import jalview.commands.EditCommand.Edit;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
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;
}
wrappedBlock = y / cHeight;
- wrappedBlock += av.getStartRes() / cwidth;
+ wrappedBlock += av.getRanges().getStartRes() / cwidth;
res = wrappedBlock * cwidth + x / av.getCharWidth();
// right-hand gutter
x = seqCanvas.getX() + seqCanvas.getWidth();
}
- res = (x / av.getCharWidth()) + av.getStartRes();
- if (res > av.getEndRes())
+ res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+ if (res > av.getRanges().getEndRes())
{
// moused off right
- res = av.getEndRes();
+ res = av.getRanges().getEndRes();
}
}
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ res = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(res);
}
return res;
}
else
{
- seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+ seq = Math.min((y / av.getCharHeight())
+ + av.getRanges().getStartSeq(),
+ av
.getAlignment().getHeight() - 1);
}
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
+
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
if (av.hasHiddenColumns()
- && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ && !hidden.isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
- while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
+ while (!hidden.isVisible(seqCanvas.cursorX)
&& seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
- || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ || !hidden.isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
}
else
{
- while (seqCanvas.cursorY < av.startSeq)
+ while (seqCanvas.cursorY < av.getRanges().getStartSeq())
{
ap.scrollUp(true);
}
- while (seqCanvas.cursorY + 1 > av.endSeq)
+ while (seqCanvas.cursorY + 1 > av.getRanges().getEndSeq())
{
ap.scrollUp(false);
}
if (!av.getWrapAlignment())
{
- while (seqCanvas.cursorX < av.getColumnSelection()
- .adjustForHiddenColumns(av.startRes))
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(av
+ .getRanges().getStartRes()))
{
if (!ap.scrollRight(false))
{
break;
}
}
- while (seqCanvas.cursorX > av.getColumnSelection()
- .adjustForHiddenColumns(av.endRes))
+ while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(av
+ .getRanges().getEndRes()))
{
if (!ap.scrollRight(true))
{
if (av.hasHiddenColumns())
{
fixedColumns = true;
- int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
- int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+ int y1 = av.getAlignment().getHiddenColumns()
+ .getHiddenBoundaryLeft(startres);
+ int y2 = av.getAlignment().getHiddenColumns()
+ .getHiddenBoundaryRight(startres);
if ((insertGap && startres > y1 && lastres < y1)
|| (!insertGap && startres < y2 && lastres > y2))
{
if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns() && startres < av
- .getColumnSelection().getHiddenBoundaryRight(startres)))
+ if ((av.hasHiddenColumns() && startres < av.getAlignment()
+ .getHiddenColumns().getHiddenBoundaryRight(startres)))
{
endEditing();
return;
}
}
+ /**
+ * Handler for double-click on a position with one or more sequence features.
+ * Opens the Amend Features dialog to allow feature details to be amended, or
+ * the feature deleted.
+ */
@Override
public void mouseClicked(MouseEvent evt)
{
.findFeaturesAtRes(sequence.getDatasetSequence(),
sequence.findPosition(findRes(evt)));
- if (features != null && features.size() > 0)
+ if (!features.isEmpty())
{
+ /*
+ * highlight the first feature at the position on the alignment
+ */
SearchResultsI highlight = new SearchResults();
highlight.addResult(sequence, features.get(0).getBegin(), features
.get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
- }
- if (features != null && features.size() > 0)
- {
- seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[] { sequence },
- features.toArray(new SequenceFeature[features.size()]),
- false, ap);
+ /*
+ * open the Amend Features dialog; clear highlighting afterwards,
+ * whether changes were made or not
+ */
+ List<SequenceI> seqs = Collections.singletonList(sequence);
+ seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
+ ap, null);
seqCanvas.highlightSearchResults(null);
}
}
stretchGroup = av.getSelectionGroup();
- if (stretchGroup == null)
+ if (stretchGroup == null || !stretchGroup.contains(sequence, res))
{
stretchGroup = av.getAlignment().findGroup(sequence, res);
- av.setSelectionGroup(stretchGroup);
- }
- if (stretchGroup == null
- || !stretchGroup.getSequences(null).contains(sequence)
- || (stretchGroup.getStartRes() > res)
- || (stretchGroup.getEndRes() < res))
- {
- stretchGroup = null;
-
- SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
-
- if (allGroups != null)
+ if (stretchGroup != null)
{
- for (int i = 0; i < allGroups.length; i++)
- {
- if ((allGroups[i].getStartRes() <= res)
- && (allGroups[i].getEndRes() >= res))
- {
- stretchGroup = allGroups[i];
- break;
- }
- }
+ // only update the current selection if the popup menu has a group to
+ // focus on
+ av.setSelectionGroup(stretchGroup);
}
-
- av.setSelectionGroup(stretchGroup);
}
if (evt.isPopupTrigger()) // Mac: mousePressed
if (av.getConservationSelected())
{
- SliderPanel.setConservationSlider(ap, av.getViewportColourScheme(),
- "Background");
+ SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+ ap.getViewName());
}
if (av.getAbovePIDThreshold())
{
- SliderPanel.setPIDSliderSource(ap, av.getViewportColourScheme(),
- "Background");
+ SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+ ap.getViewName());
}
+ // TODO: stretchGroup will always be not null. Is this a merge error ?
