import jalview.util.Comparison;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
-import jalview.util.Platform;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
* @author $author$
* @version $Revision: 1.161 $
*/
+@SuppressWarnings("serial")
public class AlignmentPanel extends GAlignmentPanel implements
AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
{
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
+// setBackground(Color.white); // BH 2019
alignFrame = af;
this.av = av;
setSeqPanel(new SeqPanel(av, this));
new Dimension(10, av.getCharHeight() + fm.getDescent()));
idwidthAdjuster.invalidate();
scalePanelHolder.invalidate();
- getIdPanel().getIdCanvas().gg = null;
+ // BH 2018 getIdPanel().getIdCanvas().gg = null;
getSeqPanel().seqCanvas.img = null;
getAnnotationPanel().adjustPanelHeight();
}
/**
- * 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 fastPaint = !(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();
av.isShowAutocalculatedAbove());
sorter.sort(getAlignment().getAlignmentAnnotation(),
av.getSortAnnotationsBy());
+ // BH 2019.04.18 this should not be necessary, but
+ // there is something wrong with the fast painting
+ // in that there is a -1 shift that should not be there.
+ // It is being covered in Java by the Consensus and Conservation
+ // threads forcing a full repaint after pasting.
+ seqPanel.seqCanvas.clearFastPaint();
repaint();
if (updateStructures)
*/
ViewportRanges ranges = av.getRanges();
setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
+ super.paintComponent(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);
*/
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);
}
/**
{
return calculationDialog;
}
+
}
git://source.jalview.org / jalview.git / blobdiff