From 7f14a135f0c03e8a01185ebfbddab5cbe11b4e4a Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Fri, 18 Aug 2023 17:16:55 +0100 Subject: [PATCH] JAL-4250 Make secondary structure annotation shapes antialiased and outlined in the same colour for better shape definition. --- src/jalview/renderer/AnnotationRenderer.java | 158 ++++++++++++++++++-------- 1 file changed, 111 insertions(+), 47 deletions(-) diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index ad1fa4a..5aea2cf 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -27,6 +27,7 @@ import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.Image; +import java.awt.RenderingHints; import java.awt.geom.AffineTransform; import java.awt.image.ImageObserver; import java.util.BitSet; @@ -37,6 +38,8 @@ 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; @@ -189,7 +192,7 @@ public class AnnotationRenderer * 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); @@ -209,7 +212,7 @@ public class AnnotationRenderer * 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); @@ -221,7 +224,7 @@ public class AnnotationRenderer } } // 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, @@ -229,7 +232,7 @@ public class AnnotationRenderer int iconOffset, int startRes, int column, boolean validRes, boolean validEnd) { - // System.out.println(nonCanColor); + // Console.info(nonCanColor); g.setColor(nonCanColor); int sCol = (lastSSX / charWidth) @@ -245,7 +248,8 @@ public class AnnotationRenderer 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 (column > 0 && Rna.isClosingParenthesis(dc)) @@ -255,7 +259,7 @@ public class AnnotationRenderer // 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 }, 3); @@ -272,7 +276,7 @@ public class AnnotationRenderer // display a forward arrow if (diffdownstream) { - 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); @@ -284,7 +288,7 @@ public class AnnotationRenderer } } // draw arrow body - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); + fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 7); } // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI @@ -447,6 +451,15 @@ public class AnnotationRenderer AlignViewportI av, Graphics g, int activeRow, int startRes, int endRes) { + Graphics2D g2d = (Graphics2D) g; + if (Cache.getDefault("ANTI_ALIAS", true)) + { + g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + g2d.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL, + RenderingHints.VALUE_STROKE_PURE); + } + long stime = System.currentTimeMillis(); boolean usedFaded = false; // NOTES: @@ -634,24 +647,24 @@ public class AnnotationRenderer { 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()); @@ -674,11 +687,11 @@ public class AnnotationRenderer 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); } /* @@ -691,19 +704,19 @@ public class AnnotationRenderer /* * 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)); } 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( @@ -711,7 +724,7 @@ public class AnnotationRenderer || (displayChar.length() < 2 && row_annotations[column].secondaryStructure == ' '))) { - gg.drawString(displayChar, 0, 0); + g2d.drawString(displayChar, 0, 0); } if (scaledToFit) { @@ -719,10 +732,10 @@ public class AnnotationRenderer * 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) @@ -784,7 +797,8 @@ public class AnnotationRenderer { // 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) { @@ -878,7 +892,7 @@ public class AnnotationRenderer // temp = x; break; default: - g.setColor(Color.gray); + g.setColor(GLYPHLINE_COLOR); g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2); // temp = x; @@ -1006,7 +1020,7 @@ public class AnnotationRenderer 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); @@ -1091,7 +1105,7 @@ public class AnnotationRenderer } else { - System.err.println( + Console.warn( "rendered with " + renderer.getClass().toString()); } } @@ -1122,17 +1136,15 @@ public class AnnotationRenderer { 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)); } ; @@ -1142,7 +1154,7 @@ public class AnnotationRenderer public static final Color GLYPHLINE_COLOR = Color.gray; - public static final Color SHEET_COLOUR = Color.green; + public static final Color SHEET_COLOUR = Color.green.darker(); public static final Color HELIX_COLOUR = Color.red; @@ -1155,6 +1167,7 @@ public class AnnotationRenderer boolean validEnd) { g.setColor(GLYPHLINE_COLOR); + unsetAntiAlias(g); g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2); } @@ -1168,9 +1181,9 @@ public class AnnotationRenderer 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( + fillRect(g, lastSSX, y + 4 + iconOffset, + (x * charWidth) - lastSSX - 4, 6); + fillPolygon(g, new int[] { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) }, new int[] @@ -1179,8 +1192,8 @@ public class AnnotationRenderer } else { - g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth - lastSSX, - 7); + fillRect(g, lastSSX, y + 4 + iconOffset, + (x + 1) * charWidth - lastSSX, 6); } } @@ -1196,12 +1209,14 @@ public class AnnotationRenderer int x1 = lastSSX; int x2 = (x * charWidth); + y--; + if (USE_FILL_ROUND_RECT) { 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 + 4 + iconOffset, x2 - x1, 8, 8, 8); if (sCol == 0 || row[sCol - 1] == null || row[sCol - 1].secondaryStructure != 'H') { @@ -1209,7 +1224,7 @@ public class AnnotationRenderer else { // g.setColor(Color.orange); - g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, + fillRoundRect(g, lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, 0, 0); } if (!validRes || row[column] == null @@ -1220,7 +1235,7 @@ public class AnnotationRenderer else { // g.setColor(Color.magenta); - g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, + fillRoundRect(g, lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, 0, 0); } @@ -1231,19 +1246,19 @@ public class AnnotationRenderer if (sCol == 0 || row[sCol - 1] == null || row[sCol - 1].secondaryStructure != 'H') { - g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180); + fillArc(g, lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180); x1 += charWidth / 2; } if (!validRes || row[column] == null || row[column].secondaryStructure != 'H') { - g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth, + fillArc(g, (x * charWidth) - charWidth, y + 4 + iconOffset, charWidth, 8, 270, 180); x2 -= charWidth / 2; } - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); + fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 8); } void drawLineGraph(Graphics g, AlignmentAnnotation _aa, @@ -1420,11 +1435,11 @@ public class AnnotationRenderer { 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 @@ -1455,7 +1470,8 @@ public class AnnotationRenderer // 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(); @@ -1598,7 +1614,7 @@ public class AnnotationRenderer { 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; @@ -1622,7 +1638,7 @@ public class AnnotationRenderer height = y; } - g.fillRect(x, y - height, charWidth, height); + fillRect(g, x, y - height, charWidth, height); } x += charWidth; } @@ -1749,9 +1765,57 @@ public class AnnotationRenderer 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 static void fillPolygon(Graphics g, int[] xpoints, int[] ypoints, + int n) + { + setAntiAlias(g); + g.fillPolygon(xpoints, ypoints, n); + g.drawPolygon(xpoints, ypoints, n); + } + + private static void fillRect(Graphics g, int a, int b, int c, int d) + { + setAntiAlias(g); + g.fillRect(a, b, c, d); + g.drawRect(a, b, c, d); + } + + private static 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); + g.drawRoundRect(a, b, c, d, e, f); + } + + private static 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); + g.drawArc(a, b, c, d, e, f); + } + + private static void setAntiAlias(Graphics g) + { + if (Cache.getDefault("ANTI_ALIAS", true)) + { + Graphics2D g2d = (Graphics2D) g; + g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + } + + private static void unsetAntiAlias(Graphics g) + { + Graphics2D g2d = (Graphics2D) g; + g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_OFF); + } } -- 1.7.10.2