import jalview.commands.EditCommand.Edit;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
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.util.ArrayList;
import java.util.List;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
private final SequenceAnnotationReport seqARep;
- StringBuffer tooltipText = new StringBuffer();
+ StringBuilder tooltipText = new StringBuilder();
String tmpString;
StructureSelectionManager ssm;
- SearchResults lastSearchResults;
+ SearchResultsI lastSearchResults;
/**
* Creates a new SeqPanel object.
}
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))
{
* the start of the highlighted region.
*/
@Override
- public void highlightSequence(SearchResults results)
+ public void highlightSequence(SearchResultsI results)
{
if (results == null || results.equals(lastSearchResults))
{
seqARep.appendFeatures(tooltipText, rpos, features,
this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
- if (tooltipText.length() == 6) // <html></html>
+ if (tooltipText.length() == 6) // <html>
{
setToolTipText(null);
lastTooltip = null;
*
* @param results
*/
- private void setStatusMessage(SearchResults results)
+ private void setStatusMessage(SearchResultsI results)
{
AlignmentI al = this.av.getAlignment();
int sequenceIndex = al.findIndex(results);
return;
}
SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
- for (Match m : results.getResults())
+ for (SearchResultMatchI m : results.getResults())
{
SequenceI seq = m.getSequence();
if (seq.getDatasetSequence() != null)
if (features != null && features.size() > 0)
{
- SearchResults highlight = new SearchResults();
+ SearchResultsI highlight = new SearchResults();
highlight.addResult(sequence, features.get(0).getBegin(), features
.get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.cannot_edit_annotations_in_wrapped_view"),
MessageManager.getString("label.wrapped_view_no_edit"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
stretchGroup = av.getSelectionGroup();
- if (stretchGroup == null)
+ if (stretchGroup == null || !stretchGroup.contains(sequence, res))
{
- stretchGroup = av.getAlignment().findGroup(sequence);
-
- if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
- && (res < stretchGroup.getEndRes()))
+ stretchGroup = av.getAlignment().findGroup(sequence, res);
+ if (stretchGroup != null)
{
+ // only update the current selection if the popup menu has a group to
+ // focus on
av.setSelectionGroup(stretchGroup);
}
- else
- {
- stretchGroup = null;
- }
- }
- else if (!stretchGroup.getSequences(null).contains(sequence)
- || (stretchGroup.getStartRes() > res)
- || (stretchGroup.getEndRes() < res))
- {
- stretchGroup = null;
-
- SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
-
- if (allGroups != null)
- {
- for (int i = 0; i < allGroups.length; i++)
- {
- if ((allGroups[i].getStartRes() <= res)
- && (allGroups[i].getEndRes() >= res))
- {
- stretchGroup = allGroups[i];
- break;
- }
- }
- }
-
- 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
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);
}