From: hansonr Date: Wed, 27 Jun 2018 10:14:00 +0000 (+0100) Subject: Consensus LOGO done X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~635 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=d6fde28142adb033d7421566a281e347a1b9e1eb Consensus LOGO done --- diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index adca17e..f883b13 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -1298,6 +1298,7 @@ public class AnnotationRenderer } } + @SuppressWarnings("unused") void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, int eRes, float min, float max, int y, boolean renderHistogram, boolean renderProfile, @@ -1382,63 +1383,58 @@ public class AnnotationRenderer boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE; float ht = normaliseProfile ? y - _aa.graphHeight : y1; double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight; - double hght; - float wdth; - double ht2 = 0; - char[] dc; /** * Render a single base for a sequence profile, a base pair for * structure profile, and a triplet for a cdna profile */ - dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)]; + char[] dc = new char[isStructureProfile ? 2 + : (isCdnaProfile ? 3 : 1)]; + + // 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()) + // + " " + (dec - lm.getDescent())); + + double asc = fm.getAscent(); + double dec = fm.getDescent(); + double fht = fm.getHeight(); - LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g); double scale = 1f / (normaliseProfile ? profl[2] : 100f); - float ofontHeight = 1f / lm.getAscent();// magnify to fill box - double scl = 0.0; + // float ofontHeight = 1f / fm.getAscent();// magnify to fill box /* * Traverse the character(s)/percentage data in the array */ - int c = 3; - int valuesProcessed = 0; + + float ht2 = ht; + // profl[1] is the number of values in the profile - while (valuesProcessed < profl[1]) + for (int i = 0, c = 3, last = profl[1]; i < last; i++) { + + String s; if (isStructureProfile) { // todo can we encode a structure pair as an int, like codons? dc[0] = (char) profl[c++]; dc[1] = (char) profl[c++]; + s = new String(dc); } else if (isCdnaProfile) { - dc = CodingUtils.decodeCodon(profl[c++]); + CodingUtils.decodeCodon2(profl[c++], dc); + s = new String(dc); } else { dc[0] = (char) profl[c++]; + s = new String(dc); } - - wdth = charWidth; - wdth /= fm.charsWidth(dc, 0, dc.length); - - ht += scl; // next profl[] position is profile % for the character(s) - scl = htn * scale * profl[c++]; - lm = ofont.getLineMetrics(dc, 0, 1, - g.getFontMetrics().getFontRenderContext()); - Font font = ofont.deriveFont(AffineTransform - .getScaleInstance(wdth, scl / lm.getAscent())); - g.setFont(font); - lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g); - - // 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 newHeight = htn * scale * profl[c++]; /* * Set character colour as per alignment colour scheme; use the @@ -1448,7 +1444,7 @@ public class AnnotationRenderer if (isCdnaProfile) { final String codonTranslation = ResidueProperties - .codonTranslate(new String(dc)); + .codonTranslate(s); colour = profcolour.findColour(codonTranslation.charAt(0), column, null); } @@ -1458,11 +1454,43 @@ public class AnnotationRenderer } g.setColor(colour == Color.white ? Color.lightGray : colour); - hght = (ht + (scl - lm.getDescent() - - lm.getBaselineOffsets()[lm.getBaselineIndex()])); + // 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()); - g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght); - valuesProcessed++; + double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length); + double sy = newHeight / asc; + double newAsc = asc * sy; + double newDec = dec * sy; + // it is not necessary to recalculated lm for the new font. + // note: lm.getBaselineOffsets()[lm.getBaselineIndex()]) must be 0 + // by definition. Was: + // int hght = (int) (ht + (newAsc - newDec - lm.getBaselineOffsets()[lm.getBaselineIndex()])); + + // original: + + if (/** @j2sNative false && */ true) { + int hght = (int) (ht + (newAsc - newDec)); // Q: why " - newDec " ? (0,0) is on the font baseline, I think + Font font = ofont.deriveFont(AffineTransform.getScaleInstance(sx, sy)); + g.setFont(font); + g.drawChars(dc, 0, dc.length, x * charWidth, hght); + ht += newHeight; + } else { + // SwingJS does not implement font.deriveFont() + // this is off by a very small amount. + int hght2 = (int) (ht2 + newAsc); + Graphics2D gg = (Graphics2D) g.create(); + gg.setFont(ofont); + gg.transform(AffineTransform.getScaleInstance(sx, sy)); + //System.out.println("sx " + sx + " sy " + sy + " " + hght + " " + lm.getDescent() + " " + dec + " " + newDec + " " + lm.getAscent() + " " + asc + " " + newAsc); + gg.drawString(s, (int) (x * charWidth / sx), + (int) (hght2 / sy)); + gg.dispose(); + ht2 += newHeight; + } + } g.setFont(ofont); } @@ -1475,7 +1503,7 @@ public class AnnotationRenderer Graphics2D g2 = (Graphics2D) g; g2.setStroke(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);