* @version $Revision: 1.161 $
*/
public class AlignmentPanel extends GAlignmentPanel implements
- AdjustmentListener, Printable, AlignmentViewPanel,
- ViewportListenerI
+ AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
{
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);
+ int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
+ getSeqPanel().seqCanvas.getWidth());
+ ranges.setViewportWidth(widthInRes);
}
else
{
/ av.getCharWidth();
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);
}
// to prevent drawing old image
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
- + fm.getDescent()));
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
- .getCharHeight() + fm.getDescent()));
-
+ scalePanelHolder.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idwidthAdjuster.invalidate();
+ scalePanelHolder.invalidate();
getIdPanel().getIdCanvas().gg = null;
getSeqPanel().seqCanvas.img = null;
getAnnotationPanel().adjustPanelHeight();
getIdPanel().getIdCanvas().setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(d);
- if (this.alignFrame.getSplitViewContainer() != null)
- {
- ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
- }
-
repaint();
}
{
Container c = new Container();
- FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
- Font.ITALIC, av.font.getSize()));
+ FontMetrics fm = c.getFontMetrics(
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
AlignmentI al = av.getAlignment();
int i = 0;
}
}
- return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
- idWidth), 12);
+ return new Dimension(
+ maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12);
}
/**
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);
}
/**
*/
if (annotationHeight + alignmentHeight > availableHeight)
{
- annotationHeight = Math.min(annotationHeight, availableHeight - 2
- * rowHeight);
+ annotationHeight = Math.min(annotationHeight,
+ availableHeight - 2 * rowHeight);
}
}
else
}
hscroll.addNotify();
- annotationScroller.setPreferredSize(new Dimension(annotationScroller
- .getWidth(), annotationHeight));
+ annotationScroller.setPreferredSize(
+ new Dimension(annotationScroller.getWidth(), annotationHeight));
Dimension e = idPanel.getSize();
alabels.setSize(new Dimension(e.width, annotationHeight));
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);
annotationSpaceFillerHolder.setVisible(true);
}
- if (wrap)
- {
- int widthInRes = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- vpRanges.setViewportWidth(widthInRes);
- }
- else
- {
- int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av
- .getCharWidth()) - 1;
- int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
- .getCharHeight()) - 1;
+ int canvasWidth = getSeqPanel().seqCanvas.getWidth();
+ if (canvasWidth > 0)
+ { // may not yet be laid out
+ if (wrap)
+ {
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(canvasWidth);
+ ranges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = (canvasWidth / av.getCharWidth());
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight());
- vpRanges.setViewportWidth(widthInRes);
- vpRanges.setViewportHeight(heightInSeq);
+ ranges.setViewportWidth(widthInRes);
+ ranges.setViewportHeight(heightInSeq);
+ }
}
idSpaceFillerPanel1.setVisible(!wrap);
repaint();
}
-
/**
* Adjust row/column scrollers to show a visible position in the alignment.
*
if (av.hasHiddenColumns())
{
// reset the width to exclude hidden columns
- width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
+ width = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(width);
}
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
@Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- int oldX = vpRanges.getStartRes();
- int oldwidth = vpRanges.getViewportWidth();
- int oldY = vpRanges.getStartSeq();
- int oldheight = vpRanges.getViewportHeight();
-
if (av.getWrapAlignment())
{
- if (evt.getSource() == hscroll)
+ adjustScrollingWrapped(evt);
+ return;
+ }
+
+ ViewportRanges ranges = av.getRanges();
+
+ if (evt.getSource() == hscroll)
+ {
+ int oldX = ranges.getStartRes();
+ int oldwidth = ranges.getViewportWidth();
+ int x = hscroll.getValue();
+ int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+
+ // 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 ((x == oldX) && (width == oldwidth))
{
- return; // no horizontal scroll when wrapped
+ return;
}
- else if (evt.getSource() == vscroll)
+ ranges.setViewportStartAndWidth(x, width);
+ }
+ else if (evt.getSource() == vscroll)
+ {
+ int oldY = ranges.getStartSeq();
+ int oldheight = ranges.getViewportHeight();
+ int y = vscroll.getValue();
+ int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
+
+ // 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 ((y == oldY) && (height == oldheight))
{
- int offy = vscroll.getValue();
- int rowSize = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().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
- int newX = offy * rowSize;
- if ((newX == oldX) && (oldwidth == rowSize))
- {
- return;
- }
- else if (offy > -1)
- {
- /*
- * throttle to one width's worth at a time (so click in
- * scrollbar doesn't jump over data)
- */
- newX = newX > oldX ? oldX + rowSize : oldX - rowSize;
- vpRanges.setViewportStartAndWidth(newX, rowSize);
- }
+ return;
}
- else
+ ranges.setViewportStartAndHeight(y, height);
+ }
+ repaint();
+ }
+
+ /**
+ * Responds to a scroll change by setting the start position of the viewport.
