X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=524e29142e272464fe2c71c4f61c48904520d720;hb=efd301320c3bd89d126980f661e4a7dbfca8bbfe;hp=c61606ef41ffbdc2eab0a7f758a4ddbcd4c3cdf6;hpb=042832306c7e7aa0484079f3bab1e141b2944de5;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index c61606e..524e291 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -20,34 +20,48 @@ */ 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.Collections; +import java.util.HashMap; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; + +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.datamodel.HiddenColumns; import jalview.datamodel.ProfilesI; +import jalview.datamodel.annotations.AnnotationColouringI; +import jalview.renderer.api.AnnotationRendererFactoryI; +import jalview.renderer.api.AnnotationRowRendererI; import jalview.schemes.ColourSchemeI; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.ResidueProperties; 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 @@ -86,6 +100,10 @@ public class AnnotationRenderer private boolean av_ignoreGapsConsensus; + private boolean renderingVectors = false; + + private boolean glyphLineDrawn = false; + /** * attributes set from AwtRenderPanelI */ @@ -127,6 +145,51 @@ public class AnnotationRenderer */ private boolean canClip = false; + /** + * Property to set text antialiasing method + */ + private static final String TEXT_ANTIALIAS_METHOD = "TEXT_ANTIALIAS_METHOD"; + + private static final Object textAntialiasMethod; + + static + { + final String textAntialiasMethodPref = Cache + .getDefault(TEXT_ANTIALIAS_METHOD, "GASP"); + switch (textAntialiasMethodPref) + { + case "ON": + textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_ON; + break; + case "GASP": + textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_GASP; + break; + case "LCD_HBGR": + textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HBGR; + break; + case "LCD_HRGB": + textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB; + break; + case "LCD_VBGR": + textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_VBGR; + break; + case "LCD_VRGB": + textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_VRGB; + break; + case "OFF": + textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_OFF; + break; + case "DEFAULT": + textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_DEFAULT; + break; + default: + jalview.bin.Console.warn(TEXT_ANTIALIAS_METHOD + " value '" + + textAntialiasMethodPref + + "' not recognised, defaulting to 'GASP'. See https://docs.oracle.com/javase/8/docs/api/java/awt/RenderingHints.html#KEY_TEXT_ANTIALIASING"); + textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_GASP; + } + } + public AnnotationRenderer() { this(false); @@ -149,18 +212,19 @@ public class AnnotationRenderer */ public void dispose() { + hiddenColumns = null; hconsensus = null; complementConsensus = null; hStrucConsensus = null; fadedImage = null; annotationPanel = null; + rendererFactoryI = null; } void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd) { - g.setColor(STEM_COLOUR); int sCol = (lastSSX / charWidth) + hiddenColumns.visibleToAbsoluteColumn(startRes); int x1 = lastSSX; @@ -170,11 +234,19 @@ public class AnnotationRenderer : row_annotations[column - 1].secondaryStructure; boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null - || dc != row_annotations[sCol - 1].secondaryStructure; + || dc != row_annotations[sCol - 1].secondaryStructure + || !validEnd; boolean diffdownstream = !validRes || !validEnd || row_annotations[column] == null || dc != row_annotations[column].secondaryStructure; + if (diffupstream || diffdownstream) + { + // draw glyphline under arrow + drawGlyphLine(g, lastSSX, x, y, iconOffset); + } + g.setColor(STEM_COLOUR); + if (column > 0 && Rna.isClosingParenthesis(dc)) { if (diffupstream) @@ -185,9 +257,10 @@ 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 }, + { y + iconOffset + 1, y + 13 + iconOffset, + y + 7 + iconOffset }, 3); x1 += 5; } @@ -205,9 +278,10 @@ 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 - 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; } @@ -217,7 +291,8 @@ 