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Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges
[jalview.git]
/
src
/
jalview
/
appletgui
/
SeqCanvas.java
diff --git
a/src/jalview/appletgui/SeqCanvas.java
b/src/jalview/appletgui/SeqCanvas.java
index
821136f
..
ae879b5
100755
(executable)
--- a/
src/jalview/appletgui/SeqCanvas.java
+++ b/
src/jalview/appletgui/SeqCanvas.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-21,12
+21,14
@@
package jalview.appletgui;
import jalview.datamodel.AlignmentI;
package jalview.appletgui;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
import jalview.viewmodel.AlignmentViewport;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Color;
import java.awt.FontMetrics;
@@
-50,8
+52,6
@@
public class SeqCanvas extends Panel
AlignViewport av;
AlignViewport av;
- SearchResults searchResults = null;
-
boolean fastPaint = false;
int cursorX = 0;
boolean fastPaint = false;
int cursorX = 0;
@@
-124,14
+124,17
@@
public class SeqCanvas extends Panel
ypos += avcharHeight;
if (av.hasHiddenColumns())
{
ypos += avcharHeight;
if (av.hasHiddenColumns())
{
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ startx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(startx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
}
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
}
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
// WEST SCALE
}
// WEST SCALE
@@
-171,7
+174,8
@@
public class SeqCanvas extends Panel
if (av.hasHiddenColumns())
{
if (av.hasHiddenColumns())
{
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
}
SequenceI seq;
}
SequenceI seq;
@@
-213,17
+217,19
@@
public class SeqCanvas extends Panel
return;
}
return;
}
+ ViewportRanges ranges = av.getRanges();
+
updateViewport();
// Its possible on certain browsers that the call to fastpaint
// is faster than it can paint, so this check here catches
// this possibility
updateViewport();
// Its possible on certain browsers that the call to fastpaint
// is faster than it can paint, so this check here catches
// this possibility
- if (lastsr + horizontal != av.startRes)
+ if (lastsr + horizontal != ranges.getStartRes())
{
{
- horizontal = av.startRes - lastsr;
+ horizontal = ranges.getStartRes() - lastsr;
}
}
- lastsr = av.startRes;
+ lastsr = ranges.getStartRes();
fastPaint = true;
gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
fastPaint = true;
gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
@@
-231,7
+237,9
@@
public class SeqCanvas extends Panel
imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
-vertical * avcharHeight);
imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
-vertical * avcharHeight);
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+ int sr = ranges.getStartRes(), er = ranges.getEndRes(), ss = ranges
+ .getStartSeq(), es = ranges
+ .getEndSeq(), transX = 0, transY = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
if (horizontal > 0) // scrollbar pulled right, image to the left
{
@@
-246,21
+254,23
@@
public class SeqCanvas extends Panel
else if (vertical > 0) // scroll down
{
ss = es - vertical;
else if (vertical > 0) // scroll down
{
ss = es - vertical;
- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+ if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
+ // at a
+ // time
{
{
- ss = av.startSeq;
+ ss = ranges.getStartSeq();
}
else
{
}
else
{
- transY = imgHeight - vertical * avcharHeight;
+ transY = imgHeight - ((vertical + 1) * avcharHeight);
}
}
else if (vertical < 0)
{
es = ss - vertical;
}
}
else if (vertical < 0)
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > ranges.getEndSeq())
{
{
- es = av.endSeq;
+ es = ranges.getEndSeq();
}
}
}
}
@@
-331,13
+341,16
@@
public class SeqCanvas extends Panel
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, imgHeight);
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, imgHeight);
+ ViewportRanges ranges = av.getRanges();
+
if (av.getWrapAlignment())
{
if (av.getWrapAlignment())
{
- drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+ drawWrappedPanel(gg, imgWidth, imgHeight, ranges.getStartRes());
}
else
{
}
else
{
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq(), 0);