if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
{
// Edit end res position of selected group
*
* @param evt
* @param res
- * @param sequence
+ * @param sequences
*/
void showPopupMenu(MouseEvent evt)
{
changeStartRes = true;
}
- if (res < av.getStartRes())
+ if (res < av.getRanges().getStartRes())
{
- res = av.getStartRes();
+ res = av.getRanges().getStartRes();
}
if (changeEndRes)
{
if (evt != null)
{
- if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
+ if (mouseDragging && (evt.getY() < 0)
+ && (av.getRanges().getStartSeq() > 0))
{
running = ap.scrollUp(true);
}
if (mouseDragging && (evt.getY() >= getHeight())
- && (av.getAlignment().getHeight() > av.getEndSeq()))
+ && (av.getAlignment().getHeight() > av.getRanges()
+ .getEndSeq()))
{
running = ap.scrollUp(false);
}
*/
@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
- SelectionSource source)
+ HiddenColumns hidden, SelectionSource source)
{
// TODO: fix this hack - source of messages is align viewport, but SeqPanel
// handles selection messages...
// shared between viewports.
boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
.getSequenceSetId().equals(av.getSequenceSetId())));
- if (iSentTheSelection || !av.followSelection)
+
+ if (iSentTheSelection)
{
- return;
+ // respond to our own event by updating dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ // process further ?
+ if (!av.followSelection)
+ {
+ return;
+ }
}
/*
* Check for selection in a view of which this one is a dna/protein
* complement.
*/
- if (selectionFromTranslation(seqsel, colsel, source))
+ if (selectionFromTranslation(seqsel, colsel, hidden, source))
{
return;
}
}
else
{
- av.getColumnSelection().setElementsFrom(colsel);
+ av.getColumnSelection().setElementsFrom(colsel,
+ av.getAlignment().getHiddenColumns());
}
}
av.isColSelChanged(true);
if (copycolsel
&& av.hasHiddenColumns()
- && (av.getColumnSelection() == null || av.getColumnSelection()
- .getHiddenColumns() == null))
+ && (av.getAlignment().getHiddenColumns() == null || av
+ .getAlignment().getHiddenColumns().getListOfCols() == null))
{
System.err.println("Bad things");
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
// ap.paintAlignment(false);
}
+
+ // lastly, update dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
}
/**
* @param source
*/
protected boolean selectionFromTranslation(SequenceGroup seqsel,
- ColumnSelection colsel, SelectionSource source)
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
{
if (!(source instanceof AlignViewportI))
{
/*
* Map column selection
*/
- ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
- av);
+ // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+ // av);
+ ColumnSelection cs = new ColumnSelection();
+ HiddenColumns hs = new HiddenColumns();
+ MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
av.setColumnSelection(cs);
+ av.getAlignment().setHiddenColumns(hs);
+
+ // lastly, update any dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
PaintRefresher.Refresh(this, av.getSequenceSetId());
git://source.jalview.org / jalview.git / blobdiff