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JAL-2388 Make startRes,startSeq,endRes,endSeq private with get/setters
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignmentPanel.java
diff --git
a/src/jalview/appletgui/AlignmentPanel.java
b/src/jalview/appletgui/AlignmentPanel.java
index
4198960
..
af7e9cd
100644
(file)
--- a/
src/jalview/appletgui/AlignmentPanel.java
+++ b/
src/jalview/appletgui/AlignmentPanel.java
@@
-323,7
+323,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
public boolean scrollToPosition(SearchResultsI results,
boolean redrawOverview)
{
public boolean scrollToPosition(SearchResultsI results,
boolean redrawOverview)
{
- return scrollToPosition(results, redrawOverview, false);
+ return scrollToPosition(results, 0, redrawOverview, false);
}
/**
}
/**
@@
-336,6
+336,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
* @return false if results were not found
*/
public boolean scrollToPosition(SearchResultsI results,
* @return false if results were not found
*/
public boolean scrollToPosition(SearchResultsI results,
+ int verticalOffset,
boolean redrawOverview, boolean centre)
{
// do we need to scroll the panel?
boolean redrawOverview, boolean centre)
{
// do we need to scroll the panel?
@@
-347,6
+348,10
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
return false;
}
{
return false;
}
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+
SequenceI seq = alignment.getSequenceAt(seqIndex);
int[] r = results.getResults(seq, 0, alignment.getWidth());
if (r == null)
SequenceI seq = alignment.getSequenceAt(seqIndex);
int[] r = results.getResults(seq, 0, alignment.getWidth());
if (r == null)
@@
-391,6
+396,11
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
return false;
}
{
return false;
}
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
return scrollTo(start, end, seqIndex, false, redrawOverview);
}
return true;
return scrollTo(start, end, seqIndex, false, redrawOverview);
}
return true;
@@
-419,6
+429,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
start = ostart;
}
{
start = ostart;
}
+
if (!av.getWrapAlignment())
{
/*
if (!av.getWrapAlignment())
{
/*
@@
-508,7
+519,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
vscroll.setValue(res / cwidth);
if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
vscroll.setValue(res / cwidth);
- av.startRes = vscroll.getValue() * cwidth;
+ av.setStartRes(vscroll.getValue() * cwidth);
}
}
}
}
@@
-621,8
+632,8
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
public void setWrapAlignment(boolean wrap)
{
public void setWrapAlignment(boolean wrap)
{
- av.startSeq = 0;
- av.startRes = 0;
+ av.setStartSeq(0);
+ av.setStartRes(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
@@
-821,8
+832,8
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
overviewPanel.setBoxPosition();
}
overviewPanel.setBoxPosition();
}
- int scrollX = av.startRes - oldX;
- int scrollY = av.startSeq - oldY;
+ int scrollX = av.getStartRes() - oldX;
+ int scrollY = av.getStartSeq() - oldY;
if (av.getWrapAlignment() || !fastPaint || av.MAC)
{
if (av.getWrapAlignment() || !fastPaint || av.MAC)
{
@@
-832,13
+843,13
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
// Make sure we're not trying to draw a panel
// larger than the visible window
{
// Make sure we're not trying to draw a panel
// larger than the visible window
- if (scrollX > av.endRes - av.startRes)
+ if (scrollX > av.getEndRes() - av.getStartRes())
{
{
- scrollX = av.endRes - av.startRes;
+ scrollX = av.getEndRes() - av.getStartRes();
}
}
- else if (scrollX < av.startRes - av.endRes)
+ else if (scrollX < av.getStartRes() - av.getEndRes())
{
{
- scrollX = av.startRes - av.endRes;
+ scrollX = av.getStartRes() - av.getEndRes();
}
idPanel.idCanvas.fastPaint(scrollY);
}
idPanel.idCanvas.fastPaint(scrollY);
@@
-909,7
+920,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
* mapped), we can make the scroll-to location a sequence above the one
* actually mapped.
*/
* mapped), we can make the scroll-to location a sequence above the one
* actually mapped.
*/
- SequenceI mappedTo = sr.getResultSequence(0);
+ SequenceI mappedTo = sr.getResults().get(0).getSequence();
List<SequenceI> seqs = av.getAlignment().getSequences();
/*
List<SequenceI> seqs = av.getAlignment().getSequences();
/*
@@
-931,23
+942,21
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
return; // failsafe, shouldn't happen
}
{
return; // failsafe, shouldn't happen
}
- sequenceIndex = Math.max(0, sequenceIndex - seqOffset);
- sr.getResults().get(0)
- .setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
/*
* Scroll to position but centring the target residue. Also set a state flag
* to prevent adjustmentValueChanged performing this recursively.
*/
setFollowingComplementScroll(true);
/*
* Scroll to position but centring the target residue. Also set a state flag
* to prevent adjustmentValueChanged performing this recursively.
*/
setFollowingComplementScroll(true);
- scrollToPosition(sr, true, true);
+ // this should be scrollToPosition(sr,verticalOffset,
+ scrollToPosition(sr, seqOffset, true, true);
}
private void sendViewPosition()
{
StructureSelectionManager.getStructureSelectionManager(av.applet)
}
private void sendViewPosition()
{
StructureSelectionManager.getStructureSelectionManager(av.applet)
- .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
- av.endSeq);
+ .sendViewPosition(this, av.getStartRes(), av.getEndRes(),
+ av.getStartSeq(), av.getEndSeq());
}
/**
}
/**