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JAL-2388 Applied ViewportRanges to code
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignmentPanel.java
diff --git
a/src/jalview/appletgui/AlignmentPanel.java
b/src/jalview/appletgui/AlignmentPanel.java
index
813ab84
..
3ae0394
100644
(file)
--- a/
src/jalview/appletgui/AlignmentPanel.java
+++ b/
src/jalview/appletgui/AlignmentPanel.java
@@
-25,9
+25,10
@@
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.JalviewLite;
import jalview.datamodel.AlignmentI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.JalviewLite;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureSelectionManager;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.BorderLayout;
import java.awt.Color;
@@
-65,6
+66,8
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
AnnotationLabels alabels;
AnnotationLabels alabels;
+ ViewportRanges vpRanges;
+
// this value is set false when selection area being dragged
boolean fastPaint = true;
// this value is set false when selection area being dragged
boolean fastPaint = true;
@@
-73,6
+76,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
alignFrame = null;
av = null;
{
alignFrame = null;
av = null;
+ vpRanges = null;
seqPanel = null;
seqPanelHolder = null;
sequenceHolderPanel = null;
seqPanel = null;
seqPanelHolder = null;
sequenceHolderPanel = null;
@@
-96,6
+100,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
alignFrame = af;
this.av = av;
alignFrame = af;
this.av = av;
+ vpRanges = av.getRanges();
seqPanel = new SeqPanel(av, this);
idPanel = new IdPanel(av, this);
scalePanel = new ScalePanel(av, this);
seqPanel = new SeqPanel(av, this);
idPanel = new IdPanel(av, this);
scalePanel = new ScalePanel(av, this);
@@
-126,7
+131,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
@Override
public void componentResized(ComponentEvent evt)
{
@Override
public void componentResized(ComponentEvent evt)
{
- setScrollValues(av.getStartRes(), av.getStartSeq());
+ setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
if (getSize().height > 0
&& annotationPanelHolder.getSize().height > 0)
{
if (getSize().height > 0
&& annotationPanelHolder.getSize().height > 0)
{
@@
-293,7
+298,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
* Highlight the given results on the alignment.
*
*/
* Highlight the given results on the alignment.
*
*/
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
scrollToPosition(results);
seqPanel.seqCanvas.highlightSearchResults(results);
{
scrollToPosition(results);
seqPanel.seqCanvas.highlightSearchResults(results);
@@
-306,7
+311,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
* @param results
* @return false if results were not found
*/
* @param results
* @return false if results were not found
*/
- public boolean scrollToPosition(SearchResults results)
+ public boolean scrollToPosition(SearchResultsI results)
{
return scrollToPosition(results, true);
}
{
return scrollToPosition(results, true);
}
@@
-320,10
+325,10
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
* - when set, the overview will be recalculated (takes longer)
* @return false if results were not found
*/
* - when set, the overview will be recalculated (takes longer)
* @return false if results were not found
*/
- public boolean scrollToPosition(SearchResults results,
+ public boolean scrollToPosition(SearchResultsI results,
boolean redrawOverview)
{
boolean redrawOverview)
{
- return scrollToPosition(results, redrawOverview, false);
+ return scrollToPosition(results, 0, redrawOverview, false);
}
/**
}
/**
@@
-335,7
+340,8
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
* - when set, the overview will be recalculated (takes longer)
* @return false if results were not found
*/
* - when set, the overview will be recalculated (takes longer)
* @return false if results were not found
*/
- public boolean scrollToPosition(SearchResults results,
+ 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
+353,10
@@
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)
@@
-378,7
+388,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
*/
if (centre)
{
*/
if (centre)
{
- int offset = (av.getEndRes() - av.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);
}
start = Math.max(start - offset, 0);
end = Math.min(end + offset, seq.getEnd() - 1);
}
@@
-391,6
+401,11
@@
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
+434,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
start = ostart;
}
{
start = ostart;
}
+
if (!av.getWrapAlignment())
{
/*
if (!av.getWrapAlignment())
{
/*
@@
-457,33
+473,34
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
// setScrollValues(start, seqIndex);
// }
// logic copied from jalview.gui.AlignmentPanel:
// setScrollValues(start, seqIndex);
// }
// logic copied from jalview.gui.AlignmentPanel:
- if ((startv = av.getStartRes()) >= start)
+ if ((startv = vpRanges.getStartRes()) >= start)
{
/*
* Scroll left to make start of search results visible
*/
setScrollValues(start - 1, seqIndex);
}
{
/*
* Scroll left to make start of search results visible
*/
setScrollValues(start - 1, seqIndex);
}
- else if ((endv = av.getEndRes()) <= end)
+ else if ((endv = vpRanges.getEndRes()) <= end)
{
/*
* Scroll right to make end of search results visible
*/
setScrollValues(startv + 1 + end - endv, seqIndex);
}
{
/*
* Scroll right to make end of search results visible
*/
setScrollValues(startv + 1 + end - endv, seqIndex);
}
- else if ((starts = av.getStartSeq()) > seqIndex)
+ else if ((starts = vpRanges.getStartSeq()) > seqIndex)
{
/*
* Scroll up to make start of search results visible
*/
{
/*
* Scroll up to make start of search results visible
*/
- setScrollValues(av.getStartRes(), seqIndex);
+ setScrollValues(vpRanges.getStartRes(), seqIndex);
