From: James Procter Date: Mon, 28 Aug 2023 11:18:09 +0000 (+0100) Subject: Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into... X-Git-Tag: Release_2_11_3_0~3^2~11^2~5 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=359e5bf258a3ed91b492941f31b6b1c735b42d2e;hp=ff8a85b4462d824e858b9ce57082455772e1a2ff;p=jalview.git Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into develop --- diff --git a/j11lib/jfreesvg-2.1.jar b/j11lib/jfreesvg-2.1.jar deleted file mode 100644 index 91d453c..0000000 Binary files a/j11lib/jfreesvg-2.1.jar and /dev/null differ diff --git a/j11lib/jfreesvg-3.4.3.jar b/j11lib/jfreesvg-3.4.3.jar new file mode 100644 index 0000000..cfd1463 Binary files /dev/null and b/j11lib/jfreesvg-3.4.3.jar differ diff --git a/j8lib/jfreesvg-2.1.jar b/j8lib/jfreesvg-2.1.jar deleted file mode 100644 index 91d453c..0000000 Binary files a/j8lib/jfreesvg-2.1.jar and /dev/null differ diff --git a/j8lib/jfreesvg-3.4.3.jar b/j8lib/jfreesvg-3.4.3.jar new file mode 100644 index 0000000..cfd1463 Binary files /dev/null and b/j8lib/jfreesvg-3.4.3.jar differ diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index d7d1ea3..dbc4953 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -103,16 +103,20 @@ public class Commands theseArgsWereParsed &= processLinked(id); processGroovyScript(id); boolean processLinkedOkay = theseArgsWereParsed; - + // wait around until alignFrame isn't busy - AlignFrame af=afMap.get(id); - while (af!=null && af.getViewport().isCalcInProgress()) + AlignFrame af = afMap.get(id); + while (af != null && af.getViewport().isCalcInProgress()) { - try { + try + { Thread.sleep(25); - } catch (Exception q) {}; + } catch (Exception q) + { + } + ; } - + theseArgsWereParsed &= processImages(id); if (processLinkedOkay) theseArgsWereParsed &= processOutput(id); @@ -263,12 +267,16 @@ public class Commands if ("" != colour) { ColourSchemeI cs = ColourSchemeProperty.getColourScheme( - af.getViewport(), af.getViewport().getAlignment(), colour); - - if (cs==null && !"None".equals(colour)) + af.getViewport(), af.getViewport().getAlignment(), + colour); + + if (cs == null && !"None".equals(colour)) + { + Console.warn( + "Couldn't parse '" + colour + "' as a colourscheme."); + } + else { - Console.warn("Couldn't parse '"+colour+"' as a colourscheme."); - } else { af.changeColour(cs); } Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour); @@ -569,15 +577,15 @@ public class Commands structureFilepath, tft, paeFilepath, false, ssFromStructure, false, viewerType); - if (sv==null) + if (sv == null) { Console.error("Failed to import and open structure view."); continue; } try { - long tries=1000; - while (sv.isBusy() && tries>0) + long tries = 1000; + while (sv.isBusy() && tries > 0) { Thread.sleep(25); if (sv.isBusy()) @@ -587,15 +595,18 @@ public class Commands "Waiting for viewer for " + structureFilepath); } } - if (tries==0 && sv.isBusy()) + if (tries == 0 && sv.isBusy()) { - Console.warn("Gave up waiting for structure viewer to load. Something may have gone wrong."); + Console.warn( + "Gave up waiting for structure viewer to load. Something may have gone wrong."); } } catch (Exception x) { - Console.warn("Exception whilst waiting for structure viewer "+structureFilepath,x); + Console.warn("Exception whilst waiting for structure viewer " + + structureFilepath, x); } - Console.debug("Successfully opened viewer for "+structureFilepath); + Console.debug( + "Successfully opened viewer for " + structureFilepath); String structureImageFilename = ArgParser.getValueFromSubValOrArg( avm, av, Arg.STRUCTUREIMAGE, subVals); if (sv != null && structureImageFilename != null) @@ -652,16 +663,18 @@ public class Commands if (sview instanceof AppJmol) { AppJmol jmol = (AppJmol) sview; - try { - Console.debug("Rendering image to "+structureImageFile); + try + { + Console.debug("Rendering image to " + structureImageFile); jmol.makePDBImage(structureImageFile, imageType, renderer, - userBis); - Console.debug("Finished Rendering image to "+structureImageFile); + userBis); + Console.debug("Finished Rendering image to " + + structureImageFile); - } - catch (ImageOutputException ioexc) + } catch (ImageOutputException ioexc) { - Console.warn("Unexpected error whilst exporting image to "+structureImageFile,ioexc); + Console.warn("Unexpected error whilst exporting image to " + + structureImageFile, ioexc); } } @@ -771,57 +784,60 @@ public class Commands Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false"); Console.info("Writing " + file); - try { - switch (type) + try { - - case "svg": - Console.debug("Outputting type '" + type + "' to " + fileName); - af.createSVG(file, renderer); - break; - - case "png": - Console.debug("Outputting type '" + type + "' to " + fileName); - af.createPNG(file, null, userBis); - break; - - case "html": - Console.debug("Outputting type '" + type + "' to " + fileName); - HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); - htmlSVG.exportHTML(fileName, renderer); - break; - - case "biojs": - Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName); - try - { - BioJsHTMLOutput.refreshVersionInfo( - BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); - } catch (URISyntaxException e) + switch (type) { - e.printStackTrace(); + + case "svg": + Console.debug("Outputting type '" + type + "' to " + fileName); + af.createSVG(file, renderer); + break; + + case "png": + Console.debug("Outputting type '" + type + "' to " + fileName); + af.createPNG(file, null, userBis); + break; + + case "html": + Console.debug("Outputting type '" + type + "' to " + fileName); + HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); + htmlSVG.exportHTML(fileName, renderer); + break; + + case "biojs": + Console.debug( + "Outputting BioJS MSA Viwer HTML file: " + fileName); + try + { + BioJsHTMLOutput.refreshVersionInfo( + BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + } catch (URISyntaxException e) + { + e.printStackTrace(); + } + BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); + bjs.exportHTML(fileName); + break; + + case "eps": + Console.debug("Outputting EPS file: " + fileName); + af.createEPS(file, renderer); + break; + + case "imagemap": + Console.debug("Outputting ImageMap file: " + fileName); + af.createImageMap(file, name); + break; + + default: + Console.warn(Arg.IMAGE.argString() + " type '" + type + + "' not known. Ignoring"); + break; } - BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); - bjs.exportHTML(fileName); - break; - - case "eps": - Console.debug("Creating EPS file: " + fileName); - af.createEPS(file, name); - break; - - case "imagemap": - Console.debug("Creating ImageMap file: " + fileName); - af.createImageMap(file, name); - break; - - default: - Console.warn(Arg.IMAGE.argString() + " type '" + type - + "' not known. Ignoring"); - break; - } - } catch (Exception ioex) { - Console.warn("Unexpected error during export",ioex); + } catch (Exception ioex) + { + Console.warn("Unexpected error during export", ioex); } } } diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 3dfb510..aa28a8c 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1175,7 +1175,8 @@ public class AlignmentPanel extends GAlignmentPanel implements return (w > 0 ? w : calculateIdWidth().width); } - void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer) throws ImageOutputException + void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer) + throws ImageOutputException { makeAlignmentImage(type, file, renderer, BitmapImageSizing.nullBitmapImageSizing()); @@ -1266,7 +1267,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } - public void makePNGImageMap(File imgMapFile, String imageName) throws ImageOutputException + public void makePNGImageMap(File imgMapFile, String imageName) + throws ImageOutputException { // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS // //////////////////////////////////////////// @@ -1391,7 +1393,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } catch (Exception ex) { - throw new ImageOutputException("couldn't write ImageMap due to unexpected error",ex); + throw new ImageOutputException( + "couldn't write ImageMap due to unexpected error", ex); } } // /////////END OF IMAGE MAP diff --git a/src/jalview/gui/ImageExporter.java b/src/jalview/gui/ImageExporter.java index 4ea30d9..8d28b1b 100644 --- a/src/jalview/gui/ImageExporter.java +++ b/src/jalview/gui/ImageExporter.java @@ -34,6 +34,7 @@ import jalview.util.ImageMaker; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.util.StringUtils; import