*/
package jalview.gui;
-import jalview.bin.Jalview;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.SequenceAnnotationReport;
-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.util.List;
import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
import javax.swing.Timer;
import javax.swing.ToolTipManager;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.SeqPanel.MousePos;
+import jalview.io.SequenceAnnotationReport;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
+
/**
* This panel hosts alignment sequence ids and responds to mouse clicks on them,
* as well as highlighting ids matched by a search from the Find menu.
ScrollThread scrollThread = null;
- String linkImageURL;
-
int offy;
// int width;
this.av = av;
alignPanel = parent;
setIdCanvas(new IdCanvas(av));
- linkImageURL = getClass().getResource("/images/link.gif").toString();
- seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
+ seqAnnotReport = new SequenceAnnotationReport(true);
setLayout(new BorderLayout());
add(getIdCanvas(), BorderLayout.CENTER);
addMouseListener(this);
}
/**
- * 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)
{
SeqPanel sp = alignPanel.getSeqPanel();
- int seq = Math.max(0, sp.findSeq(e));
- if (seq > -1 && seq < av.getAlignment().getHeight())
+ MousePos pos = sp.findMousePosition(e);
+ if (pos.isOverAnnotation())
{
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- StringBuilder tip = new StringBuilder(64);
- seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
- av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
- setToolTipText(JvSwingUtils.wrapTooltip(true,
- sequence.getDisplayId(true) + " " + tip.toString()));
+ /*
+ * mouse is over an annotation label in wrapped mode
+ */
+ AlignmentAnnotation[] anns = av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation annotation = anns[pos.annotationIndex];
+ setToolTipText(AnnotationLabels.getTooltip(annotation));
+ alignPanel.alignFrame.setStatus(
+ AnnotationLabels.getStatusMessage(annotation, anns));
+ }
+ else
+ {
+ int seq = Math.max(0, pos.seqIndex);
+ if (seq < av.getAlignment().getHeight())
+ {
+ 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, tip.toString()));
+
+ StringBuilder text = new StringBuilder();
+ text.append("Sequence ").append(String.valueOf(seq + 1))
+ .append(" ID: ").append(sequence.getName());
+ alignPanel.alignFrame.setStatus(text.toString());
+ }
}
}
{
mouseDragging = true;
- int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e));
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+ if (pos.isOverAnnotation())
+ {
+ // mouse is over annotation label in wrapped mode
+ return;
+ }
+
+ int seq = Math.max(0, pos.seqIndex);
if (seq < lastid)
{
return;
}
- int seq = alignPanel.getSeqPanel().findSeq(e);
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+ int seq = pos.seqIndex;
+ if (pos.isOverAnnotation() || seq < 0)
+ {
+ return;
+ }
+
String id = av.getAlignment().getSequenceAt(seq).getName();
String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
if (scrollThread != null)
{
scrollThread.stopScrolling();
+ scrollThread = null;
}
}
void startScrolling(boolean up)
{
scrollThread = new ScrollThread(up);
- if (!Jalview.isJS())
- {
- /*
- * Java - run in a new thread
- */
- scrollThread.start();
- }
- else
+ if (Platform.isJS())
{
/*
* for JalviewJS using Swing Timer
{
if (scrollThread == null)
{
- // finished and nulled itself
+ // IdPanel.stopScrolling called
t.stop();
}
}
});
t.start();
}
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ scrollThread.start();
+ }
}
/**
return;
}
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+
if (e.isPopupTrigger()) // Mac reports this in mousePressed
{
- showPopupMenu(e);
+ showPopupMenu(e, pos);
return;
}
av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
}
- int seq = alignPanel.getSeqPanel().findSeq(e);
if (e.isShiftDown() && (lastid != -1))
{
- selectSeqs(lastid, seq);
+ selectSeqs(lastid, pos.seqIndex);
}
else
{
- selectSeq(seq);
+ selectSeq(pos.seqIndex);
}
av.isSelectionGroupChanged(true);
*
* @param e
*/
- void showPopupMenu(MouseEvent e)
+ void showPopupMenu(MouseEvent e, MousePos pos)
{
- int seq2 = alignPanel.getSeqPanel().findSeq(e);
- Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
+ if (pos.isOverAnnotation())
+ {
+ showAnnotationMenu(e, pos);
+ return;
+ }
- /*
- * 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)
+ Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex);
+ if (sq != null)
{
- if (sf.links != null)
- {
- for (String link : sf.links)
- {
- nlinks.add(link);
- }
- }
+ PopupMenu pop = new PopupMenu(alignPanel, sq,
+ Preferences.getGroupURLLinks());
+ pop.show(this, e.getX(), e.getY());
}
+ }
- PopupMenu pop = new PopupMenu(alignPanel, sq, features,
- Preferences.getGroupURLLinks());
+ /**
+ * On right mouse click on a Consensus annotation label, shows a limited popup
+ * menu, with options to configure the consensus calculation and rendering.
+ *
+ * @param e
+ * @param pos
+ * @see AnnotationLabels#showPopupMenu(MouseEvent)
+ */
+ void showAnnotationMenu(MouseEvent e, MousePos pos)
+ {
+ if (pos.annotationIndex == -1)
+ {
+ return;
+ }
+ AlignmentAnnotation[] anns = this.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (anns == null || pos.annotationIndex >= anns.length)
+ {
+ return;
+ }
+ AlignmentAnnotation ann = anns[pos.annotationIndex];
+ if (!ann.label.contains("Consensus"))
+ {
+ return;
+ }
+
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
+ AnnotationLabels.addConsensusMenuOptions(this.alignPanel, ann, pop);
pop.show(this, e.getX(), e.getY());
}
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);
}
}
@Override
public void mouseReleased(MouseEvent e)
{
- stopScrolling();
+ if (scrollThread != null)
+ {
+ stopScrolling();
+ }
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
mouseDragging = false;
PaintRefresher.Refresh(this, av.getSequenceSetId());
if (e.isPopupTrigger()) // Windows reports this in mouseReleased
{
- showPopupMenu(e);
+ showPopupMenu(e, pos);
}
}
{
getIdCanvas().setHighlighted(list);
- if (list == null)
+ if (list == null || list.isEmpty())
{
return;
}
{
this.up = up;
setName("IdPanel$ScrollThread$" + String.valueOf(up));
- start();
}
/**
git://source.jalview.org / jalview.git / blobdiff