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); } void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, @@ -225,9 +300,8 @@ 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; @@ -237,13 +311,21 @@ public class AnnotationRenderer : row_annotations[column - 1].displayCharacter; boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null - || !dc.equals(row_annotations[sCol - 1].displayCharacter); + || !dc.equals(row_annotations[sCol - 1].displayCharacter) + || !validEnd; 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)) { @@ -251,9 +333,10 @@ 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; } @@ -268,9 +351,10 @@ 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; } @@ -280,7 +364,8 @@ 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 @@ -312,6 +397,7 @@ public class AnnotationRenderer useClip = false; } + rendererFactoryI = AnnotationRendererFactory.getRendererFactory(); updateFromAlignViewport(av); } @@ -416,6 +502,10 @@ public class AnnotationRenderer return null; } + boolean rna = false; + + private AnnotationRendererFactoryI rendererFactoryI; + /** * Render the annotation rows associated with an alignment. * @@ -438,6 +528,20 @@ public class AnnotationRenderer AlignViewportI av, Graphics g, int activeRow, int startRes, int endRes) { + return drawComponent(annotPanel, av, g, activeRow, startRes, endRes, + false); + } + + public boolean drawComponent(AwtRenderPanelI annotPanel, + AlignViewportI av, Graphics g, int activeRow, int startRes, + int endRes, boolean forExport) + { + if (g instanceof EpsGraphics2D || g instanceof SVGGraphics2D) + { + this.setVectorRendering(true); + } + Graphics2D g2d = (Graphics2D) g; + long stime = System.currentTimeMillis(); boolean usedFaded = false; // NOTES: @@ -459,8 +563,8 @@ public class AnnotationRenderer boolean validRes = false; boolean validEnd = false; boolean labelAllCols = false; -// boolean centreColLabels; -// boolean centreColLabelsDef = av.isCentreColumnLabels(); + // boolean centreColLabels; + // boolean centreColLabelsDef = av.isCentreColumnLabels(); boolean scaleColLabel = false; final AlignmentAnnotation consensusAnnot = av .getAlignmentConsensusAnnotation(); @@ -470,7 +574,6 @@ public class AnnotationRenderer .getComplementConsensusAnnotation(); BitSet graphGroupDrawn = new BitSet(); - int charOffset = 0; // offset for a label // \u03B2 \u03B1 // debug ints int yfrom = 0, f_i = 0, yto = 0, f_to = 0; @@ -506,7 +609,7 @@ public class AnnotationRenderer { continue; } -// centreColLabels = row.centreColLabels || centreColLabelsDef; + // centreColLabels = row.centreColLabels || centreColLabelsDef; labelAllCols = row.showAllColLabels; scaleColLabel = row.scaleColLabel; lastSS = ' '; @@ -583,10 +686,15 @@ 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) { if (hasHiddenColumns) @@ -617,6 +725,7 @@ public class AnnotationRenderer : null; if (x > -1) { + unsetAntialias(g); if (activeRow == i) { g.setColor(Color.red); @@ -625,26 +734,24 @@ 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); - float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0, - displayChar.length()); + float fmWidth = fm.stringWidth(displayChar); /* * shrink label width to fit in column, if that is @@ -655,46 +762,62 @@ public class AnnotationRenderer if (scaleColLabel && fmWidth > charWidth) { scaledToFit = true; - fmScaling = charWidth; - fmScaling /= fmWidth; + fmScaling = (float) charWidth / fmWidth; // and update the label's width to reflect the scaling. fmWidth = charWidth; } - charOffset = (int) ((charWidth - fmWidth) / 2f); + float charOffset = (charWidth - fmWidth) / 2f; 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); } /* * draw the label, unless it is the same secondary structure * symbol (excluding RNA Helix) as the previous column */ - final int xPos = (x * charWidth) + charOffset; - final int yPos = y + iconOffset; - + final float xPos = (x * charWidth) + charOffset; + final float yPos = y + iconOffset; + + // Act on a copy of the Graphics2d object + Graphics2D g2dCopy = (Graphics2D) g2d.create(); + // Clip to this annotation line (particularly width). + // This removes artifacts from text when side scrolling + // (particularly