jalview.util.imagemaker.BitmapImageSizing; /** @@ -111,7 +112,8 @@ public class ImageExporter } public void doExport(File file, Component parent, int width, int height, - String imageSource, String renderer, BitmapImageSizing userBis) throws ImageOutputException + String imageSource, String renderer, BitmapImageSizing userBis) + throws ImageOutputException { final long messageId = System.currentTimeMillis(); setStatus( @@ -126,8 +128,9 @@ public class ImageExporter { if (Desktop.instance.isInBatchMode()) { - // defensive error report - we could wait for user input.. I guess ? - throw(new ImageOutputException("Need an output file to render to when exporting images in batch mode!")); + // defensive error report - we could wait for user input.. I guess ? + throw (new ImageOutputException( + "Need an output file to render to when exporting images in batch mode!")); } JalviewFileChooser chooser = imageType.getFileChooser(); chooser.setFileView(new JalviewFileView()); @@ -164,9 +167,9 @@ public class ImageExporter renderStyle = "Text"; } AtomicBoolean textSelected = new AtomicBoolean( - !"Lineart".equals(renderStyle)); - if ((imageType == TYPE.EPS || imageType == TYPE.SVG) - && LineartOptions.PROMPT_EACH_TIME.equals(renderStyle) + !StringUtils.equalsIgnoreCase("lineart", renderStyle)); + if ((imageType == TYPE.EPS || imageType == TYPE.SVG) && StringUtils + .equalsIgnoreCase(LineartOptions.PROMPT_EACH_TIME, renderStyle) && !Jalview.isHeadlessMode()) { final File chosenFile = file; @@ -188,8 +191,8 @@ public class ImageExporter else { /* - * character rendering not required, or preference already set - * - just do the export + * character rendering not required, or preference already set + * or we're in headless mode - just do the export */ exportImage(file, !textSelected.get(), width, height, messageId, userBis); @@ -226,8 +229,8 @@ public class ImageExporter messageId); } catch (Exception e) { - jalview.bin.Console.error(String.format("Error creating %s file: %s", type, - e.toString()),e); + jalview.bin.Console.error(String.format("Error creating %s file: %s", + type, e.toString()), e); setStatus(MessageManager.formatMessage("info.error_creating_file", type), messageId); } diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index d15cdcf..62e48d2 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1375,8 +1375,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI } else if (inGroup) { - drawVerticals(g, sx, xwidth, visWidth, oldY, sy); - drawHorizontals(g, sx, xwidth, visWidth, top, bottom); + drawVerticals(g, sx, xwidth, visWidth, oldY, bottom); + drawHorizontals(g, sx, xwidth, visWidth, top, bottom+1); // reset top and bottom top = -1; @@ -1387,8 +1387,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI if (inGroup) { sy = verticalOffset + ((i - startSeq) * charHeight); - drawVerticals(g, sx, xwidth, visWidth, oldY, sy); - drawHorizontals(g, sx, xwidth, visWidth, top, bottom); + drawVerticals(g, sx, xwidth, visWidth, oldY, bottom); + drawHorizontals(g, sx, xwidth, visWidth, top, bottom+1); } } } diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index ad1fa4a..d943d39 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -27,16 +27,23 @@ 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; @@ -88,6 +95,10 @@ public class AnnotationRenderer private boolean av_ignoreGapsConsensus; + private boolean vectorRendition = false; + + private boolean glyphLineDrawn = false; + /** * attributes set from AwtRenderPanelI */ @@ -189,7 +200,7 @@ 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 +220,7 @@ 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 +232,7 @@ 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, @@ -229,9 +240,8 @@ 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) + hiddenColumns.visibleToAbsoluteColumn(startRes); int x1 = lastSSX; @@ -245,9 +255,16 @@ 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 (diffupstream || diffdownstream) + { + // draw glyphline under arrow + drawGlyphLine(g, lastSSX, x, y, iconOffset); + } + g.setColor(nonCanColor); if (column > 0 && Rna.isClosingParenthesis(dc)) { @@ -255,9 +272,10 @@ 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 }, + { y + iconOffset + 1, y + 13 + iconOffset, + y + 7 + iconOffset }, 3); x1 += 