import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.ResidueProperties;
import jalview.structure.SelectionListener;
import jalview.structure.SelectionSource;
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();
}
}
}
else
{
- seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+ seq = Math.min((y / av.getCharHeight())
+ + av.getRanges().getStartSeq(),
+ av
.getAlignment().getHeight() - 1);
}
}
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))
+ .adjustForHiddenColumns(av.getRanges().getStartRes()))
{
if (!ap.scrollRight(false))
{
}
}
while (seqCanvas.cursorX > av.getColumnSelection()
- .adjustForHiddenColumns(av.endRes))
+ .adjustForHiddenColumns(av.getRanges().getEndRes()))
{
if (!ap.scrollRight(true))
{
}
/**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
+ * {@inheritDoc}
*/
@Override
public void mouseDragged(MouseEvent evt)
{
if (mouseWheelPressed)
{
+ boolean inSplitFrame = ap.av.getCodingComplement() != null;
+ boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
+
int oldWidth = av.getCharWidth();
// Which is bigger, left-right or up-down?
if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
.getX() - lastMousePress.getX()))
{
+ /*
+ * on drag up or down, decrement or increment font size
+ */
int fontSize = av.font.getSize();
+ boolean fontChanged = false;
if (evt.getY() < lastMousePress.getY())
{
+ fontChanged = true;
fontSize--;
}
else if (evt.getY() > lastMousePress.getY())
{
+ fontChanged = true;
fontSize++;
}
fontSize = 1;
}
- av.setFont(
- new Font(av.font.getName(), av.font.getStyle(), fontSize),
- true);
- av.setCharWidth(oldWidth);
- ap.fontChanged();
+ if (fontChanged)
+ {
+ Font newFont = new Font(av.font.getName(), av.font.getStyle(),
+ fontSize);
+ av.setFont(newFont, true);
+ av.setCharWidth(oldWidth);
+ ap.fontChanged();
+ if (copyChanges)
+ {
+ ap.av.getCodingComplement().setFont(newFont, true);
+ SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+ .getSplitViewContainer();
+ splitFrame.adjustLayout();
+ splitFrame.repaint();
+ }
+ }
}
else
{
+ /*
+ * on drag left or right, decrement or increment character width
+ */
+ int newWidth = 0;
if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
{
- av.setCharWidth(av.getCharWidth() - 1);
+ newWidth = av.getCharWidth() - 1;
+ av.setCharWidth(newWidth);
}
else if (evt.getX() > lastMousePress.getX())
{
- av.setCharWidth(av.getCharWidth() + 1);
+ newWidth = av.getCharWidth() + 1;
+ av.setCharWidth(newWidth);
+ }
+ if (newWidth > 0)
+ {
+ ap.paintAlignment(false);
+ if (copyChanges)
+ {
+ /*
+ * need to ensure newWidth is set on cdna, regardless of which
+ * panel the mouse drag happened in; protein will compute its
+ * character width as 1:1 or 3:1
+ */
+ av.getCodingComplement().setCharWidth(newWidth);
+ SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+ .getSplitViewContainer();
+ splitFrame.adjustLayout();
+ splitFrame.repaint();
+ }
}
-
- ap.paintAlignment(false);
}
FontMetrics fm = getFontMetrics(av.getFont());
}
}
+ /**
+ * 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.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+ ap.getViewName());
}
if (av.getAbovePIDThreshold())
{
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "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)
{
stretchGroup.cs.alignmentChanged(stretchGroup,
av.getHiddenRepSequences());
+ ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme();
+ String name = stretchGroup.getName();
if (stretchGroup.cs.conservationApplied())
{
- SliderPanel.setConservationSlider(ap, stretchGroup.cs,
- stretchGroup.getName());
+ SliderPanel.setConservationSlider(ap, groupColourScheme, name);
}
- else
+ if (stretchGroup.cs.getThreshold() > 0)
{
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
- stretchGroup.getName());
+ SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
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);
}
// 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;
+ }
}
/*
PaintRefresher.Refresh(this, av.getSequenceSetId());
// ap.paintAlignment(false);
}
+
+ // lastly, update dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
}
/**
av);
av.setColumnSelection(cs);
+ // lastly, update any dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
PaintRefresher.Refresh(this, av.getSequenceSetId());
return true;