}
g.drawImage(img, 0, 0, this);
}
g.drawImage(img, 0, 0, this);
@@
-423,7
+436,7
@@
public class SeqCanvas extends Panel
av.setWrappedWidth(cWidth);
av.setWrappedWidth(cWidth);
- av.endRes = av.startRes + cWidth;
+ av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth);
int endx;
int ypos = hgap;
int endx;
int ypos = hgap;
@@
-432,7
+445,8
@@
public class SeqCanvas extends Panel
if (av.hasHiddenColumns())
{
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
while ((ypos <= canvasHeight) && (startRes < maxwidth))
}
while ((ypos <= canvasHeight) && (startRes < maxwidth))
@@
-466,12
+480,13
@@
public class SeqCanvas extends Panel
}
if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
{
}
if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
{
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
g.setColor(Color.blue);
int res;
g.setColor(Color.blue);
int res;
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
+ for (int i = 0; i < hidden.getListOfCols()
.size(); i++)
{
.size(); i++)
{
- res = av.getColumnSelection().findHiddenRegionPosition(i)
+ res = hidden.findHiddenRegionPosition(i)
- startRes;
if (res < 0 || res > endx - startRes)
- startRes;
if (res < 0 || res > endx - startRes)
@@
-493,7
+508,7
@@
public class SeqCanvas extends Panel
g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
}
g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
}
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+ drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
g.setClip(null);
if (av.isShowAnnotation())
g.setClip(null);
if (av.isShowAnnotation())
@@
-550,7
+565,8
@@
public class SeqCanvas extends Panel
if (av.hasHiddenColumns())
{
if (av.hasHiddenColumns())
{
- for (int[] region : av.getColumnSelection().getHiddenColumns())
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ for (int[] region : hidden.getListOfCols())
{
int hideStart = region[0];
int hideEnd = region[1];
{
int hideStart = region[0];
int hideEnd = region[1];
@@
-572,7
+588,7
@@
public class SeqCanvas extends Panel
g1.setColor(Color.blue);
g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
0 + offset, (blockEnd - blockStart + 1) * avcharWidth
g1.setColor(Color.blue);
g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
0 + offset, (blockEnd - blockStart + 1) * avcharWidth
- - 1, (endSeq - startSeq) * avcharHeight
+ - 1, (endSeq - startSeq + 1) * avcharHeight
+ offset);
}
+ offset);
}
@@
-612,7
+628,7
@@
public class SeqCanvas extends Panel
// / First draw the sequences
// ///////////////////////////
// / First draw the sequences
// ///////////////////////////
- for (int i = startSeq; i < endSeq; i++)
+ for (int i = startSeq; i <= endSeq; i++)
{
nextSeq = av.getAlignment().getSequenceAt(i);
{
nextSeq = av.getAlignment().getSequenceAt(i);
@@
-627,14
+643,15
@@
public class SeqCanvas extends Panel
if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * avcharHeight));
+ + ((i - startSeq) * avcharHeight), false);
}
// / Highlight search Results once all sequences have been drawn
// ////////////////////////////////////////////////////////
}
// / Highlight search Results once all sequences have been drawn
// ////////////////////////////////////////////////////////
- if (searchResults != null)
+ if (av.hasSearchResults())
{
{
- int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+ int[] visibleResults = av.getSearchResults().getResults(nextSeq,
+ startRes,
endRes);
if (visibleResults != null)
{
endRes);
if (visibleResults != null)
{
@@
-695,7
+712,7
@@
public class SeqCanvas extends Panel
int bottom = -1;
int alHeight = av.getAlignment().getHeight() - 1;
int bottom = -1;
int alHeight = av.getAlignment().getHeight() - 1;
- for (i = startSeq; i < endSeq; i++)
+ for (i = startSeq; i <= endSeq; i++)
{
sx = (group.getStartRes() - startRes) * avcharWidth;
sy = offset + ((i - startSeq) * avcharHeight);
{
sx = (group.getStartRes() - startRes) * avcharWidth;
sy = offset + ((i - startSeq) * avcharHeight);
@@
-843,10
+860,9
@@
public class SeqCanvas extends Panel
}
}
}
}
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
{
- searchResults = results;
-
+ av.setSearchResults(results);
repaint();
}
repaint();
}