int end = sg.findEndRes(sg.getSequenceAt(i));
if (start <= end)
{
- seqs[rsize] = sg.getSequenceAt(i);
- features[rsize] = new SequenceFeature(null, null, start,
- end, "Jalview");
- rsize++;
+ seqs.add(sg.getSequenceAt(i));
- features.add(new SequenceFeature(null, null, null, start, end,
++ features.add(new SequenceFeature(null, null, start, end,
+ "Jalview"));
}
}
- rseqs = new SequenceI[rsize];
- tfeatures = new SequenceFeature[rsize];
- System.arraycopy(seqs, 0, rseqs, 0, rsize);
- System.arraycopy(features, 0, tfeatures, 0, rsize);
- features = tfeatures;
- seqs = rseqs;
if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
features, true, ap))
if (!create)
{
- SequenceFeature sf = features[featureIndex];
+ SequenceFeature sf = features.get(featureIndex);
if (dialog.accept)
{
- sf.type = enteredType;
- sf.featureGroup = group.getText().trim();
- if (sf.featureGroup != null && sf.featureGroup.length() < 1)
- {
- sf.featureGroup = null;
- }
- sf.description = description.getText().replace('\n', ' ');
if (!colourPanel.isGcol)
{
// update colour - otherwise its already done.
setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
}
+ int newBegin = sf.begin;
+ int newEnd = sf.end;
try
{
- sf.begin = Integer.parseInt(start.getText());
- sf.end = Integer.parseInt(end.getText());
+ newBegin = Integer.parseInt(start.getText());
+ newEnd = Integer.parseInt(end.getText());
} catch (NumberFormatException ex)
{
- //
+ //
}
+
+ /*
+ * replace the feature by deleting it and adding a new one
+ * (to ensure integrity of SequenceFeatures data store)
+ */
- sequences[0].deleteFeature(sf);
++ sequences.get(0).deleteFeature(sf);
+ SequenceFeature newSf = new SequenceFeature(sf, newBegin, newEnd,
+ enteredGroup, sf.getScore());
+ newSf.setDescription(enteredDesc);
+ ffile.parseDescriptionHTML(newSf, false);
+ // amend features dialog only updates one sequence at a time
- sequences[0].addSequenceFeature(newSf);
++ sequences.get(0).addSequenceFeature(newSf);
boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup
.equals(sf.featureGroup));
*/
if (dialog.accept && name.getText().length() > 0)
{
- for (int i = 0; i < sequences.length; i++)
+ for (int i = 0; i < sequences.size(); i++)
{
- SequenceFeature sf = features[i];
- features.get(i).type = enteredType;
- features.get(i).featureGroup = group.getText().trim();
- features.get(i).description = description.getText()
- .replace('\n', ' ');
- sequences.get(i).addSequenceFeature(features.get(i));
- ffile.parseDescriptionHTML(features.get(i), false);
++ SequenceFeature sf = features.get(i);
+ SequenceFeature sf2 = new SequenceFeature(enteredType,
+ enteredDesc, sf.getBegin(), sf.getEnd(), enteredGroup);
+ ffile.parseDescriptionHTML(sf2, false);
- sequences[i].addSequenceFeature(sf2);
++ sequences.get(i).addSequenceFeature(sf2);
}
Color newColour = colourPanel.getBackground();
public void createNewGroup_actionPerformed()
{
- SequenceI[] seqs = new SequenceI[searchResults.getSize()];
- SequenceFeature[] features = new SequenceFeature[searchResults
- .getSize()];
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceFeature> features = new ArrayList<SequenceFeature>();
String searchString = textfield.getText().trim();
- int i = 0;
for (SearchResultMatchI match : searchResults.getResults())
{
- seqs[i] = match.getSequence().getDatasetSequence();
-
- features[i] = new SequenceFeature(searchString, "Search Results",
- match.getStart(), match.getEnd(), "Search Results");
- i++;
+ seqs.add(match.getSequence().getDatasetSequence());
- features.add(new SequenceFeature(searchString,
- "Search Results", null, match.getStart(), match.getEnd(),
- "Search Results"));
++ features.add(new SequenceFeature(searchString, "Search Results",
++ match.getStart(), match.getEnd(), "Search Results"));
}
if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
-import java.util.ArrayList;
+ import java.util.Collections;
import java.util.List;
+ import java.util.ListIterator;
import java.util.Vector;
public class SeqPanel extends Panel implements MouseMotionListener,
highlight.addResult(sequence, features.get(0).getBegin(), features
.get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
- SequenceFeature[] featuresArray = features
- .toArray(new SequenceFeature[features.size()]);
seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[] { sequence }, featuresArray, false, ap);
-
+ Collections.singletonList(sequence), features, false, ap);
-
seqCanvas.highlightSearchResults(null);
}
}
}
/*
- * 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())
{
List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
- sequence.findPosition(column));
+ respos);
+ if (isGapped)
+ {
+ removeAdjacentFeatures(allFeatures, column + 1, sequence);
+ }
for (SequenceFeature sf : allFeatures)
{
tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
}
}
+ 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)
+ {
+ // TODO should this be an AlignViewController method (shared by gui)?
+ ListIterator<SequenceFeature> it = features.listIterator();
+ while (it.hasNext())
+ {
+ SequenceFeature sf = it.next();
+ if (sequence.findIndex(sf.getBegin()) > column
+ || sequence.findIndex(sf.getEnd()) < column)
+ {
+ it.remove();
+ }
+ }
+ }
+
- List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
- {
- List<SequenceFeature> result = new ArrayList<SequenceFeature>();
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- 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))
- {
- result.add(features[i]);
- }
- }
- }
-
- return result;
- }
-
Tooltip tooltip;
/**
}
else
{
- if (lastTooltip == null
- || !lastTooltip.equals(tooltipText.toString()))
+ String textString = tooltipText.toString();
+ if (lastTooltip == null || !lastTooltip.equals(textString))
{
-- String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
- tooltipText.toString());
- // String formatedTooltipText = tooltipText.toString();
- setToolTipText(formatedTooltipText);
- lastTooltip = tooltipText.toString();
++ String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
+ textString);
- setToolTipText(formatedTooltipText);
++ setToolTipText(formattedTooltipText);
+ lastTooltip = textString;
}
-
}
-
}
+ /**
+ * 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,
+ final int column, SequenceI sequence)
+ {
+ // TODO should this be an AlignViewController method (and reused by applet)?
+ ListIterator<SequenceFeature> it = features.listIterator();
+ while (it.hasNext())
+ {
+ SequenceFeature sf = it.next();
+ if (sequence.findIndex(sf.getBegin()) > column
+ || sequence.findIndex(sf.getEnd()) < column)
+ {
+ it.remove();
+ }
+ }
+ }
+
private Point lastp = null;
/*
git://source.jalview.org / jalview.git / commitdiff