+ * Does
+ *
+ * @param evt
+ */
+ protected void adjustScrollingWrapped(AdjustmentEvent evt)
+ {
+ if (evt.getSource() == hscroll)
+ {
+ return; // no horizontal scroll when wrapped
+ }
+ final ViewportRanges ranges = av.getRanges();
+
+ if (evt.getSource() == vscroll)
+ {
+ int newY = vscroll.getValue();
+
+ /*
+ * 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 = ranges.getStartRes();
+ int oldY = ranges.getWrappedScrollPosition(oldX);
+ if (oldY == newY)
{
- // This is only called if file loaded is a jar file that
- // was wrapped when saved and user has wrap alignment true
- // as preference setting
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- // When updating scrolling to use ViewportChange events, this code
- // could not be validated and it is not clear if it is now being
- // called. Log warning here in case it is called and unforeseen
- // problems occur
- Cache.log
- .warn("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);
- }
- });
+ return;
+ }
+ if (newY > -1)
+ {
+ /*
+ * limit page up/down to one width's worth of positions
+ */
+ int rowSize = ranges.getViewportWidth();
+ int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
+ ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
}
- repaint();
}
else
{
- // horizontal scroll
- if (evt.getSource() == hscroll)
+ // This is only called if file loaded is a jar file that
+ // was wrapped when saved and user has wrap alignment true
+ // as preference setting
+ SwingUtilities.invokeLater(new Runnable()
{
- int x = hscroll.getValue();
- int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
-
- // 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 ((x == oldX) && (width == oldwidth))
- {
- return;
- }
- vpRanges.setViewportStartAndWidth(x, width);
- }
- else if (evt.getSource() == vscroll)
- {
- int y = vscroll.getValue();
- int height = getSeqPanel().seqCanvas.getHeight()
- / av.getCharHeight();
-
- // 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 ((y == oldY) && (height == oldheight))
+ @Override
+ public void run()
{
- return;
+ // When updating scrolling to use ViewportChange events, this code
+ // could not be validated and it is not clear if it is now being
+ // called. Log warning here in case it is called and unforeseen
+ // problems occur
+ Cache.log.warn(
+ "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+
+ // scroll to start of panel
+ ranges.setStartRes(0);
+ ranges.setStartSeq(0);
}
- vpRanges.setViewportStartAndHeight(y, height);
- }
- if (!fastPaint)
- {
- repaint();
- }
+ });
}
+ 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)
{
@Override
public void paintComponent(Graphics g)
{
- invalidate();
+ invalidate(); // needed so that the id width adjuster works correctly
Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
idPanelHolder.setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
- validate();
+
+ validate(); // needed so that the id width adjuster works correctly
/*
- * set scroll bar positions
+ * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+ * though I still think this call should be elsewhere.
*/
- setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+ ViewportRanges ranges = av.getRanges();
+ setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
}
- /*
- * Set vertical scroll bar parameters for wrapped panel
- * @param res
- * the residue to scroll to
+ /**
+ * Set vertical scroll bar position, and number of increments, for wrapped
+ * panel
+ *
+ * @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.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
- }
+ ViewportRanges ranges = av.getRanges();
+ int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
+ int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
- // get the width of the canvas in residues
- int canvasWidth = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- 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);
}
/**
* Get the horizontal offset to where we draw the sequences.
* This is idWidth if using a single Graphics context, else zero.
