import java.awt.FontMetrics;
import java.awt.Graphics;
+import org.jfree.graphics2d.svg.SVGGraphics2D;
+import org.jibble.epsgraphics.EpsGraphics2D;
+
public class SequenceRenderer implements jalview.api.SequenceRenderer
{
final static int CHAR_TO_UPPER = 'A' - 'a';
{
allGroups = av.getAlignment().findAllGroups(seq);
return resColourFinder.getResidueColour(av.getShowBoxes(),
- av.getResidueShading(),
- allGroups, seq, position,
- finder);
+ av.getResidueShading(), allGroups, seq, position, finder);
}
/**
if (i < length)
{
SequenceGroup currentSequenceGroup = resColourFinder
- .getCurrentSequenceGroup(
- allGroups, i);
+ .getCurrentSequenceGroup(allGroups, i);
if (currentSequenceGroup != null)
{
if (currentSequenceGroup.getDisplayBoxes())
{
resBoxColour = resColourFinder.getBoxColour(
- currentSequenceGroup.getGroupColourScheme(), seq,
- i);
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
}
}
else if (av.getShowBoxes())
}
graphics.setColor(av.getTextColour());
- if (monospacedFont && av.getShowText() && allGroups.length == 0
- && !av.getColourText() && av.getThresholdTextColour() == 0)
+ boolean drawAllText = monospacedFont && av.getShowText()
+ && allGroups.length == 0 && !av.getColourText()
+ && av.getThresholdTextColour() == 0;
+
+ /*
+ * EPS or SVG misaligns monospaced strings (JAL-3239)
+ * so always draw these one character at a time
+ */
+ if (graphics instanceof EpsGraphics2D
+ || graphics instanceof SVGGraphics2D)
+ {
+ drawAllText = false;
+ }
+ if (drawAllText)
{
if (av.isRenderGaps())
{
}
SequenceGroup currentSequenceGroup = resColourFinder
- .getCurrentSequenceGroup(
- allGroups, i);
+ .getCurrentSequenceGroup(allGroups, i);
if (currentSequenceGroup != null)
{
if (!currentSequenceGroup.getDisplayText())
{
getboxColour = true;
resBoxColour = resColourFinder.getBoxColour(
- currentSequenceGroup.getGroupColourScheme(), seq,
- i);
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
if (currentSequenceGroup.getColourText())
{
graphics.setColor(currentSequenceGroup.textColour);
}
boolean isgrep = currentSequenceGroup != null
- ? currentSequenceGroup.getSeqrep() == seq : false;
+ ? currentSequenceGroup.getSeqrep() == seq
+ : false;
if (!isarep && !isgrep
&& currentSequenceGroup.getShowNonconserved()) // todo
// optimize
}
}
- public void drawCursor(SequenceI seq, int res, int x1, int y1)
+ /**
+ * Draw a sequence canvas cursor
+ *
+ * @param g
+ * graphics context to draw on
+ * @param s
+ * character to draw at cursor
+ * @param x1
+ * x position of cursor in graphics context
+ * @param y1
+ * y position of cursor in graphics context
+ */
+ public void drawCursor(Graphics g, char s, int x1, int y1)
{
int pady = av.getCharHeight() / 5;
int charOffset = 0;
- graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
+ g.setColor(Color.black);
+ g.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
if (av.isValidCharWidth())
{
- graphics.setColor(Color.white);
-
- char s = seq.getCharAt(res);
-
+ g.setColor(Color.white);
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + x1,
+ g.drawString(String.valueOf(s), charOffset + x1,
(y1 + av.getCharHeight()) - pady);
}