*/
package jalview.gui;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.commands.EditCommand;
import jalview.viewmodel.ViewportRanges;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Point;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.awt.event.MouseWheelEvent;
-import java.awt.event.MouseWheelListener;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import javax.swing.JPanel;
-import javax.swing.SwingUtilities;
-import javax.swing.ToolTipManager;
-
/**
* DOCUMENT ME!
*
StringBuffer keyboardNo2;
- java.net.URL linkImageURL;
-
private final SequenceAnnotationReport seqARep;
StringBuilder tooltipText = new StringBuilder();
*/
public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
{
- linkImageURL = getClass().getResource("/images/link.gif");
- seqARep = new SequenceAnnotationReport(linkImageURL.toString());
+ seqARep = new SequenceAnnotationReport(true);
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
.findComplementFeaturesAtResidue(ds, pos);
if (mf != null)
{
- List<String> pv = mf.findProteinVariants();
- for (String s : pv)
+ for (SequenceFeature sf : mf.features)
{
- if (!infos.contains(s))
+ String pv = mf.findProteinVariants(sf);
+ if (pv.length() > 0 && !infos.contains(pv))
{
- infos.addAll(pv);
+ infos.add(pv);
}
}
}
* add features that straddle the gap (pos may be the residue before or
* after the gap)
*/
+ int unshownFeatures = 0;
if (av.isShowSequenceFeatures())
{
List<SequenceFeature> features = ap.getFeatureRenderer()
.findFeaturesAtColumn(sequence, column + 1);
- seqARep.appendFeatures(tooltipText, pos, features,
- this.ap.getSeqPanel().seqCanvas.fr);
+ unshownFeatures = seqARep.appendFeatures(tooltipText, pos,
+ features, this.ap.getSeqPanel().seqCanvas.fr,
+ MAX_TOOLTIP_LENGTH);
/*
* add features in CDS/protein complement at the corresponding
pos);
if (mf != null)
{
- seqARep.appendFeatures(tooltipText, pos, mf.features, fr2);
+ unshownFeatures = seqARep.appendFeatures(tooltipText,
+ pos, mf, fr2, MAX_TOOLTIP_LENGTH);
}
}
}
}
- if (tooltipText.length() == 6) // <html>
+ if (tooltipText.length() == 6) // "<html>"
{
setToolTipText(null);
lastTooltip = null;
}
else
{
- if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
+ if (tooltipText.length() > MAX_TOOLTIP_LENGTH)
{
tooltipText.setLength(MAX_TOOLTIP_LENGTH);
tooltipText.append("...");
}
+ if (unshownFeatures > 0)
+ {
+ tooltipText.append("<br/>").append("... ").append("<i>")
+ .append(MessageManager.formatMessage(
+ "label.features_not_shown", unshownFeatures))
+ .append("</i>");
+ }
String textString = tooltipText.toString();
if (lastTooltip == null || !lastTooltip.equals(textString))
{
{
char sequenceChar = sequence.getCharAt(column);
int pos = sequence.findPosition(column);
- setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+ setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos);
return pos;
}
* Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
* </pre>
*
- * @param sequence
+ * @param seqName
* @param seqIndex
* sequence position in the alignment (1..)
* @param sequenceChar
* @param residuePos
* the sequence residue position (if not over a gap)
*/
- protected void setStatusMessage(SequenceI sequence, int seqIndex,
+ protected void setStatusMessage(String seqName, int seqIndex,
char sequenceChar, int residuePos)
{
StringBuilder text = new StringBuilder(32);
*/
String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
text.append("Sequence").append(seqno).append(" ID: ")
- .append(sequence.getName());
+ .append(seqName);
String residue = null;
{
return;
}
- SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+ SequenceI alignedSeq = al.getSequenceAt(sequenceIndex);
+ SequenceI ds = alignedSeq.getDatasetSequence();
for (SearchResultMatchI m : results.getResults())
{
SequenceI seq = m.getSequence();
if (seq == ds)
{
int start = m.getStart();
- setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
- start);
+ setStatusMessage(alignedSeq.getName(), sequenceIndex,
+ seq.getCharAt(start - 1), start);
return;
}
}
return;
}
- if (evt.getClickCount() > 1)
+ if (evt.getClickCount() > 1 && av.isShowSequenceFeatures())
{
sg = av.getSelectionGroup();
if (sg != null && sg.getSize() == 1
final int column = pos.column;
final int seq = pos.seqIndex;
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- List<SequenceFeature> features = ap.getFeatureRenderer()
- .findFeaturesAtColumn(sequence, column + 1);
-
- PopupMenu pop = new PopupMenu(ap, null, features);
- pop.show(this, evt.getX(), evt.getY());
+ if (sequence != null)
+ {
+ PopupMenu pop = new PopupMenu(ap, sequence, column);
+ pop.show(this, evt.getX(), evt.getY());
+ }
}
/**
* Map sequence selection
*/
SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
- av.setSelectionGroup(sg);
+ av.setSelectionGroup(sg != null && sg.getSize() > 0 ? sg : null);
av.isSelectionGroupChanged(true);
/*