{
public AlignViewport av;
- ViewportRanges vpRanges;
-
OverviewPanel overviewPanel;
private SeqPanel seqPanel;
private AnnotationLabels alabels;
- // this value is set false when selection area being dragged
- boolean fastPaint = true;
-
private int hextent = 0;
private int vextent = 0;
{
alignFrame = af;
this.av = av;
- vpRanges = av.getRanges();
setSeqPanel(new SeqPanel(av, this));
setIdPanel(new IdPanel(av, this));
// reset the viewport ranges when the alignment panel is resized
// in particular, this initialises the end residue value when Jalview
// is initialised
+ ViewportRanges ranges = av.getRanges();
if (av.getWrapAlignment())
{
int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
getSeqPanel().seqCanvas.getWidth());
- vpRanges.setViewportWidth(widthInRes);
+ ranges.setViewportWidth(widthInRes);
}
else
{
int heightInSeq = getSeqPanel().seqCanvas.getHeight()
/ av.getCharHeight();
- vpRanges.setViewportWidth(widthInRes);
- vpRanges.setViewportHeight(heightInSeq);
+ ranges.setViewportWidth(widthInRes);
+ ranges.setViewportHeight(heightInSeq);
}
}
alignFrame.updateEditMenuBar();
- paintAlignment(true);
+ // no idea if we need to update structure
+ paintAlignment(true, true);
}
int verticalOffset, boolean redrawOverview, boolean centre)
{
int startv, endv, starts, ends;
+ ViewportRanges ranges = av.getRanges();
if (results == null || results.isEmpty() || av == null
|| av.getAlignment() == null)
*/
if (centre)
{
- int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
+ int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
start = Math.max(start - offset, 0);
end = end + offset - 1;
}
if (!av.getWrapAlignment())
{
- if ((startv = vpRanges.getStartRes()) >= start)
+ if ((startv = ranges.getStartRes()) >= start)
{
/*
* Scroll left to make start of search results visible
*/
setScrollValues(start, seqIndex);
}
- else if ((endv = vpRanges.getEndRes()) <= end)
+ else if ((endv = ranges.getEndRes()) <= end)
{
/*
* Scroll right to make end of search results visible
*/
setScrollValues(startv + end - endv, seqIndex);
}
- else if ((starts = vpRanges.getStartSeq()) > seqIndex)
+ else if ((starts = ranges.getStartSeq()) > seqIndex)
{
/*
* Scroll up to make start of search results visible
*/
- setScrollValues(vpRanges.getStartRes(), seqIndex);
+ setScrollValues(ranges.getStartRes(), seqIndex);
}
- else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
+ else if ((ends = ranges.getEndSeq()) <= seqIndex)
{
/*
* Scroll down to make end of search results visible
*/
- setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+ setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
+ 1);
}
/*
}
else
{
- scrollNeeded = vpRanges.scrollToWrappedVisible(start);
+ scrollNeeded = ranges.scrollToWrappedVisible(start);
}
- paintAlignment(redrawOverview);
+ paintAlignment(redrawOverview, false);
return scrollNeeded;
}
}
validateAnnotationDimensions(true);
addNotify();
- paintAlignment(true);
+ // TODO: many places call this method and also paintAlignment with various
+ // different settings. this means multiple redraws are triggered...
