import java.beans.PropertyChangeEvent;
import java.util.List;
-public class AlignmentPanel extends Panel implements AdjustmentListener,
- AlignmentViewPanel, ViewportListenerI
+public class AlignmentPanel extends Panel
+ implements AdjustmentListener, AlignmentViewPanel, ViewportListenerI
{
public AlignViewport av;
// this value is set false when selection area being dragged
boolean fastPaint = true;
- @Override
- public void finalize() throws Throwable
- {
- alignFrame = null;
- av = null;
- vpRanges = null;
- seqPanel = null;
- seqPanelHolder = null;
- sequenceHolderPanel = null;
- scalePanel = null;
- scalePanelHolder = null;
- annotationPanel = null;
- annotationPanelHolder = null;
- annotationSpaceFillerHolder = null;
- super.finalize();
- }
-
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
try
idPanel.idCanvas.image = null;
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanel.setSize(new Dimension(10, av.getCharHeight()
- + fm.getDescent()));
- idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight()
- + fm.getDescent()));
+ scalePanel.setSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idwidthAdjuster.setSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
av.updateSequenceIdColours();
annotationPanel.image = null;
int ap = annotationPanel.adjustPanelHeight(false);
* @return false if results were not found
*/
public boolean scrollToPosition(SearchResultsI results,
- int verticalOffset,
- boolean redrawOverview, boolean centre)
+ int verticalOffset, boolean redrawOverview, boolean centre)
{
// do we need to scroll the panel?
- if (results != null && results.getSize() > 0)
+ if (results != null && results.getCount() > 0)
{
AlignmentI alignment = av.getAlignment();
int seqIndex = alignment.findIndex(results);
{
if (JalviewLite.debug)
{// DEBUG
- System.out
- .println("DEBUG: scroll didn't happen - results not within alignment : "
+ System.out.println(
+ "DEBUG: scroll didn't happen - results not within alignment : "
+ seq.getStart() + "," + seq.getEnd());
}
return false;
*/
if (centre)
{
- int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
+ int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
+ - 1;
start = Math.max(start - offset, 0);
- end = Math.min(end + offset, seq.getEnd() - 1);
+ end = end + offset - 1;
+ // end = Math.min(end + offset, seq.getEnd() - 1);
}
if (start < 0)
int start = -1;
if (av.hasHiddenColumns())
{
- start = av.getColumnSelection().findColumnPosition(ostart);
- end = av.getColumnSelection().findColumnPosition(end);
+ AlignmentI al = av.getAlignment();
+ start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
+ end = al.getHiddenColumns().absoluteToVisibleColumn(end);
if (start == end)
{
- if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
+ if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
{
// don't scroll - position isn't visible
return false;
/*
* Scroll down to make end of search results visible
*/
- setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
- + 1);
+ setScrollValues(vpRanges.getStartRes(),
+ starts + seqIndex - ends + 1);
}
/*
* Else results are already visible - no need to scroll
vpRanges.scrollToWrappedVisible(start);
}
- paintAlignment(redrawOverview);
+ paintAlignment(redrawOverview, false);
return true;
}
// this is called after loading new annotation onto alignment
if (alignFrame.getSize().height == 0)
{
- System.out
- .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
+ System.out.println(
+ "adjustAnnotationHeight frame size zero NEEDS FIXING");
}
fontChanged();
validateAnnotationDimensions(true);
apvscroll.addNotify();
hscroll.addNotify();
validate();
- paintAlignment(true);
+ paintAlignment(true, false);
}
/**
*/
if (annotationHeight + alignmentHeight > availableHeight)
{
- annotationHeight = Math.min(annotationHeight, availableHeight - 2
- * rowHeight);
+ annotationHeight = Math.min(annotationHeight,
+ availableHeight - 2 * rowHeight);
}
}
else
annotationPanel.setSize(new Dimension(d.width, annotationHeight));
annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight));
// seqPanelHolder.setSize(d.width, seqandannot - height);
- seqPanel.seqCanvas
- .setSize(d.width, seqPanel.seqCanvas.getSize().height);
+ seqPanel.seqCanvas.setSize(d.width,
+ seqPanel.seqCanvas.getSize().height);
Dimension e = idPanel.getSize();
alabels.setSize(new Dimension(e.width, annotationHeight));
- annotationSpaceFillerHolder.setSize(new Dimension(e.width,
- annotationHeight));
+ annotationSpaceFillerHolder
+ .setSize(new Dimension(e.width, annotationHeight));
int s = apvscroll.getValue();
if (s > mheight - annotationHeight)
public void setWrapAlignment(boolean wrap)
{
- vpRanges.setStartSeq(0);
+ vpRanges.setStartEndSeq(0, vpRanges.getVisibleAlignmentHeight());
vpRanges.setStartRes(0);
scalePanelHolder.setVisible(!wrap);
int vextent = 0;
- public void setScrollValues(int x, int y)
+ public void setScrollValues(int xpos, int ypos)
{
+ int x = xpos;
+ int y = ypos;
+
if (av.getWrapAlignment())
{
setScrollingForWrappedPanel(x);
}
else
{
-
- int width = av.getAlignment().getWidth();
+ int width = av.getAlignment().getVisibleWidth();
int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- width = av.getColumnSelection().findColumnPosition(width);
- }
if (x < 0)
{
x = 0;
}
}
+ /**
+ * Respond to adjustment event when horizontal or vertical scrollbar is
+ * changed
+ *
+ * @param evt
+ * adjustment event encoding whether apvscroll, hscroll or vscroll
+ * changed
+ */
@Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
+ // Note that this event is NOT fired by the AWT scrollbar when setValues is
+ // called. Instead manually call adjustHorizontal and adjustVertical
+ // directly.
