import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
+import java.util.Collections;
+import java.util.List;
+import java.util.ListIterator;
import java.util.Vector;
public class SeqPanel extends Panel implements MouseMotionListener,
av.setSelectionGroup(null);
}
- SequenceFeature[] features = findFeaturesAtRes(sequence,
- sequence.findPosition(findRes(evt)));
+ int column = findRes(evt);
+ boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+ List<SequenceFeature> features = findFeaturesAtRes(sequence,
+ sequence.findPosition(column));
+ if (isGapped)
+ {
+ removeAdjacentFeatures(features, column + 1, sequence);
+ }
- if (features != null && features.length > 0)
+ if (!features.isEmpty())
{
SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequence, features[0].getBegin(),
- features[0].getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(), features
+ .get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
- }
- if (features != null && features.length > 0)
- {
seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[] { sequence }, features, false, ap);
-
+ Collections.singletonList(sequence), features, false, ap);
seqCanvas.highlightSearchResults(null);
}
}
}
final char ch = sequence.getCharAt(column);
- int respos = Comparison.isGap(ch) ? -1 : sequence.findPosition(column);
+ boolean isGapped = Comparison.isGap(ch);
+ // find residue at column (or nearest if at a gap)
+ int respos = sequence.findPosition(column);
- if (ssm != null && respos != -1)
+ if (ssm != null && !isGapped)
{
mouseOverSequence(sequence, column, respos);
}
text.append("Sequence ").append(Integer.toString(seq + 1))
.append(" ID: ").append(sequence.getName());
- String obj = null;
- if (respos != -1)
+ if (!isGapped)
{
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(ch);
- if (obj != null)
- {
- text.append(" Nucleotide: ").append(obj);
- }
+ String base = ResidueProperties.nucleotideName.get(ch);
+ text.append(" Nucleotide: ").append(base == null ? ch : base);
}
else
{
- obj = (ch == 'x' || ch == 'X') ? "X" : ResidueProperties.aa2Triplet
+ String residue = (ch == 'x' || ch == 'X') ? "X"
+ : ResidueProperties.aa2Triplet
.get(String.valueOf(ch));
- if (obj != null)
- {
- text.append(" Residue: ").append(obj);
- }
- }
- if (obj != null)
- {
- text.append(" (").append(Integer.toString(respos)).append(")");
+ text.append(" Residue: ").append(residue == null ? ch : residue);
}
+ text.append(" (").append(Integer.toString(respos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
}
/*
- * add feature details to tooltip if over one or more features
+ * add feature details to tooltip, including any that straddle
+ * a gapped position
*/
- if (respos != -1)
+ if (av.isShowSequenceFeatures())
{
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
- sequence.findPosition(column));
-
- int index = 0;
- while (index < allFeatures.length)
+ List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
+ respos);
+ if (isGapped)
+ {
+ removeAdjacentFeatures(allFeatures, column + 1, sequence);
+ }
+ for (SequenceFeature sf : allFeatures)
{
- SequenceFeature sf = allFeatures[index];
-
tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
if (sf.getDescription() != null)
}
}
tooltipText.append("\n");
-
- index++;
}
}
}
}
- SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+ List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
+ {
+ return seqCanvas.getFeatureRenderer().findFeaturesAtRes(sequence, res);
+ }
+
+ /**
+ * Removes from the list of features any that start after, or end before, the
+ * given column position. This allows us to retain only those features
+ * adjacent to a gapped position that straddle the position.
+ *
+ * @param features
+ * @param column
+ * alignment column (1..)
+ * @param sequence
+ */
+ protected void removeAdjacentFeatures(List<SequenceFeature> features,
+ int column, SequenceI sequence)
{
- Vector tmp = new Vector();
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (features != null)
+ // TODO should this be an AlignViewController method (shared by gui)?
+ ListIterator<SequenceFeature> it = features.listIterator();
+ while (it.hasNext())
{
- for (int i = 0; i < features.length; i++)
+ SequenceFeature sf = it.next();
+ if (sequence.findIndex(sf.getBegin()) > column
+ || sequence.findIndex(sf.getEnd()) < column)
{
- if (av.getFeaturesDisplayed() == null
- || !av.getFeaturesDisplayed().isVisible(
- features[i].getType()))
- {
- continue;
- }
-
- if (features[i].featureGroup != null
- && !seqCanvas.fr.checkGroupVisibility(
- features[i].featureGroup, false))
- {
- continue;
- }
-
- if ((features[i].getBegin() <= res)
- && (features[i].getEnd() >= res))
- {
- tmp.addElement(features[i]);
- }
+ it.remove();
}
}
-
- features = new SequenceFeature[tmp.size()];
- tmp.copyInto(features);
-
- return features;
}
Tooltip tooltip;
// DETECT RIGHT MOUSE BUTTON IN AWT
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+ List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
sequence.findPosition(res));
Vector<String> links = null;
- if (allFeatures != null)
+ for (SequenceFeature sf : allFeatures)
{
- for (int i = 0; i < allFeatures.length; i++)
+ if (sf.links != null)
{
- if (allFeatures[i].links != null)
+ if (links == null)
{
- if (links == null)
- {
- links = new Vector<>();
- }
- for (int j = 0; j < allFeatures[i].links.size(); j++)
- {
- links.addElement(allFeatures[i].links.elementAt(j));
- }
+ links = new Vector<String>();
}
+ links.addAll(sf.links);
}
}
APopupMenu popup = new APopupMenu(ap, null, links);
git://source.jalview.org / jalview.git / blobdiff