*/
package jalview.renderer;
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.image.ImageObserver;
+import java.util.BitSet;
+import java.util.Hashtable;
+
+import org.jfree.graphics2d.svg.SVGGraphics2D;
+import org.jibble.epsgraphics.EpsGraphics2D;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.CodingUtils;
import jalview.analysis.Rna;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ZappoColourScheme;
import jalview.util.Platform;
-import java.awt.BasicStroke;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.Image;
-import java.awt.geom.AffineTransform;
-import java.awt.image.ImageObserver;
-import java.util.BitSet;
-import java.util.Hashtable;
-
public class AnnotationRenderer
{
private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
private boolean av_ignoreGapsConsensus;
+ private boolean vectorRendition = false;
+
+ private boolean glyphLineDrawn = false;
+
/**
* attributes set from AwtRenderPanelI
*/
* if new annotation with a closing base pair half of the stem,
* display a backward arrow
*/
- g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
new int[]
{ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
3);
* if annotation ending with an opeing base pair half of the stem,
* display a forward arrow
*/
- g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
+ fillPolygon(g, new int[] { x2 - 5, x2 - 5, x2 },
new int[]
{ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
3);
}
}
// draw arrow body
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 7);
}
void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
int iconOffset, int startRes, int column, boolean validRes,
boolean validEnd)
{
- // System.out.println(nonCanColor);
+ // Console.info(nonCanColor);
- g.setColor(nonCanColor);
int sCol = (lastSSX / charWidth)
+ hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| !dc.equals(row_annotations[column].displayCharacter);
- // System.out.println("Column "+column+" diff up: "+diffupstream+"
+ // Console.info("Column "+column+" diff up:
+ // "+diffupstream+"
// down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
+ if (diffupstream || diffdownstream)
+ {
+ // draw glyphline under arrow
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+ }
+ g.setColor(nonCanColor);
if (column > 0 && Rna.isClosingParenthesis(dc))
{
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
{
- g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ 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;
}
// display a forward arrow
if (diffdownstream)
{
- g.fillPolygon(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
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ unsetAntialias(g);
+ fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
}
// public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
AlignViewportI av, Graphics g, int activeRow, int startRes,
int endRes)
{
+ if (g instanceof EpsGraphics2D || g instanceof SVGGraphics2D)
+ {
+ this.setVectorRendition(true);
+ }
+ Graphics2D g2d = (Graphics2D) g;
+
long stime = System.currentTimeMillis();
boolean usedFaded = false;
// NOTES:
*
* continue; }
*/
+
// first pass sets up state for drawing continuation from left-hand
// column
// of startRes
+
+ // flag used for vector rendition
+ this.glyphLineDrawn = false;
x = (startRes == 0) ? 0 : -1;
while (x < endRes - startRes)
{
: null;
if (x > -1)
{
+ unsetAntialias(g);
if (activeRow == i)
{
g.setColor(Color.red);
{
if (columnSelection.contains(column))
{
- g.fillRect(x * charWidth, y, charWidth, charHeight);
+ fillRect(g, x * charWidth, y, charWidth, charHeight);
}
}
}
if (row.getInvalidStrucPos() > x)
{
g.setColor(Color.orange);
- g.fillRect(x * charWidth, y, charWidth, charHeight);
+ fillRect(g, x * charWidth, y, charWidth, charHeight);
}
else if (row.getInvalidStrucPos() == x)
{
g.setColor(Color.orange.darker());
- g.fillRect(x * charWidth, y, charWidth, charHeight);
+ fillRect(g, x * charWidth, y, charWidth, charHeight);
}
if (validCharWidth && validRes && displayChar != null
&& (displayChar.length() > 0))
{
- Graphics2D gg = ((Graphics2D) g);
+ // Graphics2D gg = (g);
float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
displayChar.length());
if (row_annotations[column].colour == null)
{
- gg.setColor(Color.black);
+ g2d.setColor(Color.black);
}
else
{
- gg.setColor(row_annotations[column].colour);
+ g2d.setColor(row_annotations[column].colour);
}
/*
/*
* translate to drawing position _before_ applying any scaling
*/
- gg.translate(xPos, yPos);
+ g2d.translate(xPos, yPos);
if (scaledToFit)
{
/*
* use a scaling transform to make the label narrower
* (JalviewJS doesn't have Font.deriveFont(AffineTransform))
*/
- gg.transform(
+ g2d.transform(
AffineTransform.getScaleInstance(fmScaling, 1.0));
}
+ setAntialias(g);
if (column == 0 || row.graph > 0)
{
- gg.drawString(displayChar, 0, 0);
+ g2d.drawString(displayChar, 0, 0);
}
else if (row_annotations[column - 1] == null || (labelAllCols
|| !displayChar.equals(
|| (displayChar.length() < 2
&& row_annotations[column].secondaryStructure == ' ')))
{
- gg.drawString(displayChar, 0, 0);
+ g2d.drawString(displayChar, 0, 0);
}
if (scaledToFit)
{
* undo scaling before translating back
* (restoring saved transform does NOT work in JS PDFGraphics!)