*/
- final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
+ final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
+ : idWidth;
FontMetrics fm = getFontMetrics(av.getFont());
int charHeight = av.getCharHeight();
endSeq = alignmentHeight;
}
- int pagesHigh = ((alignmentHeight / totalSeq) + 1)
- * pageHeight;
+ int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
if (av.isShowAnnotation())
{
{
return Printable.NO_SUCH_PAGE;
}
- final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
- + 3;
+ final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
/*
* draw the Scale at horizontal offset, then reset to top left (0, 0)
if (av.isRightAlignIds())
{
fm = idGraphics.getFontMetrics();
- xPos = idWidth
- - fm.stringWidth(displayId)
- - 4;
+ xPos = idWidth - fm.stringWidth(displayId) - 4;
}
idGraphics.drawString(displayId, xPos,
* single graphics context), then reset to (0, scale height)
*/
alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
- getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
- startSeq, endSeq, 0);
+ getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
+ endRes, startSeq, endSeq);
alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
if (av.isShowAnnotation() && (endSeq == alignmentHeight))
* draw the annotations starting at
* (idOffset, alignmentHeight) from (0, scaleHeight)
*/
- alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
+ alignmentGraphics.translate(alignmentGraphicsOffset,
+ alignmentDrawnHeight);
getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
alignmentGraphics, -1, startRes, endRes + 1);
}
.findColumnPosition(maxwidth) - 1;
}
- int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
- - idWidth);
+ int resWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(pwidth - idWidth);
int totalHeight = cHeight * (maxwidth / resWidth + 1);
}
if (labels != null)
{
- pg.translate(-3,
- ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
+ pg.translate(-3, ypos
+ + (av.getAlignment().getHeight() * av.getCharHeight()));
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
- pg.translate(
- +3,
- -ypos
- - (av.getAlignment().getHeight() * av
- .getCharHeight()));
+ pg.translate(+3, -ypos
+ - (av.getAlignment().getHeight() * av.getCharHeight()));
}
ypos += cHeight;
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+ getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth,
totalHeight, 0);
if ((pi * pheight) < totalHeight)
return calculateIdWidth(-1).width + 4;
}
Integer idwidth = null;
- if (onscreen
- || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+ if (onscreen || (idwidth = Cache
+ .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
int w = getIdPanel().getWidth();
return (w > 0 ? w : calculateIdWidth().width + 4);
{
int boarderBottomOffset = 5;
long pSessionId = System.currentTimeMillis();
- headless = (System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true"));
+ headless = (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"));
if (alignFrame != null && !headless)
{
if (file != null)
{
- alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file", new Object[] { type.getLabel() }),
- pSessionId);
+ alignFrame.setProgressBar(MessageManager
+ .formatMessage("status.saving_file", new Object[]
+ { type.getLabel() }), pSessionId);
}
}
try
}
im = new jalview.util.ImageMaker(this, type, imageAction,
- aDimension.getWidth(), aDimension.getHeight()
- + boarderBottomOffset, file, imageTitle,
- alignFrame, pSessionId, headless);
+ aDimension.getWidth(),
+ aDimension.getHeight() + boarderBottomOffset, file,
+ imageTitle, alignFrame, pSessionId, headless);
Graphics graphics = im.getGraphics();
if (av.getWrapAlignment())
{
{
if (graphics != null)
{
- printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
- 0, graphics, graphics);
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ graphics, graphics);
im.writeImage();
}
}
// this duplicates the calculation in getWrappedHeight but adjusts for
// offscreen idWith
width = alignFrame.getWidth() - vscroll.getPreferredSize().width
- - alignFrame.getInsets().left
- - alignFrame.getInsets().right - getVisibleIdWidth()
- + getVisibleIdWidth(false);
+ - alignFrame.getInsets().left - alignFrame.getInsets().right
+ - getVisibleIdWidth() + getVisibleIdWidth(false);
}
else
{
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;
}
}
*/
protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
- /*
- * To avoid jumpy vertical scrolling (if some sequences are gapped or not
- * mapped), we can make the scroll-to location a sequence above the one
- * actually mapped.
- */
- SequenceI mappedTo = sr.getResults().get(0).getSequence();
- List<SequenceI> seqs = av.getAlignment().getSequences();
-
- /*
- * This is like AlignmentI.findIndex(seq) but here we are matching the
- * dataset sequence not the aligned sequence
- */
- boolean matched = false;
- for (SequenceI seq : seqs)
- {
- if (mappedTo == seq.getDatasetSequence())
- {
- matched = true;
- break;
- }
- }
- if (!matched)
- {
- return; // failsafe, shouldn't happen
- }
-
- /*
- * Scroll to position but centring the target residue.
- */
scrollToPosition(sr, verticalOffset, true, true);
}
if (adjustHeight)
{
// sort, repaint, update overview
- paintAlignment(true);
+ paintAlignment(true, false);
}
else
{
@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)
{
// 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