import static jalview.math.RotatableMatrix.Axis.Y;
import static jalview.math.RotatableMatrix.Axis.Z;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.analysis.PCA;
import jalview.analysis.scoremodels.ScoreModels;
view.setRenderGaps(av.isRenderGaps());
view.setShowAnnotation(av.isShowAnnotation());
view.setShowBoxes(av.getShowBoxes());
+ view.setShowAutocalcAbove(av.isShowAutocalculatedAbove());
+ view.setSortAnnotationsBy(av.getSortAnnotationsBy().name());
view.setShowColourText(av.getColourText());
view.setShowFullId(av.getShowJVSuffix());
view.setRightAlignIds(av.isRightAlignIds());
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al,
+ cs = ColourSchemeProperty.getColourScheme(null, al,
jGroup.getColour());
}
}
{
af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
uniqueSeqSetId, viewId, autoAlan);
+ // TODO resort annotations here to their order in the project?
av = af.getViewport();
ap = af.alignPanel;
}
// TODO: verify 'associate with all views' works still
tp.getTreeCanvas().setViewport(av); // af.viewport;
tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
- // FIXME: should we use safeBoolean here ?
- tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
-
}
+ tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
if (tp == null)
{
warn("There was a problem recovering stored Newick tree: \n"
viewport.setColourText(safeBoolean(view.isShowColourText()));
- viewport
- .setConservationSelected(
- safeBoolean(view.isConservationSelected()));
+ viewport.setConservationSelected(
+ safeBoolean(view.isConservationSelected()));
viewport.setIncrement(safeInt(view.getConsThreshold()));
viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
- viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
+ Boolean autocalcFirst = view.isShowAutocalcAbove();
+ if (autocalcFirst != null)
+ {
+ af.setShowAutoCalculatedAbove(autocalcFirst.booleanValue());
+ }
+ String sortBy = view.getSortAnnotationsBy();
+ if (sortBy != null)
+ {
+ try
+ {
+ viewport.setSortAnnotationsBy(
+ SequenceAnnotationOrder.valueOf(sortBy));
+ } catch (IllegalArgumentException e)
+ {
+ Cache.log.error(
+ "Invalid annotation sort specifier in project: " + sortBy);
+ }
+ }
+ viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
viewport.setShowText(safeBoolean(view.isShowText()));
-
viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+ cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
+ view.getBgColour());
}
}
// recompute any autoannotation
af.alignPanel.updateAnnotation(false, true);
reorderAutoannotation(af, al, autoAlan);
+ af.sortAnnotations(false);
af.alignPanel.alignmentChanged();
}
else
else
{
cs = new AnnotationColourGradient(matchedAnnotation,
- ColourSchemeProperty.getColourScheme(al,
+ ColourSchemeProperty.getColourScheme(af.getViewport(), al,
viewAnnColour.getColourScheme()),
safeInt(viewAnnColour.getAboveThreshold()));
}