if (evt == null || evt.getSource() == apvscroll)
{
annotationPanel.setScrollOffset(apvscroll.getValue(), false);
}
vpRanges.setViewportStartAndWidth(x, width);
- if (av.getWrapAlignment() || !fastPaint || av.MAC)
+ if (av.getWrapAlignment() || !fastPaint)
{
repaint();
}
sendViewPosition();
}
- private void adjustVertical(int offy)
+ private void adjustVertical(int newY)
{
- int oldX = vpRanges.getStartRes();
- int oldwidth = vpRanges.getViewportWidth();
- int oldY = vpRanges.getStartSeq();
- int oldheight = vpRanges.getViewportHeight();
-
if (av.getWrapAlignment())
{
- int rowSize = seqPanel.seqCanvas
- .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-
- // if we're scrolling to the position we're already at, stop
- // this prevents infinite recursion of events when the scroll/viewport
- // ranges values are the same
- if ((offy * rowSize == oldX) && (oldwidth == rowSize))
+ /*
+ * if we're scrolling to the position we're already at, stop
+ * this prevents infinite recursion of events when the scroll/viewport
+ * ranges values are the same
+ */
+ int oldX = vpRanges.getStartRes();
+ int oldY = vpRanges.getWrappedScrollPosition(oldX);
+ if (oldY == newY)
{
return;
}
- else if (offy > -1)
+ if (newY > -1)
{
- vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
+ /*
+ * limit page up/down to one width's worth of positions
+ */
+ int rowSize = vpRanges.getViewportWidth();
+ int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
+ vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
}
}
else
{
int height = seqPanel.seqCanvas.getHeight() / av.getCharHeight();
+ int oldY = vpRanges.getStartSeq();
+ int oldheight = vpRanges.getViewportHeight();
// if we're scrolling to the position we're already at, stop
// this prevents infinite recursion of events when the scroll/viewport
// ranges values are the same
- if ((offy == oldY) && (height == oldheight))
+ if ((newY == oldY) && (height == oldheight))
{
return;
}
- vpRanges.setViewportStartAndHeight(offy, height);
+ vpRanges.setViewportStartAndHeight(newY, height);
}
- if (av.getWrapAlignment() || !fastPaint || av.MAC)
+ if (av.getWrapAlignment() || !fastPaint)
{
repaint();
}
* Scroll to position but centring the target residue. Also set a state flag
* to prevent adjustmentValueChanged performing this recursively.
*/
- // setFollowingComplementScroll(true);
- // this should be scrollToPosition(sr,verticalOffset,
scrollToPosition(sr, seqOffset, true, true);
}
* Repaint the alignment and annotations, and, optionally, any overview window
*/
@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
jalview.structure.StructureSelectionManager
.getStructureSelectionManager(av.applet)
.sequenceColoursChanged(this);
-
+ }
+ if (updateOverview)
+ {
if (overviewPanel != null)
{
overviewPanel.updateOverviewImage();
}
- /*
+ /**
* Set vertical scroll bar parameters for wrapped panel
- * @param res
- * the residue to scroll to
+ *
+ * @param topLeftColumn
+ * the column position at top left (0..)
*/
- private void setScrollingForWrappedPanel(int res)
+ private void setScrollingForWrappedPanel(int topLeftColumn)
{
- // get the width of the alignment in residues
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
+ int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn);
+ int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn);
- // get the width of the canvas in residues
- int canvasWidth = seqPanel.seqCanvas
- .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
- if (canvasWidth > 0)
- {
- // position we want to scroll to is number of canvasWidth's to get there
- int current = res / canvasWidth;
-
- // max scroll position: add one because extent is 1 and scrollbar value
- // can only be set to at most max - extent
- int max = maxwidth / canvasWidth + 1;
- vscroll.setUnitIncrement(1);
- vscroll.setValues(current, 1, 0, max);
- }
+ /*
+ * a scrollbar's value can be set to at most (maximum-extent)
+ * so we add extent (1) to the maxScroll value
+ */
+ vscroll.setUnitIncrement(1);
+ vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
}
protected Panel sequenceHolderPanel = new Panel();
/*
* Flag set while scrolling to follow complementary cDNA/protein scroll. When
- * true, suppresses invoking the same method recursively.
+ * false, suppresses invoking the same method recursively.
*/
- private boolean followingComplementScroll = true;
+ private boolean scrollComplementaryPanel = true;
private void jbInit() throws Exception
{
*
* @param b
*/
- protected void setFollowingComplementScroll(boolean b)
+ protected void setToScrollComplementPanel(boolean b)
{
- this.followingComplementScroll = b;
+ this.scrollComplementaryPanel = b;
}
- protected boolean isFollowingComplementScroll()
+ /**
+ * Get whether to scroll complement panel
+ *
+ * @return true if cDNA/protein complement panels should be scrolled
+ */
+ protected boolean isSetToScrollComplementPanel()
{
- return this.followingComplementScroll;
+ return this.scrollComplementaryPanel;
}
@Override
/**
- * Property change event fired when a change is made to the viewport ranges
+ * Property change event fired when a change is made to the viewport ranges
* object associated with this alignment panel's viewport
*/
public void propertyChange(PropertyChangeEvent evt)
// now update any complementary alignment (its viewport ranges object
// is different so does not get automatically updated)
- if (isFollowingComplementScroll())
+ if (isSetToScrollComplementPanel())
{
- setFollowingComplementScroll(false);
+ setToScrollComplementPanel(false);
av.scrollComplementaryAlignment(getComplementPanel());
- setFollowingComplementScroll(true);
+ setToScrollComplementPanel(true);
}
}
git://source.jalview.org / jalview.git / blobdiff