+ paintAlignment(true, false);
}
/**
fontChanged();
setAnnotationVisible(av.isShowAnnotation());
boolean wrap = av.getWrapAlignment();
- vpRanges.setStartSeq(0);
+ ViewportRanges ranges = av.getRanges();
+ ranges.setStartSeq(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
idwidthAdjuster.setVisible(!wrap);
{
int widthInRes = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(canvasWidth);
- vpRanges.setViewportWidth(widthInRes);
+ ranges.setViewportWidth(widthInRes);
}
else
{
- int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
+ int widthInRes = (canvasWidth / av.getCharWidth());
int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
- / av.getCharHeight()) - 1;
+ / av.getCharHeight());
- vpRanges.setViewportWidth(widthInRes);
- vpRanges.setViewportHeight(heightInSeq);
+ ranges.setViewportWidth(widthInRes);
+ ranges.setViewportHeight(heightInSeq);
}
}
return;
}
+ ViewportRanges ranges = av.getRanges();
+
if (evt.getSource() == hscroll)
{
- int oldX = vpRanges.getStartRes();
- int oldwidth = vpRanges.getViewportWidth();
+ int oldX = ranges.getStartRes();
+ int oldwidth = ranges.getViewportWidth();
int x = hscroll.getValue();
int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
{
return;
}
- vpRanges.setViewportStartAndWidth(x, width);
+ ranges.setViewportStartAndWidth(x, width);
}
else if (evt.getSource() == vscroll)
{
- int oldY = vpRanges.getStartSeq();
- int oldheight = vpRanges.getViewportHeight();
+ int oldY = ranges.getStartSeq();
+ int oldheight = ranges.getViewportHeight();
int y = vscroll.getValue();
int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
{
return;
}
- vpRanges.setViewportStartAndHeight(y, height);
- }
- if (!fastPaint)
- {
- repaint();
+ ranges.setViewportStartAndHeight(y, height);
}
+ repaint();
}
/**
{
return; // no horizontal scroll when wrapped
}
+ final ViewportRanges ranges = av.getRanges();
+
if (evt.getSource() == vscroll)
{
int newY = vscroll.getValue();
* this prevents infinite recursion of events when the scroll/viewport
* ranges values are the same
*/
- int oldX = vpRanges.getStartRes();
- int oldY = vpRanges.getWrappedScrollPosition(oldX);
+ int oldX = ranges.getStartRes();
+ int oldY = ranges.getWrappedScrollPosition(oldX);
if (oldY == newY)
{
return;
/*
* limit page up/down to one width's worth of positions
*/
- int rowSize = vpRanges.getViewportWidth();
+ int rowSize = ranges.getViewportWidth();
int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
- vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
+ ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
}
}
else
"Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
// scroll to start of panel
- vpRanges.setStartRes(0);
- vpRanges.setStartSeq(0);
+ ranges.setStartRes(0);
+ ranges.setStartSeq(0);
}
});
}
repaint();
}
- /**
- * Repaint the alignment including the annotations and overview panels (if
- * shown).
+ /* (non-Javadoc)
+ * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
*/
@Override
- public void paintAlignment(boolean updateOverview)
+ public void paintAlignment(boolean updateOverview,
+ boolean updateStructures)
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
av.isShowAutocalculatedAbove());
av.getSortAnnotationsBy());
repaint();
- if (updateOverview)
+ if (updateStructures)
{
- // TODO: determine if this paintAlignment changed structure colours
av.getStructureSelectionManager().sequenceColoursChanged(this);
+ }
+ if (updateOverview)
+ {
if (overviewPanel != null)
{
/*
* set scroll bar positions
*/
- setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+ ViewportRanges ranges = av.getRanges();
+ setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
}
/**
*/
private void setScrollingForWrappedPanel(int topLeftColumn)
{
- int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn);
- int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn);
+ ViewportRanges ranges = av.getRanges();
+ int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
+ int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
/*
* a scrollbar's value can be set to at most (maximum-extent)
if (annotationPanel != null)
{
annotationPanel.dispose();
+ annotationPanel = null;
}
if (av != null)
{
av.removePropertyChangeListener(propertyChangeListener);
- jalview.structure.StructureSelectionManager ssm = av
- .getStructureSelectionManager();
+ propertyChangeListener = null;
+ StructureSelectionManager ssm = av.getStructureSelectionManager();
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeSelectionListener(getSeqPanel());
ssm.removeCommandListener(av);
*/
protected void closeChildFrames()
{
+ if (overviewPanel != null)
+ {
+ overviewPanel.dispose();
+ overviewPanel = null;
+ }
if (calculationDialog != null)
{
calculationDialog.closeFrame();
+ calculationDialog = null;
}
}
if (adjustHeight)
{
// sort, repaint, update overview
- paintAlignment(true);
+ paintAlignment(true, false);
}
else
{
public void propertyChange(PropertyChangeEvent evt)
{
// update this panel's scroll values based on the new viewport ranges values
- int x = vpRanges.getStartRes();
- int y = vpRanges.getStartSeq();
+ ViewportRanges ranges = av.getRanges();
+ int x = ranges.getStartRes();
+ int y = ranges.getStartSeq();
setScrollValues(x, y);
// now update any complementary alignment (its viewport ranges object
git://source.jalview.org / jalview.git / blobdiff