5; } @@ -272,9 +290,10 @@ public class AnnotationRenderer // 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; } @@ -284,7 +303,8 @@ public class AnnotationRenderer } } // 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 @@ -447,6 +467,12 @@ public class AnnotationRenderer 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: @@ -592,9 +618,13 @@ public class AnnotationRenderer * * 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) { @@ -626,6 +656,7 @@ public class AnnotationRenderer : null; if (x > -1) { + unsetAntialias(g); if (activeRow == i) { g.setColor(Color.red); @@ -634,24 +665,24 @@ 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 +705,11 @@ 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 +722,20 @@ 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)); } + 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( @@ -711,7 +743,7 @@ public class AnnotationRenderer || (displayChar.length() < 2 && row_annotations[column].secondaryStructure == ' '))) { - gg.drawString(displayChar, 0, 0); + g2d.drawString(displayChar, 0, 0); } if (scaledToFit) { @@ -719,10 +751,10 @@ 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 +816,8 @@ 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) { @@ -878,10 +911,17 @@ public class AnnotationRenderer // 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; } } @@ -1006,14 +1046,23 @@ 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); 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; } } @@ -1091,7 +1140,7 @@ public class AnnotationRenderer } else { - System.err.println( + Console.warn( "rendered with " + renderer.getClass().toString()); } } @@ -1122,17 +1171,15 @@ 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)); } ; @@ -1150,10 +1197,15 @@ public class AnnotationRenderer // 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); } @@ -1163,45 +1215,52 @@ public class AnnotationRenderer 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') { @@ -1209,8 +1268,8 @@ public class AnnotationRenderer 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') @@ -1220,30 +1279,38 @@ public class AnnotationRenderer 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, @@ -1254,6 +1321,13 @@ public class AnnotationRenderer { 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; @@ -1280,7 +1354,8 @@ public class AnnotationRenderer } 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); @@ -1322,7 +1397,7 @@ public class AnnotationRenderer // standalone value y1 = y - (int) (((aa_annotations[column].value - min) / range) * graphHeight); - g.drawLine(x * charWidth + charWidth / 4, y1, + drawLine(g, x * charWidth + charWidth / 4, y1, x * charWidth + 3 * charWidth / 4, y1); x++; continue; @@ -1339,7 +1414,7 @@ public class AnnotationRenderer 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++; } @@ -1348,14 +1423,14 @@ public class AnnotationRenderer { 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") @@ -1382,7 +1457,7 @@ public class AnnotationRenderer 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; @@ -1420,11 +1495,11 @@ 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 +1530,8 @@ 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(); @@ -1580,15 +1656,13 @@ public class AnnotationRenderer 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); } } @@ -1598,7 +1672,7 @@ 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 +1696,7 @@ public class AnnotationRenderer height = y; } - g.fillRect(x, y - height, charWidth, height); + fillRect(g, x, y - height, charWidth, height); } x += charWidth; } @@ -1749,9 +1823,92 @@ 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 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; + } } diff --git a/src/jalview/util/StringUtils.java b/src/jalview/util/StringUtils.java index 1c67c92..7cbbe1c 100644 --- a/src/jalview/util/StringUtils.java +++ b/src/jalview/util/StringUtils.java @@ -586,6 +586,15 @@ public class StringUtils return min < text.length() + 1 ? min : -1; } + public static boolean equalsIgnoreCase(String s1, String s2) + { + if (s1 == null || s2 == null) + { + return s1 == s2; + } + return s1.toLowerCase(Locale.ROOT).equals(s2.toLowerCase(Locale.ROOT)); + } + public static int indexOfFirstWhitespace(String text) { int index = -1;