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;
: row_annotations[column - 1].secondaryStructure;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || dc != row_annotations[sCol - 1].secondaryStructure;
+ || dc != row_annotations[sCol - 1].secondaryStructure
+ || !validEnd;
boolean diffdownstream = !validRes || !validEnd
|| 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)
*/
fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ { y + iconOffset + 1, y + 13 + iconOffset,
+ y + 7 + iconOffset },
3);
x1 += 5;
}
* 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[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ { y + iconOffset + 1, y + 13 + iconOffset,
+ y + 7 + iconOffset },
3);
x2 -= 5;
}
}
}
// draw arrow body
- fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 7);
+ unsetAntialias(g);
+ fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
}
void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
: row_annotations[column - 1].displayCharacter;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+ || !dc.equals(row_annotations[sCol - 1].displayCharacter)
+ || !validEnd;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| !dc.equals(row_annotations[column].displayCharacter);
}
else
{
- // g.setColor(Color.orange);
fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0,
0);
}
}
else
{
- // g.setColor(Color.magenta);
fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs,
8, 0, 0);
}