}
}
- else if ((ends = av.getEndSeq()) <= seqIndex)
+ else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
{
/*
* Scroll down to make end of search results visible
*/
{
/*
* Scroll down to make end of search results visible
*/
- setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+ + 1);
}
/*
* Else results are already visible - no need to scroll
}
/*
* Else results are already visible - no need to scroll
@@
-505,10
+522,11
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
int cwidth = seqPanel.seqCanvas
.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
{
int cwidth = seqPanel.seqCanvas
.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
- if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+ if (res <= vpRanges.getStartRes()
+ || res >= (vpRanges.getStartRes() + cwidth))
{
vscroll.setValue(res / cwidth);
{
vscroll.setValue(res / cwidth);
- av.startRes = vscroll.getValue() * cwidth;
+ vpRanges.setStartRes(vscroll.getValue() * cwidth);
}
}
}
}
@@
-621,8
+639,8
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
public void setWrapAlignment(boolean wrap)
{
public void setWrapAlignment(boolean wrap)
{
- av.startSeq = 0;
- av.startRes = 0;
+ vpRanges.setStartSeq(0);
+ vpRanges.setStartRes(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
@@
-713,7
+731,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
x = 0;
}
{
x = 0;
}
- ;
+
hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
@@
-751,17
+769,10
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
x = 0;
}
x = 0;
}
- av.setStartSeq(y);
-
- int endSeq = y + vextent;
- if (endSeq > av.getAlignment().getHeight())
- {
- endSeq = av.getAlignment().getHeight();
- }
-
- av.setEndSeq(endSeq);
- av.setStartRes(x);
- av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
+ vpRanges.setStartSeq(y);
+ vpRanges.setEndSeq(y + vextent);
+ vpRanges.setStartRes(x);
+ vpRanges.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
.getCharWidth())) - 1);
hscroll.setValues(x, hextent, 0, width);
.getCharWidth())) - 1);
hscroll.setValues(x, hextent, 0, width);
@@
-778,8
+789,8
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
@Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
@Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
+ int oldX = vpRanges.getStartRes();
+ int oldY = vpRanges.getStartSeq();
if (evt == null || evt.getSource() == apvscroll)
{
if (evt == null || evt.getSource() == apvscroll)
{
@@
-793,8
+804,8
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
if (evt == null || evt.getSource() == hscroll)
{
int x = hscroll.getValue();
if (evt == null || evt.getSource() == hscroll)
{
int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes(x + seqPanel.seqCanvas.getSize().width
+ vpRanges.setStartRes(x);
+ vpRanges.setEndRes(x + seqPanel.seqCanvas.getSize().width
/ av.getCharWidth() - 1);
}
/ av.getCharWidth() - 1);
}
@@
-805,14
+816,14
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
{
int rowSize = seqPanel.seqCanvas
.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
{
int rowSize = seqPanel.seqCanvas
.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
- av.setStartRes(vscroll.getValue() * rowSize);
- av.setEndRes((vscroll.getValue() + 1) * rowSize);
+ vpRanges.setStartRes(vscroll.getValue() * rowSize);
+ vpRanges.setEndRes((vscroll.getValue() + 1) * rowSize);
}
else
{
}
else
{
- av.setStartSeq(offy);
- av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
- / av.getCharHeight());
+ vpRanges.setStartSeq(offy);
+ vpRanges.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
+ / av.getCharHeight() - 1);
}
}
}
}
@@
-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 = vpRanges.getStartRes() - oldX;
+ int scrollY = vpRanges.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 > vpRanges.getEndRes() - vpRanges.getStartRes())
{
{
- scrollX = av.endRes - av.startRes;
+ scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
}
}
- else if (scrollX < av.startRes - av.endRes)
+ else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
{
{
- scrollX = av.startRes - av.endRes;
+ scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
}
idPanel.idCanvas.fastPaint(scrollY);
}
idPanel.idCanvas.fastPaint(scrollY);
@@
-847,7
+858,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
scalePanel.repaint();
if (av.isShowAnnotation())
{
scalePanel.repaint();
if (av.isShowAnnotation())
{
- annotationPanel.fastPaint(av.getStartRes() - oldX);
+ annotationPanel.fastPaint(vpRanges.getStartRes() - oldX);
}
}
sendViewPosition();
}
}
sendViewPosition();
@@
-902,14
+913,14
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
* @param seqOffset
* the number of visible sequences to show above the mapped region
*/
* @param seqOffset
* the number of visible sequences to show above the mapped region
*/
- protected void scrollToCentre(SearchResults sr, int seqOffset)
+ protected void scrollToCentre(SearchResultsI sr, int seqOffset)
{
/*
* 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.
*/
{
/*
* 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.getResultSequence(0);
+ SequenceI mappedTo = sr.getResults().get(0).getSequence();
List<SequenceI> seqs = av.getAlignment().getSequences();
/*
List<SequenceI> seqs = av.getAlignment().getSequences();
/*
@@
-931,23
+942,22
@@
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, vpRanges.getStartRes(),
+ vpRanges.getEndRes(), vpRanges.getStartSeq(),
+ vpRanges.getEndSeq());
}
/**
}
/**
@@
-1015,7
+1025,7
@@
public class AlignmentPanel extends Panel implements AdjustmentListener,
}
else
{
}
else
{
- setScrollValues(av.getStartRes(), av.getStartSeq());
+ setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
}
seqPanel.seqCanvas.repaint();
}
seqPanel.seqCanvas.repaint();