*/
- gg.transform(AffineTransform
+ g2d.transform(AffineTransform
.getScaleInstance(1D / fmScaling, 1.0));
}
- gg.translate(-xPos, -yPos);
+ g2d.translate(-xPos, -yPos);
}
}
if (row.hasIcons)
{
// int nb_annot = x - temp;
- // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
+ // Console.info("\t type :"+lastSS+"\t x
+ // :"+x+"\t nbre
// annot :"+nb_annot);
switch (lastSS)
{
// temp = x;
break;
default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * charWidth) - lastSSX, 2);
- // temp = x;
+ if (isVectorRendition())
+ {
+ // draw single full width glyphline
+ drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset);
+ // disable more glyph lines
+ this.glyphLineDrawn = true;
+ }
+ else
+ {
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+ }
break;
}
}
case 'y':
case 'Z':
case 'z':
- // System.out.println(lastSS);
+ // Console.info(lastSS);
Color nonCanColor = getNotCanonicalColor(lastSS);
drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
x, y, iconOffset, startRes, column, validRes, validEnd);
break;
default:
- drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
+ if (isVectorRendition())
+ {
+ // draw single full width glyphline
+ drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset);
+ // disable more glyph lines
+ this.glyphLineDrawn = true;
+ }
+ else
+ {
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+ }
break;
}
}
.getRendererFor(row);
if (renderer != null)
{
- renderer.renderRow(g, charWidth, charHeight,
- hasHiddenColumns, av, hiddenColumns, columnSelection,
- row, row_annotations, startRes, endRes, row.graphMin,
+ renderer.renderRow(g, charWidth, charHeight, hasHiddenColumns,
+ av, hiddenColumns, columnSelection, row,
+ row_annotations, startRes, endRes, row.graphMin,
row.graphMax, y);
}
if (debugRedraw)
{
if (renderer == null)
{
- System.err.println("No renderer found for "
- + row.toString());
+ System.err
+ .println("No renderer found for " + row.toString());
}
else
{
- System.err.println("rendered with "
- + renderer.getClass().toString());
+ Console.warn(
+ "rendered with " + renderer.getClass().toString());
}
}
{
if (clipst)
{
- System.err.println(
- "Start clip at : " + yfrom + " (index " + f_i + ")");
+ Console.warn("Start clip at : " + yfrom + " (index " + f_i + ")");
}
if (clipend)
{
- System.err.println(
- "End clip at : " + yto + " (index " + f_to + ")");
+ Console.warn("End clip at : " + yto + " (index " + f_to + ")");
}
}
;
- System.err.println("Annotation Rendering time:"
+ Console.warn("Annotation Rendering time:"
+ (System.currentTimeMillis() - stime));
}
;
// private Color sdNOTCANONICAL_COLOUR;
- void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
- int y, int iconOffset, int startRes, int column, boolean validRes,
- boolean validEnd)
+ void drawGlyphLine(Graphics g, int lastSSX, int x, int y, int iconOffset)
{
+ if (glyphLineDrawn)
+ {
+ // if we've drawn a single long glyphline for an export, don't draw the
+ // bits
+ return;
+ }
+ unsetAntialias(g);
g.setColor(GLYPHLINE_COLOR);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
}
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
- g.setColor(SHEET_COLOUR);
-
if (!validEnd || !validRes || row == null || row[column] == null
|| row[column].secondaryStructure != 'E')
{
- g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX - 4,
- 7);
- g.fillPolygon(
+ // draw the glyphline underneath
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+
+ g.setColor(SHEET_COLOUR);
+ fillRect(g, lastSSX, y + 4 + iconOffset,
+ (x * charWidth) - lastSSX - 4, 6);
+ fillPolygon(g,
new int[]
- { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
+ { (x * charWidth) - 6, (x * charWidth) - 6,
+ (x * charWidth - 1) },
new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
+ { y + iconOffset + 1, y + 13 + iconOffset,
+ y + 7 + iconOffset },
3);
}
else
{
- g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth - lastSSX,
- 7);
+ g.setColor(SHEET_COLOUR);
