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Merge branch 'develop' into patch/JAL-3088_finalbracenotinrightplace
[jalview.git]
/
src
/
jalview
/
renderer
/
AnnotationRenderer.java
diff --git
a/src/jalview/renderer/AnnotationRenderer.java
b/src/jalview/renderer/AnnotationRenderer.java
index
cba36d2
..
9438e9a
100644
(file)
--- a/
src/jalview/renderer/AnnotationRenderer.java
+++ b/
src/jalview/renderer/AnnotationRenderer.java
@@
-175,7
+175,6
@@
public class AnnotationRenderer
int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
- g.setColor(STEM_COLOUR);
int sCol = (lastSSX / charWidth)
+ hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int sCol = (lastSSX / charWidth)
+ hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
@@
-190,6
+189,13
@@
public class AnnotationRenderer
|| row_annotations[column] == null
|| dc != row_annotations[column].secondaryStructure;
|| row_annotations[column] == null
|| dc != row_annotations[column].secondaryStructure;
+ if (diffupstream || diffdownstream)
+ {
+ // draw glyphline under arrow
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+ }
+ g.setColor(STEM_COLOUR);
+
if (column > 0 && Rna.isClosingParenthesis(dc))
{
if (diffupstream)
if (column > 0 && Rna.isClosingParenthesis(dc))
{
if (diffupstream)
@@
-202,7
+208,8
@@
public class AnnotationRenderer
*/
fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
new int[]
*/
fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
new int[]
- { y + iconOffset, y + 13 + iconOffset, y + 7 + iconOffset },
+ { y + iconOffset + 1, y + 13 + iconOffset,
+ y + 7 + iconOffset },
3);
x1 += 5;
}
3);
x1 += 5;
}
@@
-220,9
+227,10
@@
public class AnnotationRenderer
* if annotation ending with an opeing base pair half of the stem,
* display a forward arrow
*/
* if annotation ending with an opeing base pair half of the stem,
* display a forward arrow
*/
- fillPolygon(g, new int[] { x2 - 5, x2 - 5, x2 },
+ fillPolygon(g, new int[] { x2 - 6, x2 - 6, x2 - 1 },
new int[]
new int[]
- { y + iconOffset, y + 13 + iconOffset, y + 7 + iconOffset },
+ { y + iconOffset + 1, y + 13 + iconOffset,
+ y + 7 + iconOffset },
3);
x2 -= 5;
}
3);
x2 -= 5;
}
@@
-232,6
+240,7
@@
public class AnnotationRenderer
}
}
// draw arrow body
}
}
// draw arrow body
+ unsetAntialias(g);
fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
}
fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
}
@@
-1267,7
+1276,6
@@
public class AnnotationRenderer
}
else
{
}
else
{
- // g.setColor(Color.orange);
fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0,
0);
}
fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0,
0);
}
@@
-1278,7
+1286,6
@@
public class AnnotationRenderer
}
else
{
}
else
{
- // g.setColor(Color.magenta);
fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs,
8, 0, 0);
}
fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs,
8, 0, 0);
}