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Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings
[jalview.git]
/
src
/
jalview
/
gui
/
AlignmentPanel.java
diff --git
a/src/jalview/gui/AlignmentPanel.java
b/src/jalview/gui/AlignmentPanel.java
index
c03b56d
..
92b9a50
100644
(file)
--- a/
src/jalview/gui/AlignmentPanel.java
+++ b/
src/jalview/gui/AlignmentPanel.java
@@
-328,12
+328,12
@@
public class AlignmentPanel extends GAlignmentPanel implements
}
/**
}
/**
- * Highlight the given results on the alignment.
+ * Highlight the given results on the alignment
*
*/
public void highlightSearchResults(SearchResultsI results)
{
*
*/
public void highlightSearchResults(SearchResultsI results)
{
- boolean scrolled = scrollToPosition(results, 0, true, false);
+ boolean scrolled = scrollToPosition(results, 0, false);
boolean noFastPaint = scrolled && av.getWrapAlignment();
boolean noFastPaint = scrolled && av.getWrapAlignment();
@@
-345,13
+345,11
@@
public class AlignmentPanel extends GAlignmentPanel implements
* (if any)
*
* @param searchResults
* (if any)
*
* @param searchResults
- * @param redrawOverview
* @return
*/
* @return
*/
- public boolean scrollToPosition(SearchResultsI searchResults,
- boolean redrawOverview)
+ public boolean scrollToPosition(SearchResultsI searchResults)
{
{
- return scrollToPosition(searchResults, 0, redrawOverview, false);
+ return scrollToPosition(searchResults, 0, false);
}
/**
}
/**
@@
-364,14
+362,12
@@
public class AlignmentPanel extends GAlignmentPanel implements
* @param verticalOffset
* if greater than zero, allows scrolling to a position below the
* first displayed sequence
* @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,
* @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();
{
int startv, endv, starts, ends;
ViewportRanges ranges = av.getRanges();
@@
-477,7
+473,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
scrollNeeded = ranges.scrollToWrappedVisible(start);
}
scrollNeeded = ranges.scrollToWrappedVisible(start);
}
- paintAlignment(redrawOverview, false);
+ paintAlignment(false, false);
return scrollNeeded;
}
return scrollNeeded;
}
@@
-536,7
+532,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
addNotify();
// TODO: many places call this method and also paintAlignment with various
// different settings. this means multiple redraws are triggered...
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());
}
/**
}
/**
@@
-641,16
+637,9
@@
public class AlignmentPanel extends GAlignmentPanel implements
}
else
{
}
else
{
- int width = av.getAlignment().getWidth();
+ int width = av.getAlignment().getVisibleWidth();
int height = av.getAlignment().getHeight();
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();
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
@@
-962,8
+951,8
@@
public class AlignmentPanel extends GAlignmentPanel implements
final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
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,
final int startRes = (pageIndex % pagesWide) * totalRes;
final int endRes = Math.min(startRes + totalRes - 1,
@@
-1080,12
+1069,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
int idWidth = getVisibleIdWidth(false);
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);
int resWidth = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(pageWidth - idWidth);
@@
-1247,12
+1231,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
public AlignmentDimension getAlignmentDimension()
{
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();
int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ getScalePanel().getHeight();
@@
-1698,7
+1677,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
*/
protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
*/
protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
- scrollToPosition(sr, verticalOffset, true, true);
+ scrollToPosition(sr, verticalOffset, true);
}
/**
}
/**