+ fillRect(g, lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX,
+ 6);
}
-
}
void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
int y, int iconOffset, int startRes, int column, boolean validRes,
boolean validEnd)
{
- g.setColor(HELIX_COLOUR);
-
int sCol = (lastSSX / charWidth)
+ hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
- if (USE_FILL_ROUND_RECT)
+ if (USE_FILL_ROUND_RECT || isVectorRendition())
{
+ // draw glyph line behind helix (visible in EPS or SVG output)
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+
+ g.setColor(HELIX_COLOUR);
+ setAntialias(g);
int ofs = charWidth / 2;
// Off by 1 offset when drawing rects and ovals
// to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
+ fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - 1, 8, 8, 8);
if (sCol == 0 || row[sCol - 1] == null
|| row[sCol - 1].secondaryStructure != 'H')
{
else
{
// g.setColor(Color.orange);
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
- 0, 0);
+ fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0,
+ 0);
}
if (!validRes || row[column] == null
|| row[column].secondaryStructure != 'H')
else
{
// g.setColor(Color.magenta);
- g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset,
- x2 - x1 - ofs + 1, 8, 0, 0);
-
+ fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs,
+ 8, 0, 0);
}
return;
}
- if (sCol == 0 || row[sCol - 1] == null
- || row[sCol - 1].secondaryStructure != 'H')
+ boolean leftEnd = sCol == 0 || row[sCol - 1] == null
+ || row[sCol - 1].secondaryStructure != 'H';
+ boolean rightEnd = !validRes || row[column] == null
+ || row[column].secondaryStructure != 'H';
+
+ if (leftEnd || rightEnd)
+ {
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+ }
+ g.setColor(HELIX_COLOUR);
+
+ if (leftEnd)
{
- g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
+ fillArc(g, lastSSX, y + 3 + iconOffset, charWidth, 8, 90, 180);
x1 += charWidth / 2;
}
- if (!validRes || row[column] == null
- || row[column].secondaryStructure != 'H')
+ if (rightEnd)
{
- g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
- 8, 270, 180);
+ fillArc(g, ((x - 1) * charWidth), y + 3 + iconOffset, charWidth, 8,
+ 270, 180);
x2 -= charWidth / 2;
}
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+ fillRect(g, x1, y + 3 + iconOffset, x2 - x1, 8);
}
void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
{
return;
}
+ Stroke roundStroke = new BasicStroke(1, BasicStroke.CAP_ROUND,
+ BasicStroke.JOIN_ROUND);
+ Stroke squareStroke = new BasicStroke(1, BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_MITER);
+ Graphics2D g2d = (Graphics2D) g;
+ Stroke prevStroke = g2d.getStroke();
+ g2d.setStroke(roundStroke);
int x = 0;
}
g.setColor(Color.gray);
- g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
+ drawLine(g, squareStroke, x * charWidth - charWidth, y2,
+ (eRes - sRes) * charWidth, y2);
eRes = Math.min(eRes, aa_annotations.length);
break;
}
- if (aa_annotations[column] == null
- || aa_annotations[column - 1] == null)
+ if (aa_annotations[column] == null)
{
x++;
continue;
g.setColor(aa_annotations[column].colour);
}
+ if (aa_annotations[column - 1] == null
+ && aa_annotations.length > column + 1
+ && aa_annotations[column + 1] == null)
+ {
+ // standalone value
+ y1 = y - (int) (((aa_annotations[column].value - min) / range)
+ * graphHeight);
+ drawLine(g, x * charWidth + charWidth / 4, y1,
+ x * charWidth + 3 * charWidth / 4, y1);
+ x++;
+ continue;
+ }
+
+ if (aa_annotations[column - 1] == null)
+ {
+ x++;
+ continue;
+ }
+
y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
* graphHeight);
y2 = y - (int) (((aa_annotations[column].value - min) / range)
* graphHeight);
- g.drawLine(x * charWidth - charWidth / 2, y1,
+ drawLine(g, (x - 1) * charWidth + charWidth / 2, y1,
x * charWidth + charWidth / 2, y2);
x++;
}
{
g.setColor(_aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
- g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
