSeq() > 0)
+ {
+ startScrolling(true);
+ }
+ else if (e.getY() >= getHeight()
+ && ranges.getEndSeq() <= av.getAlignment().getHeight())
+ {
+ startScrolling(false);
+ }
}
+ }
- if (mouseDragging && (e.getY() >= getHeight())
- && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
+ /**
+ * Starts scrolling either up or down
+ *
+ * @param up
+ */
+ void startScrolling(boolean up)
+ {
+ scrollThread = new ScrollThread(up);
+ if (Platform.isJS())
+ {
+ /*
+ * for JalviewJS using Swing Timer
+ */
+ Timer t = new Timer(20, new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (scrollThread != null)
+ {
+ // if (!scrollOnce() {t.stop();}) gives compiler error :-(
+ scrollThread.scrollOnce();
+ }
+ }
+ });
+ t.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (scrollThread == null)
+ {
+ // IdPanel.stopScrolling called
+ t.stop();
+ }
+ }
+ });
+ t.start();
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- scrollThread = new ScrollThread(false);
+ scrollThread.start();
}
}
* (where isPopupTrigger() will answer true)
* NB isRightMouseButton is also true for Cmd-click on Mac
*/
- if (SwingUtilities.isRightMouseButton(e) && !Platform.isAMac())
+ if (Platform.isWinRightButton(e))
{
return;
}
}
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex);
-
- /*
- * build a new links menu based on the current links
- * and any non-positional features
- */
- List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
- List<SequenceFeature> features = sq.getFeatures().getNonPositionalFeatures();
- for (SequenceFeature sf : features)
+ if (sq != null)
{
- if (sf.links != null)
- {
- nlinks.addAll(sf.links);
+ PopupMenu pop = new PopupMenu(alignPanel, sq,
+ Preferences.getGroupURLLinks());
+ pop.show(this, e.getX(), e.getY());
}
}
- PopupMenu pop = new PopupMenu(alignPanel, sq, features,
- Preferences.getGroupURLLinks());
- pop.show(this, e.getX(), e.getY());
- }
-
/**
* On right mouse click on a Consensus annotation label, shows a limited popup
* menu, with options to configure the consensus calculation and rendering.
lastid = seq;
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, true);
+ av.getSelectionGroup().addOrRemove(pickedSeq, false);
}
/**
for (int i = start; i <= end; i++)
{
av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
- i == end);
+ false);
}
}
{
if (scrollThread != null)
{
- scrollThread.running = false;
+ stopScrolling();
}
MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
{
getIdCanvas().setHighlighted(list);
- if (list == null)
+ if (list == null || list.isEmpty())
{
return;
}
this.idCanvas = idCanvas;
}
- // this class allows scrolling off the bottom of the visible alignment
+ /**
+ * Performs scrolling of the visible alignment up or down, adding newly
+ * visible sequences to the current selection
+ */
class ScrollThread extends Thread
{
- boolean running = false;
+ private boolean running = false;
- boolean up = true;
+ private boolean up;
+ /**
+ * Constructor for a thread that scrolls either up or down
+ *
+ * @param up
+ */
public ScrollThread(boolean up)
{
this.up = up;
- start();
+ setName("IdPanel$ScrollThread$" + String.valueOf(up));
}
+ /**
+ * Sets a flag to stop the scrolling
+ */
public void stopScrolling()
{
running = false;
}
+ /**
+ * Scrolls the alignment either up or down, one row at a time, adding newly
+ * visible sequences to the current selection. Speed is limited to a maximum
+ * of ten rows per second. The thread exits when the end of the alignment is
+ * reached or a flag is set to stop it by a call to stopScrolling.
+ */
@Override
public void run()
{
while (running)
{
- if (av.getRanges().scrollUp(up))
- {
- // scroll was ok, so add new sequence to selection
- int seq = av.getRanges().getStartSeq();
-
- if (!up)
- {
- seq = av.getRanges().getEndSeq();
- }
-
- if (seq < lastid)
- {
- selectSeqs(lastid - 1, seq);
- }
- else if (seq > lastid)
- {
- selectSeqs(lastid + 1, seq);
- }
-
- lastid = seq;
- }
- else
- {
- running = false;
- }
-
- alignPanel.paintAlignment(false, false);
-
+ running = scrollOnce();
try
{
Thread.sleep(100);
{
}
}
+ IdPanel.this.scrollThread = null;
+ }
+
+ /**
+ * Scrolls one row up or down. Answers true if a scroll could be done, false
+ * if not (top or bottom of alignment reached).
+ */
+ boolean scrollOnce()
+ {
+ ViewportRanges ranges = IdPanel.this.av.getRanges();
+ if (ranges.scrollUp(up))
+ {
+ int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq();
+ int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1;
+ IdPanel.this.selectSeqs(fromSeq, toSeq);
+ lastid = toSeq;
+ alignPanel.paintAlignment(false, false);
+ return true;
+ }
+
+ return false;
}
}
}
git://source.jalview.org / jalview.git / blobdiff