/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class SequenceRenderer
{
AlignViewport av;
+
FontMetrics fm;
+
boolean renderGaps = true;
+
SequenceGroup currentSequenceGroup = null;
+
SequenceGroup[] allGroups = null;
+
Color resBoxColour;
+
Graphics graphics;
+
boolean monospacedFont;
+
boolean forOverview = false;
/**
* Creates a new SequenceRenderer object.
- *
- * @param av DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
*/
public SequenceRenderer(AlignViewport av)
{
/**
* DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
*/
public void prepare(Graphics g, boolean renderGaps)
{
// If EPS graphics, stringWidth will be a double, not an int
double dwidth = fm.getStringBounds("M", g).getWidth();
- monospacedFont =
- (dwidth == fm.getStringBounds("|", g).getWidth()
- && (float) av.charWidth == dwidth);
+ monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && (float) av.charWidth == dwidth);
this.renderGaps = renderGaps;
}
/**
* DOCUMENT ME!
- *
- * @param cs DOCUMENT ME!
- * @param seq DOCUMENT ME!
- * @param i DOCUMENT ME!
+ *
+ * @param cs
+ * DOCUMENT ME!
+ * @param seq
+ * DOCUMENT ME!
+ * @param i
+ * DOCUMENT ME!
*/
void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
{
{
resBoxColour = cs.findColour(seq.getCharAt(i), i);
}
- else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+ else if (forOverview
+ && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
{
resBoxColour = Color.lightGray;
}
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param seq DOCUMENT ME!
- * @param sg DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- * @param x1 DOCUMENT ME!
- * @param y1 DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param height DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param seq
+ * DOCUMENT ME!
+ * @param sg
+ * DOCUMENT ME!
+ * @param start
+ * DOCUMENT ME!
+ * @param end
+ * DOCUMENT ME!
+ * @param x1
+ * DOCUMENT ME!
+ * @param y1
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param height
+ * DOCUMENT ME!
*/
- public void drawSequence(SequenceI seq, SequenceGroup[] sg,
- int start, int end, int y1)
+ public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
+ int end, int y1)
{
allGroups = sg;
/**
* DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- * @param x1 DOCUMENT ME!
- * @param y1 DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param height DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
+ * @param start
+ * DOCUMENT ME!
+ * @param end
+ * DOCUMENT ME!
+ * @param x1
+ * DOCUMENT ME!
+ * @param y1
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param height
+ * DOCUMENT ME!
*/
- public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
+ public synchronized void drawBoxes(SequenceI seq, int start, int end,
+ int y1)
{
int i = start;
int length = seq.getLength();
if (tempColour != null)
{
graphics.fillRect(av.charWidth * (curStart - start), y1,
- curWidth, av.charHeight);
+ curWidth, av.charHeight);
}
graphics.setColor(resBoxColour);
}
graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
- av.charHeight);
+ av.charHeight);
}
/**
* DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- * @param x1 DOCUMENT ME!
- * @param y1 DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param height DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
+ * @param start
+ * DOCUMENT ME!
+ * @param end
+ * DOCUMENT ME!
+ * @param x1
+ * DOCUMENT ME!
+ * @param y1
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param height
+ * DOCUMENT ME!
*/
public void drawText(SequenceI seq, int start, int end, int y1)
{
}
graphics.setColor(av.textColour);
- if (monospacedFont
- && av.showText
- && allGroups.length == 0
- && !av.getColourText()
- && av.thresholdTextColour == 0)
+ if (monospacedFont && av.showText && allGroups.length == 0
+ && !av.getColourText() && av.thresholdTextColour == 0)
{
if (av.renderGaps)
{
else
{
char gap = av.getGapCharacter();
- graphics.drawString(seq.getSequenceAsString(start, end + 1).replace(gap,
- ' '), 0, y1);
+ graphics.drawString(seq.getSequenceAsString(start, end + 1)
+ .replace(gap, ' '), 0, y1);
}
}
else
}
if (currentSequenceGroup.thresholdTextColour > 0
- || currentSequenceGroup.getColourText())
+ || currentSequenceGroup.getColourText())
{
getboxColour = true;
getBoxColour(currentSequenceGroup.cs, seq, i);
if (currentSequenceGroup.thresholdTextColour > 0)
{
- if (resBoxColour.getRed() +
- resBoxColour.getBlue() +
- resBoxColour.getGreen() <
- currentSequenceGroup.thresholdTextColour)
+ if (resBoxColour.getRed() + resBoxColour.getBlue()
+ + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
{
graphics.setColor(currentSequenceGroup.textColour2);
}
getBoxColour(av.globalColourScheme, seq, i);
}
- if (resBoxColour.getRed() +
- resBoxColour.getBlue() +
- resBoxColour.getGreen() < av.thresholdTextColour)
+ if (resBoxColour.getRed() + resBoxColour.getBlue()
+ + resBoxColour.getGreen() < av.thresholdTextColour)
{
graphics.setColor(av.textColour2);
}
}
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s),
- charOffset + av.charWidth * (i - start),
- y1);
+ graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+ * (i - start), y1);
}
}
/**
* DOCUMENT ME!
- *
- * @param res DOCUMENT ME!
- *
+ *
+ * @param res
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
boolean inCurrentSequenceGroup(int res)
for (int i = 0; i < allGroups.length; i++)
{
- if ( (allGroups[i].getStartRes() <= res) &&
- (allGroups[i].getEndRes() >= res))
+ if ((allGroups[i].getStartRes() <= res)
+ && (allGroups[i].getEndRes() >= res))
{
currentSequenceGroup = allGroups[i];
/**
* DOCUMENT ME!
- *
- * @param seq DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- * @param x1 DOCUMENT ME!
- * @param y1 DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param height DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
+ * @param start
+ * DOCUMENT ME!
+ * @param end
+ * DOCUMENT ME!
+ * @param x1
+ * DOCUMENT ME!
+ * @param y1
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param height
+ * DOCUMENT ME!
*/
- public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
- int y1)
+ public void drawHighlightedText(SequenceI seq, int start, int end,
+ int x1, int y1)
{
int pady = av.charHeight / 5;
int charOffset = 0;
graphics.setColor(Color.BLACK);
- graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
+ graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
+ av.charHeight);
graphics.setColor(Color.white);
char s = '~';
}
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s),
- charOffset + x1 + (av.charWidth * (i - start)),
- (y1 + av.charHeight) - pady);
+ graphics
+ .drawString(String.valueOf(s), charOffset + x1
+ + (av.charWidth * (i - start)),
+ (y1 + av.charHeight) - pady);
}
}
}
char s = seq.getCharAt(res);
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s),
- charOffset + x1,
- (y1 + av.charHeight) - pady);
+ graphics.drawString(String.valueOf(s), charOffset + x1,
+ (y1 + av.charHeight) - pady);
}
}