X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=0fbfb0250e80feb7c0f8721b31fbb73f1465214c;hb=0a20590a673993f11b664bf9d6747d1360ee54b5;hp=d943d3932fb4de3f980151e09b09bc4b0c0f82ae;hpb=c209e4de401c4c8ff1b566b2ae8158a116ee9f72;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index d943d39..0fbfb02 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -32,7 +32,9 @@ import java.awt.Stroke; import java.awt.geom.AffineTransform; import java.awt.image.ImageObserver; import java.util.BitSet; +import java.util.HashMap; import java.util.Hashtable; +import java.util.Map; import org.jfree.graphics2d.svg.SVGGraphics2D; import org.jibble.epsgraphics.EpsGraphics2D; @@ -95,7 +97,7 @@ public class AnnotationRenderer private boolean av_ignoreGapsConsensus; - private boolean vectorRendition = false; + private boolean renderingVectors = false; private boolean glyphLineDrawn = false; @@ -175,7 +177,6 @@ public class AnnotationRenderer 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; @@ -185,11 +186,19 @@ 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) @@ -202,7 +211,8 @@ public class AnnotationRenderer */ 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; } @@ -220,9 +230,10 @@ public class AnnotationRenderer * if annotation ending with an opeing base pair half of the stem, * display a forward arrow */ - fillPolygon(g, 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; } @@ -232,7 +243,8 @@ public class AnnotationRenderer } } // draw arrow body - fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 7); + unsetAntialias(g); + fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6); } void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, @@ -251,7 +263,8 @@ 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); @@ -469,7 +482,7 @@ public class AnnotationRenderer { if (g instanceof EpsGraphics2D || g instanceof SVGGraphics2D) { - this.setVectorRendition(true); + this.setVectorRendering(true); } Graphics2D g2d = (Graphics2D) g; @@ -812,7 +825,7 @@ public class AnnotationRenderer if (!validRes || (ss != lastSS)) { - if (x > -1) + if (x > 0) { // int nb_annot = x - temp; @@ -911,7 +924,7 @@ public class AnnotationRenderer // temp = x; break; default: - if (isVectorRendition()) + if (isVectorRendering()) { // draw single full width glyphline drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset); @@ -1052,7 +1065,7 @@ public class AnnotationRenderer x, y, iconOffset, startRes, column, validRes, validEnd); break; default: - if (isVectorRendition()) + if (isVectorRendering()) { // draw single full width glyphline drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset); @@ -1129,7 +1142,7 @@ public class AnnotationRenderer renderer.renderRow(g, charWidth, charHeight, hasHiddenColumns, av, hiddenColumns, columnSelection, row, row_annotations, startRes, endRes, row.graphMin, - row.graphMax, y); + row.graphMax, y, isVectorRendering()); } if (debugRedraw) { @@ -1250,7 +1263,7 @@ public class AnnotationRenderer int x1 = lastSSX; int x2 = (x * charWidth); - if (USE_FILL_ROUND_RECT || isVectorRendition()) + if (USE_FILL_ROUND_RECT || isVectorRendering()) { // draw glyph line behind helix (visible in EPS or SVG output) drawGlyphLine(g, lastSSX, x, y, iconOffset); @@ -1267,7 +1280,6 @@ public class AnnotationRenderer } else { - // g.setColor(Color.orange); fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0, 0); } @@ -1278,7 +1290,6 @@ public class AnnotationRenderer } else { - // g.setColor(Color.magenta); fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0, 0); } @@ -1339,11 +1350,6 @@ public class AnnotationRenderer eRes = Math.min(eRes, aa_annotations.length); - if (sRes == 0) - { - x++; - } - int y1 = y, y2 = y; float range = max - min; @@ -1354,15 +1360,20 @@ public class AnnotationRenderer } g.setColor(Color.gray); - drawLine(g, squareStroke, x * charWidth - charWidth, y2, - (eRes - sRes) * 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) @@ -1390,32 +1401,55 @@ public class AnnotationRenderer g.setColor(aa_annotations[column].colour); } - if (aa_annotations[column - 1] == null - && aa_annotations.length > column + 1 - && aa_annotations[column + 1] == null) + boolean previousValueExists = column > 0 + && aa_annotations[column - 1] != null; + float previousValue = previousValueExists + ? aa_annotations[column - 1].value + : 0; + float thisValue = aa_annotations[column].value; + boolean nextValueExists = aa_annotations.length > column + 1 + && aa_annotations[column + 1] != null; + float nextValue = nextValueExists ? aa_annotations[column + 1].value + : 0; + + // check for standalone value + if (!previousValueExists && !nextValueExists) { - // 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); + y2 = y - yValueToPixelHeight(thisValue, min, range, graphHeight); + drawLine(g, x * charWidth + charWidth / 4, y2, + x * charWidth + 3 * charWidth / 4, y2); x++; continue; } - if (aa_annotations[column - 1] == null) + if (!previousValueExists) { x++; continue; } - y1 = y - (int) (((aa_annotations[column - 1].value - min) / range) - * graphHeight); - y2 = y - (int) (((aa_annotations[column].value - min) / range) - * graphHeight); + y1 = y - yValueToPixelHeight(previousValue, min, range, graphHeight); + y2 = y - yValueToPixelHeight(thisValue, min, range, graphHeight); - drawLine(g, (x - 1) * charWidth + charWidth / 2, y1, - x * charWidth + charWidth / 2, y2); + if (x == 0) + { + // only draw an initial half-line + drawLine(g, x * charWidth, y1 + (y2 - y1) / 2, + x * charWidth + charWidth / 2, y2); + + } + else if (x == eRes - sRes) + { + // this is one past the end to draw -- only draw a half line + drawLine(g, (x - 1) * charWidth + charWidth / 2, y1, + x * charWidth - 1, y1 + (y2 - y1) / 2); + + } + else + { + drawLine(g, (x - 1) * charWidth + charWidth / 2, y1, + x * charWidth + charWidth / 2, y2); + } x++; } @@ -1423,16 +1457,50 @@ public class AnnotationRenderer { g.setColor(_aa.threshold.colour); Graphics2D g2 = (Graphics2D) g; - Stroke s = new BasicStroke(1, BasicStroke.CAP_SQUARE, - BasicStroke.JOIN_ROUND, 3f, new float[] - { 5f, 3f }, 0f); - y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight); - drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2); + 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 static int yValueToPixelHeight(float value, float min, + float range, int graphHeight) + { + return (int) (((value - min) / range) * graphHeight); + } + @SuppressWarnings("unused") void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, int eRes, float min, @@ -1597,12 +1665,6 @@ 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; @@ -1877,7 +1939,7 @@ public class AnnotationRenderer private void setAntialias(Graphics g) { - if (isVectorRendition()) + if (isVectorRendering()) { // no need to antialias vector drawings return; @@ -1892,7 +1954,7 @@ public class AnnotationRenderer private void unsetAntialias(Graphics g) { - if (isVectorRendition()) + if (isVectorRendering()) { // no need to antialias vector drawings return; @@ -1902,13 +1964,13 @@ public class AnnotationRenderer RenderingHints.VALUE_ANTIALIAS_OFF); } - public void setVectorRendition(boolean b) + public void setVectorRendering(boolean b) { - vectorRendition = b; + renderingVectors = b; } - public boolean isVectorRendition() + public boolean isVectorRendering() { - return vectorRendition; + return renderingVectors; } }