package jalview.gui;
import jalview.analysis.AnnotationSorter;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import jalview.util.MessageManager;
-import jalview.util.Platform;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
}
/**
- * Highlight the given results on the alignment.
+ * Highlight the given results on the alignment
*
*/
public void highlightSearchResults(SearchResultsI results)
{
- boolean scrolled = scrollToPosition(results, 0, true, false);
+ boolean scrolled = scrollToPosition(results, 0, false);
boolean noFastPaint = scrolled && av.getWrapAlignment();
* (if any)
*
* @param searchResults
- * @param redrawOverview
* @return
*/
- public boolean scrollToPosition(SearchResultsI searchResults,
- boolean redrawOverview)
+ public boolean scrollToPosition(SearchResultsI searchResults)
{
- return scrollToPosition(searchResults, 0, redrawOverview, false);
+ return scrollToPosition(searchResults, 0, false);
}
/**
* @param verticalOffset
* if greater than zero, allows scrolling to a position below the
* first displayed sequence
- * @param redrawOverview
- * - when set, the overview will be recalculated (takes longer)
* @param centre
* if true, try to centre the search results horizontally in the view
* @return
*/
protected boolean scrollToPosition(SearchResultsI results,
- int verticalOffset, boolean redrawOverview, boolean centre)
+ int verticalOffset, boolean centre)
{
int startv, endv, starts, ends;
ViewportRanges ranges = av.getRanges();
scrollNeeded = ranges.scrollToWrappedVisible(start);
}
- paintAlignment(redrawOverview, false);
+ paintAlignment(false, false);
return scrollNeeded;
}
addNotify();
// TODO: many places call this method and also paintAlignment with various
// different settings. this means multiple redraws are triggered...
- paintAlignment(true, false);
+ paintAlignment(true, av.needToUpdateStructureViews());
}
/**
protected void validateAnnotationDimensions(boolean adjustPanelHeight)
{
int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ annotationHeight = getAnnotationPanel()
+ .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
- if (adjustPanelHeight)
- {
- int rowHeight = av.getCharHeight();
- int alignmentHeight = rowHeight * av.getAlignment().getHeight();
-
- /*
- * Estimate available height in the AlignFrame for alignment +
- * annotations. Deduct an estimate for title bar, menu bar, scale panel,
- * hscroll, status bar, insets.
- */
- int stuff = Platform.isAMac() ? 120 : 140;
- int availableHeight = alignFrame.getHeight() - stuff;
-
- /*
- * If not enough vertical space, maximize annotation height while keeping
- * at least two rows of alignment visible
- */
- if (annotationHeight + alignmentHeight > availableHeight)
- {
- annotationHeight = Math.min(annotationHeight,
- availableHeight - 2 * rowHeight);
- }
- }
- else
- {
- // maintain same window layout whilst updating sliders
- annotationHeight = annotationScroller.getSize().height;
- }
hscroll.addNotify();
-
annotationScroller.setPreferredSize(
new Dimension(annotationScroller.getWidth(), annotationHeight));
{
annotationScroller.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
+ validateAnnotationDimensions(false);
}
int canvasWidth = getSeqPanel().seqCanvas.getWidth();
}
else
{
- int width = av.getAlignment().getWidth();
+ int width = av.getAlignment().getVisibleWidth();
int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- // reset the width to exclude hidden columns
- width = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(width);
- }
-
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
public void paintAlignment(boolean updateOverview,
boolean updateStructures)
{
- final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
- av.isShowAutocalculatedAbove());
- sorter.sort(getAlignment().getAlignmentAnnotation(),
- av.getSortAnnotationsBy());
repaint();
if (updateStructures)
}
/**
+ * Sorts annotations according to currently selected preferences. Does nothing
+ * if currently set to 'Custom' (manual) ordering.
+ */
+ void sortAnnotations()
+ {
+ SequenceAnnotationOrder sortBy = av.getSortAnnotationsBy();
+ if (sortBy != SequenceAnnotationOrder.CUSTOM)
+ {
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment().getAlignmentAnnotation(), sortBy);
+ }
+ }
+
+ /**
* DOCUMENT ME!
*
* @param g
final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
- final int alignmentWidth = av.getAlignment().getWidth();
- final int pagesWide = (alignmentWidth / totalRes) + 1;
+ final int alignmentWidth = av.getAlignment().getVisibleWidth();
+ int pagesWide = (alignmentWidth / totalRes) + 1;
final int startRes = (pageIndex % pagesWide) * totalRes;
final int endRes = Math.min(startRes + totalRes - 1,
int idWidth = getVisibleIdWidth(false);
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth) - 1;
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
int resWidth = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(pageWidth - idWidth);
g.setFont(av.getFont());
g.setColor(Color.black);
+ /*
+ * method: print the whole wrapped alignment, but with a clip region that
+ * is restricted to the requested page; this supports selective print of
+ * single pages or ranges, (at the cost of some repeated processing in
+ * the 'normal' case, when all pages are printed)
+ */
g.translate(0, -pageNumber * pageHeight);
g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
public AlignmentDimension getAlignmentDimension()
{
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth);
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ getScalePanel().getHeight();
@Override
public String getViewName()
{
- return av.viewName;
+ return av.getViewName();
}
/**
*/
protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
- scrollToPosition(sr, verticalOffset, true, true);
+ scrollToPosition(sr, verticalOffset, true);
}
/**