import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import java.awt.BorderLayout;
import java.awt.Color;
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;
if (av.hasHiddenColumns())
{
res = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(res);
+ .visibleToAbsoluteColumn(res);
}
return res;
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
- // TODO: once JAL-2759 is ready, change this loop to something more
- // efficient
- while (!hidden.isVisible(seqCanvas.cursorX)
- && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0
- && dx != 0)
+ if (!hidden.isVisible(seqCanvas.cursorX))
{
- seqCanvas.cursorX += dx;
+ int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
+ int[] region = hidden.getRegionWithEdgeAtRes(visx);
+
+ if (region != null) // just in case
+ {
+ if (dx == 1)
+ {
+ // moving right
+ seqCanvas.cursorX = region[1] + 1;
+ }
+ else if (dx == -1)
+ {
+ // moving left
+ seqCanvas.cursorX = region[0] - 1;
+ }
+ }
+ seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
}
if (seqCanvas.cursorX >= maxWidth
{
// scrollToWrappedVisible expects x-value to have hidden cols subtracted
int x = av.getAlignment().getHiddenColumns()
- .findColumnPosition(seqCanvas.cursorX);
+ .absoluteToVisibleColumn(seqCanvas.cursorX);
av.getRanges().scrollToWrappedVisible(x);
}
else
* the start of the highlighted region.
*/
@Override
- public void highlightSequence(SearchResultsI results)
+ public String highlightSequence(SearchResultsI results)
{
if (results == null || results.equals(lastSearchResults))
{
- return;
+ return null;
}
lastSearchResults = results;
{
setStatusMessage(results);
}
+ return results.isEmpty() ? null : getHighlightInfo(results);
+ }
+
+ /**
+ * temporary hack: answers a message suitable to show on structure hover
+ * label. This is normally null. It is a peptide variation description if
+ * <ul>
+ * <li>results are a single residue in a protein alignment</li>
+ * <li>there is a mapping to a coding sequence (codon)</li>
+ * <li>there are one or more SNP variant features on the codon</li>
+ * </ul>
+ * in which case the answer is of the format (e.g.) "p.Glu388Asp"
+ *
+ * @param results
+ * @return
+ */
+ private String getHighlightInfo(SearchResultsI results)
+ {
+ /*
+ * ideally, just find mapped CDS (as we don't care about render style here);
+ * for now, go via split frame complement's FeatureRenderer
+ */
+ AlignViewportI complement = ap.getAlignViewport().getCodingComplement();
+ if (complement == null)
+ {
+ return null;
+ }
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+
+ int j = results.getSize();
+ List<String> infos = new ArrayList<>();
+ for (int i = 0; i < j; i++)
+ {
+ SearchResultMatchI match = results.getResults().get(i);
+ int pos = match.getStart();
+ if (pos == match.getEnd())
+ {
+ SequenceI seq = match.getSequence();
+ SequenceI ds = seq.getDatasetSequence() == null ? seq
+ : seq.getDatasetSequence();
+ MappedFeatures mf = fr2
+ .findComplementFeaturesAtResidue(ds, pos);
+ if (mf != null)
+ {
+ List<String> pv = mf.findProteinVariants();
+ for (String s : pv)
+ {
+ if (!infos.contains(s))
+ {
+ infos.addAll(pv);
+ }
+ }
+ }
+ }
+ }
+
+ if (infos.isEmpty())
+ {
+ return null;
+ }
+ StringBuilder sb = new StringBuilder();
+ for (String info : infos)
+ {
+ if (sb.length() > 0)
+ {
+ sb.append("|");
+ }
+ sb.append(info);
+ }
+ return sb.toString();
}
@Override
.findFeaturesAtColumn(sequence, column + 1);
seqARep.appendFeatures(tooltipText, pos, features,
this.ap.getSeqPanel().seqCanvas.fr);
+
+ /*
+ * add features in CDS/protein complement at the corresponding
+ * position if configured to do so
+ */
+ if (av.isShowComplementFeatures())
+ {
+ if (!Comparison.isGap(sequence.getCharAt(column)))
+ {
+ AlignViewportI complement = ap.getAlignViewport()
+ .getCodingComplement();
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(sequence,
+ pos);
+ if (mf != null)
+ {
+ seqARep.appendFeatures(tooltipText, pos, mf.features, fr2);
+ }
+ }
+ }
}
if (tooltipText.length() == 6) // <html>
{
{
fixedColumns = true;
int y1 = av.getAlignment().getHiddenColumns()
- .getHiddenBoundaryLeft(startres);
+ .getNextHiddenBoundary(true, startres);
int y2 = av.getAlignment().getHiddenColumns()
- .getHiddenBoundaryRight(startres);
+ .getNextHiddenBoundary(false, startres);
if ((insertGap && startres > y1 && lastres < y1)
|| (!insertGap && startres < y2 && lastres > y2))
if (sg.getSize() == av.getAlignment().getHeight())
{
if ((av.hasHiddenColumns() && startres < av.getAlignment()
- .getHiddenColumns().getHiddenBoundaryRight(startres)))
+ .getHiddenColumns()
+ .getNextHiddenBoundary(false, startres)))
{
endEditing();
return;
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
- if (e.getWheelRotation() > 0)
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
{
if (e.isShiftDown())
{
av.getRanges().scrollUp(false);
}
}
- else
+ else if (wheelRotation < 0)
{
if (e.isShiftDown())
{
return true;
}
+
+ /**
+ *
+ * @return null or last search results handled by this panel
+ */
+ public SearchResultsI getLastSearchResults()
+ {
+ return lastSearchResults;
+ }
}
git://source.jalview.org / jalview.git / blobdiff