import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
/*
* 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 dontScrollComplement = false;
+ private boolean scrollComplementaryPanel = true;
private PropertyChangeListener propertyChangeListener;
+ private CalculationChooser calculationDialog;
+
/**
* Creates a new AlignmentPanel object.
*
{
av.alignmentChanged(this);
+ if (getCalculationDialog() != null)
+ {
+ getCalculationDialog().validateCalcTypes();
+ }
+
alignFrame.updateEditMenuBar();
paintAlignment(true);
}
int start = r[0];
int end = r[1];
- // DEBUG
- // System.err.println(this.av.viewName + " Seq : " + seqIndex
- // + " Scroll to " + start + "," + end);
/*
* To centre results, scroll to positions half the visible width
*/
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 = end + offset - 1;
}
}
if (av.hasHiddenColumns())
{
- start = av.getColumnSelection().findColumnPosition(start);
- end = av.getColumnSelection().findColumnPosition(end);
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ start = hidden.findColumnPosition(start);
+ end = hidden.findColumnPosition(end);
if (start == end)
{
- if (!av.getColumnSelection().isVisible(r[0]))
+ if (!hidden.isVisible(r[0]))
{
// don't scroll - position isn't visible
return false;
*/
seqIndex = Math.max(0, seqIndex - verticalOffset);
- // System.out.println("start=" + start + ", end=" + end + ", startv="
- // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
- // + av.getStartSeq() + ", ends=" + av.getEndSeq());
if (!av.getWrapAlignment())
{
if ((startv = vpRanges.getStartRes()) >= start)
/*
* Scroll left to make start of search results visible
*/
- // setScrollValues(start - 1, seqIndex); // plus one residue
setScrollValues(start, seqIndex);
}
else if ((endv = vpRanges.getEndRes()) <= end)
/*
* Scroll right to make end of search results visible
*/
- // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
setScrollValues(startv + end - endv, seqIndex);
}
else if ((starts = vpRanges.getStartSeq()) > seqIndex)
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);
+ vpRanges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
+ .getCharHeight()) - 1;
- vpRanges.setViewportWidth(widthInRes);
- vpRanges.setViewportHeight(heightInSeq);
+ vpRanges.setViewportWidth(widthInRes);
+ vpRanges.setViewportHeight(heightInSeq);
+ }
}
idSpaceFillerPanel1.setVisible(!wrap);
* visible row to scroll to
*
*/
- public void setScrollValues(int x, int y)
+ public void setScrollValues(int xpos, int ypos)
{
+ int x = xpos;
+ int y = ypos;
+
if (av == null || av.getAlignment() == null)
{
return;
}
else
{
-
int width = av.getAlignment().getWidth();
int height = av.getAlignment().getHeight();
if (av.hasHiddenColumns())
{
// reset the width to exclude hidden columns
- width = av.getColumnSelection().findColumnPosition(width);
+ width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
}
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
}
/**
- * DOCUMENT ME!
+ * Respond to adjustment event when horizontal or vertical scrollbar is
+ * changed
*
* @param evt
- * DOCUMENT ME!
+ * adjustment event encoding whether hscroll or vscroll changed
*/
@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)
- {
- return; // no horizontal scroll when wrapped
- }
- else if (evt.getSource() == vscroll)
+ adjustScrollingWrapped(evt);
+ return;
+ }
+
+ if (evt.getSource() == hscroll)
+ {
+ int oldX = vpRanges.getStartRes();
+ int oldwidth = vpRanges.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))
{
- 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
- if ((offy * rowSize == oldX) && (oldwidth == rowSize))
- {
- return;
- }
- else if (offy > -1)
- {
- vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
- }
+ return;
}
- else
+ vpRanges.setViewportStartAndWidth(x, width);
+ }
+ else if (evt.getSource() == vscroll)
+ {
+ int oldY = vpRanges.getStartSeq();
+ int oldheight = vpRanges.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))
{
- // 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()
- {
- setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
- }
- });
+ return;
}
+ vpRanges.setViewportStartAndHeight(y, height);
+ }
+ if (!fastPaint)
+ {
repaint();
}
- else
+ }
+
+ /**
+ * 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)
{
- // horizontal scroll
- if (evt.getSource() == hscroll)
- {
- int x = hscroll.getValue();
- int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ return; // no horizontal scroll when wrapped
+ }
+ 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
- if ((x == oldX) && (width == oldwidth))
- {
- return;
- }
- vpRanges.setViewportStartAndWidth(x, width);
- }
- else if (evt.getSource() == vscroll)
+ /*
+ * 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)
{
- 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))
- {
- return;
- }
- vpRanges.setViewportStartAndHeight(y, height);
+ return;
}
- if (!fastPaint)
+ if (newY > -1)
{
- repaint();
+ /*
+ * 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
+ {
+ // 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);
+ }
+ });
+ }
+ repaint();
}
/**
setScrollValues(vpRanges.getStartRes(), vpRanges.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.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
-
- // 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;
+ int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn);
+ int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn);
- // 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);
}
/**
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
}
int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
int height = ((maxwidth / chunkWidth) + 1) * cHeight;
PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
PaintRefresher.RemoveComponent(this);
+ closeChildFrames();
+
/*
* try to ensure references are nulled
*/
}
/**
+ * Close any open dialogs that would be orphaned when this one is closed
+ */
+ protected void closeChildFrames()
+ {
+ if (calculationDialog != null)
+ {
+ calculationDialog.closeFrame();
+ }
+ }
+
+ /**
* hides or shows dynamic annotation rows based on groups and av state flags
*/
public void updateAnnotation()
*
* @param b
*/
- protected void setDontScrollComplement(boolean b)
+ protected void setToScrollComplementPanel(boolean b)
{
- this.dontScrollComplement = b;
+ this.scrollComplementaryPanel = b;
}
- protected boolean isDontScrollComplement()
+ /**
+ * Get whether to scroll complement panel
+ *
+ * @return true if cDNA/protein complement panels should be scrolled
+ */
+ protected boolean isSetToScrollComplementPanel()
{
- return this.dontScrollComplement;
+ return this.scrollComplementaryPanel;
}
/**
// now update any complementary alignment (its viewport ranges object
// is different so does not get automatically updated)
- if (!isDontScrollComplement())
+ if (isSetToScrollComplementPanel())
{
- setDontScrollComplement(true);
+ setToScrollComplementPanel(false);
av.scrollComplementaryAlignment();
- setDontScrollComplement(false);
+ setToScrollComplementPanel(true);
}
}
+
+ /**
+ * Set the reference to the PCA/Tree chooser dialog for this panel. This
+ * reference should be nulled when the dialog is closed.
+ *
+ * @param calculationChooser
+ */
+ public void setCalculationDialog(CalculationChooser calculationChooser)
+ {
+ calculationDialog = calculationChooser;
+ }
+
+ /**
+ * Returns the reference to the PCA/Tree chooser dialog for this panel (null
+ * if none is open)
+ */
+ public CalculationChooser getCalculationDialog()
+ {
+ return calculationDialog;
+ }
}
git://source.jalview.org / jalview.git / blobdiff