in wrap format), but can result in clipped + // characters until a full paint is drawn. + // Add charHeight allowance above and below annotation for + // character overhang. + // If we're in an image export, set the clip width to be the + // entire width of the annotation. + + int clipWidth = forExport + ? row_annotations.length * charWidth - 1 + : imgWidth - 1; + g2dCopy.setClip(0, (int) yPos - 2 * charHeight, clipWidth, + charHeight * 3); /* * translate to drawing position _before_ applying any scaling */ - gg.translate(xPos, yPos); + g2dCopy.translate(xPos, yPos); if (scaledToFit) { /* * use a scaling transform to make the label narrower * (JalviewJS doesn't have Font.deriveFont(AffineTransform)) */ - gg.transform( + g2dCopy.transform( AffineTransform.getScaleInstance(fmScaling, 1.0)); } + setAntialias(g2dCopy, true); if (column == 0 || row.graph > 0) { - gg.drawString(displayChar, 0, 0); + g2dCopy.drawString(displayChar, 0, 0); } else if (row_annotations[column - 1] == null || (labelAllCols || !displayChar.equals( @@ -702,18 +825,9 @@ public class AnnotationRenderer || (displayChar.length() < 2 && row_annotations[column].secondaryStructure == ' '))) { - gg.drawString(displayChar, 0, 0); - } - if (scaledToFit) - { - /* - * undo scaling before translating back - * (restoring saved transform does NOT work in JS PDFGraphics!) - */ - gg.transform(AffineTransform - .getScaleInstance(1D / fmScaling, 1.0)); + g2dCopy.drawString(displayChar, 0, 0); } - gg.translate(-xPos, -yPos); + g2dCopy.dispose(); } } if (row.hasIcons) @@ -771,11 +885,12 @@ public class AnnotationRenderer if (!validRes || (ss != lastSS)) { - if (x > -1) + if (x > 0) { // 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) { @@ -869,10 +984,17 @@ public class AnnotationRenderer // temp = x; break; default: - g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, - (x * charWidth) - lastSSX, 2); - // temp = x; + if (isVectorRendering()) + { + // 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; } } @@ -997,14 +1119,23 @@ 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 (isVectorRendering()) + { + // 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; } } @@ -1062,6 +1193,32 @@ public class AnnotationRenderer row.graphMin, row.graphMax, y, renderHistogram, renderProfile, normaliseProfile); } + else + { + AnnotationRowRendererI renderer = rendererFactoryI + .getRendererFor(row); + if (renderer != null) + { + renderer.renderRow(g, charWidth, charHeight, hasHiddenColumns, + av, hiddenColumns, columnSelection, row, + row_annotations, startRes, endRes, row.graphMin, + row.graphMax, y, isVectorRendering()); + } + if (debugRedraw) + { + if (renderer == null) + { + System.err + .println("No renderer found for " + row.toString()); + } + else + { + Console.warn( + "rendered with " + renderer.getClass().toString()); + } + } + + } } } else @@ -1087,17 +1244,15 @@ 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)); } ; @@ -1115,10 +1270,15 @@ 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); } @@ -1128,54 +1288,60 @@ 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 || isVectorRendering()) { + // 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') @@ -1184,31 +1350,38 @@ 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) { - g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180); + drawGlyphLine(g, lastSSX, x, y, iconOffset); + } + g.setColor(HELIX_COLOUR); + + if (leftEnd) + { + 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, @@ -1219,6 +1392,13 @@ 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; @@ -1230,11 +1410,6 @@ public class AnnotationRenderer eRes = Math.min(eRes, aa_annotations.length); - if (sRes == 0) - { - x++; - } - int y1 = y, y2 = y; float range = max - min; @@ -1245,14 +1420,20 @@ public class AnnotationRenderer } g.setColor(Color.gray); - g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2); + drawLine(g, squareStroke, x * charWidth, y2, (eRes - sRes) * charWidth, + y2); + + if (sRes == 0) + { + x++; + } eRes = Math.min(eRes, aa_annotations.length); int column; int aaMax = aa_annotations.length - 1; - while (x < eRes - sRes) + while (x <= eRes - sRes) { column = sRes + x; if (hasHiddenColumns) @@ -1265,13 +1446,13 @@ public class AnnotationRenderer break; } - if (aa_annotations[column] == null - || aa_annotations[column - 1] == null) + if (aa_annotations[column] == null) { x++; continue; } + boolean individualColour = false; if (aa_annotations[column].colour == null) { g.setColor(Color.black); @@ -1279,15 +1460,77 @@ public class AnnotationRenderer else { g.setColor(aa_annotations[column].colour); + individualColour = true; + } + + boolean value1Exists = column > 0 + && aa_annotations[column - 1] != null; + float value1 = 0f; + Color color1 = null; + if (value1Exists) + { + value1 = aa_annotations[column - 1].value; + color1 = aa_annotations[column - 1].colour; } + float value2 = aa_annotations[column].value; + boolean nextValueExists = aa_annotations.length > column + 1 + && aa_annotations[column + 1] != null; - y1 = y - (int) (((aa_annotations[column - 1].value - min) / range) - * graphHeight); - y2 = y - (int) (((aa_annotations[column].value - min) / range) - * graphHeight); + // check for standalone value + if (!value1Exists && !nextValueExists) + { + y2 = y - yValueToPixelHeight(value2, min, range, graphHeight); + drawLine(g, x * charWidth + charWidth / 4, y2, + x * charWidth + 3 * charWidth / 4, y2); + x++; + continue; + } + + if (!value1Exists) + { + x++; + continue; + } - g.drawLine(x * charWidth - charWidth / 2, y1, - x * charWidth + charWidth / 2, y2); + y1 = y - yValueToPixelHeight(value1, min, range, graphHeight); + y2 = y - yValueToPixelHeight(value2, min, range, graphHeight); + + float v1 = value1; + float v2 = value2; + int a1 = (x - 1) * charWidth + charWidth / 2; + int b1 = y1; + int a2 = x * charWidth + charWidth / 2; + int b2 = y2; + if (x == 0) + { + // only draw an initial half-line + a1 = x * charWidth; + b1 = y1 + (y2 - y1) / 2; + v1 = value1 + (value2 - value1) / 2; + } + else if (x == eRes - sRes) + { + // this is one past the end to draw -- only draw the first half of the + // line + a2 = x * charWidth - 1; + b2 = y1 + (y2 - y1) / 2; + v2 = value1 + (value2 - value1) / 2; + } + else + { + } + AnnotationColouringI ac = aa_annotations[column] + .getAnnotationColouring(); + List> valCols = ac == null ? null + : ac.rangeColours(v1, v2); + if (valCols != null) + { + drawSegmentedLine(g, valCols, a1, b1, a2, b2); + } + else + { + drawLine(g, a1, b1, a2, b2); + } x++; } @@ -1295,14 +1538,135 @@ public class AnnotationRenderer { g.setColor(_aa.threshold.colour); Graphics2D g2 = (Graphics2D) g; - g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE, - BasicStroke.JOIN_ROUND, 3f, new float[] - { 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, dashedLine(charWidth), 0, y2, (eRes - sRes) * charWidth, + y2); + } + g2d.setStroke(prevStroke); + } + + private static double log2 = Math.log(2); + + // Cached dashed line Strokes + private static Map dashedLineLookup = new HashMap<>(); + + /** + * Returns a dashed line stroke as close to 6-4 pixels as fits within the + * charWidth. This allows translations of multiples of charWidth without + * disrupting the dashed line. The exact values are 0.6-0.4 proportions of + * charWidth for charWidth under 16. For charWidth 16 or over, the number of + * dashes doubles as charWidth doubles. + * + * @param charWidth + * @return Stroke with appropriate dashed line fitting exactly within the + * charWidth + */ + private static Stroke dashedLine(int charWidth) + { + if (!dashedLineLookup.containsKey(charWidth)) + { + int power2 = charWidth >= 8 ? (int) (Math.log(charWidth) / log2) : 2; + float width = ((float) charWidth) / ((float) Math.pow(2, power2 - 3)); + float segment1 = width * 0.6f; + float segment2 = width - segment1; + dashedLineLookup.put(charWidth, new BasicStroke(1, + BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[] + { segment1, segment2 }, 0f)); + } + return dashedLineLookup.get(charWidth); + } + + private void drawSegmentedLine(Graphics g, + List> valCols, int x1, int y1, int x2, + int y2) + { + if (valCols == null || valCols.size() == 0) + { + return; + } + // let's only go forwards+up|down -- try and avoid providing right to left + // x values + if (x2 < x1) + { + int tmp = y2; + y2 = y1; + y1 = tmp; + tmp = x2; + x2 = x1; + x1 = tmp; + Collections.reverse(valCols); + } + Graphics2D g2d = (Graphics2D) g.create(); + float yd = y2 - y1; + boolean reverse = yd > 0; // reverse => line going DOWN (y increasing) + Map.Entry firstValCol = valCols.remove(0); + float firstVal = firstValCol.getKey(); + Color firstCol = firstValCol.getValue(); + int yy1 = 0; + yy1 = reverse ? (int) Math.ceil(y1 + firstVal * yd) + : (int) Math.floor(y1 + firstVal * yd); + Color thisCol = firstCol; + for (int i = 0; i < valCols.size(); i++) + { + Map.Entry valCol = valCols.get(i); + float val = valCol.getKey(); + Color col = valCol.getValue(); + int clipX = x1 - 1; + int clipW = x2 - x1 + 2; + int clipY = 0; + int clipH = 0; + int yy2 = 0; + if (reverse) // line going down + { + yy2 = (int) Math.ceil(y1 + val * yd); + g2d.setColor(thisCol); + clipY = yy1 - 1; + clipH = yy2 - yy1; + if (i == 0) + { + // highest segment, don't clip at the top + clipY -= 2; + clipH += 2; + } + if (i == valCols.size() - 1) + { + // lowest segment, don't clip at the bottom + clipH += 2; + } + } + else // line going up (or level) + { + yy2 = (int) Math.floor(y1 + val * yd); + // g2d.setColor(Color.cyan); g2d.drawRect(x1 - 1, yy1, x2 - x1 + 1, yy2 + // - + // yy1 + 1); + g2d.setColor(col); + clipY = yy2; + clipH = yy1 - yy2; + if (i == 0) + { + // lowest segment, don't clip at the bottom + clipH += 2; + } + if (i == valCols.size() - 1) + { + // highest segment, don't clip at the top + clipY -= 2; + clipH += 2; + } + } + g2d.setClip(clipX, clipY, clipW, clipH); + drawLine(g2d, x1, y1, x2, y2); + yy1 = yy2; + thisCol = col; } + g2d.dispose(); + } + + private static int yValueToPixelHeight(float value, float min, + float range, int graphHeight) + { + return (int) (((value - min) / range) * graphHeight); } @SuppressWarnings("unused") @@ -1329,7 +1693,7 @@ 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; @@ -1367,11 +1731,11 @@ 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 @@ -1402,7 +1766,8 @@ 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(); @@ -1468,12 +1833,6 @@ public class AnnotationRenderer } g.setColor(colour == Color.white ? Color.lightGray : colour); - // Debug - render boxes around characters - // g.setColor(Color.red); - // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, - // (int)(scl)); - // g.setColor(profcolour.findColour(dc[0]).darker()); - double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length); double sy = newHeight / asc; double newAsc = asc * sy; @@ -1515,6 +1874,8 @@ public class AnnotationRenderer .deriveFont(AffineTransform.getScaleInstance(sx, sy)); g.setFont(font); g.drawChars(dc, 0, dc.length, x * charWidth, hght); + g.setFont(ofont); + ht += newHeight; } } @@ -1525,15 +1886,13 @@ 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); } } @@ -1543,7 +1902,7 @@ 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; @@ -1567,7 +1926,7 @@ public class AnnotationRenderer height = y; } - g.fillRect(x, y - height, charWidth, height); + fillRect(g, x, y - height, charWidth, height); } x += charWidth; } @@ -1694,9 +2053,105 @@ 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 x1, int y1, int x2, int y2) + { + setAntialias(g); + g.drawLine(x1, y1, x2, y2); + } + + private void setAntialias(Graphics g) + { + setAntialias(g, false); + } + + private void setAntialias(Graphics g, boolean text) + { + if (isVectorRendering()) + { + // no need to antialias vector drawings + return; + } + if (Cache.getDefault("ANTI_ALIAS", true)) + { + Graphics2D g2d = (Graphics2D) g; + if (text) + { + g2d.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, + this.textAntialiasMethod); + } + else + { + g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + } + } + + private void unsetAntialias(Graphics g) + { + if (isVectorRendering()) + { + // no need to antialias vector drawings + return; + } + Graphics2D g2d = (Graphics2D) g; + g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_OFF); + } + + public void setVectorRendering(boolean b) + { + renderingVectors = b; + } + + public boolean isVectorRendering() + { + return renderingVectors; + } }