+ Stroke s = new BasicStroke(1, BasicStroke.CAP_SQUARE,
BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ { 5f, 3f }, 0f);
y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
- g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
- g2.setStroke(new BasicStroke());
+ drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2);
}
+ g2d.setStroke(prevStroke);
}
@SuppressWarnings("unused")
g.setColor(Color.gray);
- g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
+ drawLine(g, x, y2, (eRes - sRes) * charWidth, y2);
int column;
int aaMax = aa_annotations.length - 1;
{
if (y1 - y2 > 0)
{
- g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
+ fillRect(g, x * charWidth, y2, charWidth, y1 - y2);
}
else
{
- g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
+ fillRect(g, x * charWidth, y1, charWidth, y2 - y1);
}
}
// draw profile if available
// lm is not necessary - we can just use fm - could be off by no more
// than 0.5 px
// LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
- // System.out.println(asc + " " + dec + " " + (asc - lm.getAscent())
+ // Console.info(asc + " " + dec + " " + (asc -
+ // lm.getAscent())
// + " " + (dec - lm.getDescent()));
double asc = fm.getAscent();
if (_aa.threshold != null)
{
g.setColor(_aa.threshold.colour);
- Graphics2D g2 = (Graphics2D) g;
- g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
+ Stroke s = new BasicStroke(1, BasicStroke.CAP_SQUARE,
BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ { 5f, 3f }, 0f);
y2 = (int) (y
- ((_aa.threshold.value - min) / range) * _aa.graphHeight);
- g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
- g2.setStroke(new BasicStroke());
+ drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2);
}
}
{
eRes = Math.min(eRes, aa_annotations.length);
g.setColor(Color.white);
- g.fillRect(0, 0, width, y);
+ fillRect(g, 0, 0, width, y);
g.setColor(new Color(0, 0, 180));
int x = 0, height;
height = y;
}
- g.fillRect(x, y - height, charWidth, height);
+ fillRect(g, x, y - height, charWidth, height);
}
x += charWidth;
}
return new Color(0, 80, 255);
default:
- System.out.println("This is not a interaction : " + lastss);
+ Console.info("This is not a interaction : " + lastss);
return null;
}
}
+
+ private void fillPolygon(Graphics g, int[] xpoints, int[] ypoints, int n)
+ {
+ setAntialias(g);
+ g.fillPolygon(xpoints, ypoints, n);
+ }
+
+ /*
+ private void fillRect(Graphics g, int a, int b, int c, int d)
+ {
+ fillRect(g, false, a, b, c, d);
+ }*/
+
+ private void fillRect(Graphics g, int a, int b, int c, int d)
+ {
+ unsetAntialias(g);
+ g.fillRect(a, b, c, d);
+ }
+
+ private void fillRoundRect(Graphics g, int a, int b, int c, int d, int e,
+ int f)
+ {
+ setAntialias(g);
+ g.fillRoundRect(a, b, c, d, e, f);
+ }
+
+ private void fillArc(Graphics g, int a, int b, int c, int d, int e, int f)
+ {
+ setAntialias(g);
+ g.fillArc(a, b, c, d, e, f);
+ }
+
+ private void drawLine(Graphics g, Stroke s, int a, int b, int c, int d)
+ {
+ Graphics2D g2d = (Graphics2D) g;
+ Stroke p = g2d.getStroke();
+ g2d.setStroke(s);
+ drawLine(g, a, b, c, d);
+ g2d.setStroke(p);
+ }
+
+ private void drawLine(Graphics g, int a, int b, int c, int d)
+ {
+ setAntialias(g);
+ g.drawLine(a, b, c, d);
+ }
+
+ private void setAntialias(Graphics g)
+ {
+ if (isVectorRendition())
+ {
+ // no need to antialias vector drawings
+ return;
+ }
+ if (Cache.getDefault("ANTI_ALIAS", true))
+ {
+ Graphics2D g2d = (Graphics2D) g;
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+ }
+
+ private void unsetAntialias(Graphics g)
+ {
+ if (isVectorRendition())
+ {
+ // no need to antialias vector drawings
+ return;
+ }
+ Graphics2D g2d = (Graphics2D) g;
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_OFF);
+ }
+
+ public void setVectorRendition(boolean b)
+ {
+ vectorRendition = b;
+ }
+
+ public boolean isVectorRendition()
+ {
+ return vectorRendition;
+ }
}
git://source.jalview.org / jalview.git / blobdiff