X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=0aeb45ab8b511a8387c9c8cee0b6394a4261b965;hb=7dd4345867987ee35d061be13ca3ad37bc179b94;hp=25a81f9ea6ff70f5f6957e354b0f064cc03bea45;hpb=b24a7070977bdbb780ec0a0e218935966af94b65;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 25a81f9..0aeb45a 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -25,6 +25,7 @@ import jalview.analysis.CodingUtils; import jalview.analysis.Rna; import jalview.analysis.StructureFrequency; import jalview.api.AlignViewportI; +import jalview.bin.Jalview; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; @@ -43,7 +44,6 @@ import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.Image; -import java.awt.font.LineMetrics; import java.awt.geom.AffineTransform; import java.awt.image.ImageObserver; import java.util.BitSet; @@ -162,7 +162,8 @@ public class AnnotationRenderer boolean validRes, boolean validEnd) { g.setColor(STEM_COLOUR); - int sCol = (lastSSX / charWidth) + startRes; + int sCol = (lastSSX / charWidth) + + hiddenColumns.visibleToAbsoluteColumn(startRes); int x1 = lastSSX; int x2 = (x * charWidth); @@ -228,7 +229,8 @@ public class AnnotationRenderer // System.out.println(nonCanColor); g.setColor(nonCanColor); - int sCol = (lastSSX / charWidth) + startRes; + int sCol = (lastSSX / charWidth) + + hiddenColumns.visibleToAbsoluteColumn(startRes); int x1 = lastSSX; int x2 = (x * charWidth); @@ -474,9 +476,6 @@ public class AnnotationRenderer BitSet graphGroupDrawn = new BitSet(); int charOffset = 0; // offset for a label - float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a - // column. - Font ofont = g.getFont(); // \u03B2 \u03B1 // debug ints int yfrom = 0, f_i = 0, yto = 0, f_to = 0; @@ -651,49 +650,56 @@ public class AnnotationRenderer if (validCharWidth && validRes && displayChar != null && (displayChar.length() > 0)) { - - fmWidth = fm.charsWidth(displayChar.toCharArray(), 0, + Graphics2D gg = ((Graphics2D) g); + AffineTransform oldTransform = gg.getTransform(); + float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0, displayChar.length()); - if (/* centreColLabels || */scaleColLabel) + + /* + * shrink label width to fit in column, if that is + * both configured and necessary + */ + boolean scaledToFit = false; + float fmScaling = 1f; + if (scaleColLabel && fmWidth > charWidth) { - // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0, - // displayChar.length()); - // - // if (scaleColLabel) - // { - // justify the label and scale to fit in column - if (fmWidth > charWidth) - { - // scale only if the current font isn't already small enough - fmScaling = charWidth; - fmScaling /= fmWidth; - g.setFont(ofont.deriveFont(AffineTransform - .getScaleInstance(fmScaling, 1.0))); - // and update the label's width to reflect the scaling. - fmWidth = charWidth; - } - // } + scaledToFit = true; + fmScaling = charWidth; + fmScaling /= fmWidth; + // and update the label's width to reflect the scaling. + fmWidth = charWidth; } - // TODO is it ok to use width of / show all characters here? - // else - // { - // fmWidth = fm.charWidth(displayChar.charAt(0)); - // } + charOffset = (int) ((charWidth - fmWidth) / 2f); if (row_annotations[column].colour == null) { - g.setColor(Color.black); + gg.setColor(Color.black); } else { - g.setColor(row_annotations[column].colour); + gg.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; + gg.translate(xPos, yPos); + if (scaledToFit) + { + /* + * use a scaling transform to make the label narrower + * (JalviewJS doesn't have Font.deriveFont(AffineTransform)) + */ + gg.transform( + AffineTransform.getScaleInstance(fmScaling, 1.0)); + } if (column == 0 || row.graph > 0) { - g.drawString(displayChar, (x * charWidth) + charOffset, - y + iconOffset); + gg.drawString(displayChar, 0, 0); } else if (row_annotations[column - 1] == null || (labelAllCols || !displayChar.equals( @@ -701,10 +707,10 @@ public class AnnotationRenderer || (displayChar.length() < 2 && row_annotations[column].secondaryStructure == ' '))) { - g.drawString(displayChar, x * charWidth + charOffset, - y + iconOffset); + gg.drawString(displayChar, 0, 0); } - g.setFont(ofont); + gg.translate(-xPos, -yPos); + gg.setTransform(oldTransform); } } if (row.hasIcons) @@ -1147,7 +1153,8 @@ public class AnnotationRenderer { g.setColor(HELIX_COLOUR); - int sCol = (lastSSX / charWidth) + startRes; + int sCol = (lastSSX / charWidth) + + hiddenColumns.visibleToAbsoluteColumn(startRes); int x1 = lastSSX; int x2 = (x * charWidth); @@ -1295,6 +1302,7 @@ 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, @@ -1379,63 +1387,58 @@ 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 @@ -1445,7 +1448,7 @@ public class AnnotationRenderer if (isCdnaProfile) { final String codonTranslation = ResidueProperties - .codonTranslate(new String(dc)); + .codonTranslate(s); colour = profcolour.findColour(codonTranslation.charAt(0), column, null); } @@ -1455,11 +1458,48 @@ 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 recalculate 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()])); + + if (Jalview.isJS()) + { + /* + * SwingJS does not implement font.deriveFont() + * so use a scaling transform to draw instead, + * this is off by a very small amount + */ + final int hght = (int) (ht2 + (newAsc - newDec)); + Graphics2D gg = (Graphics2D) g.create(); + gg.setFont(ofont); + int xShift = (int) (x * charWidth / sx); + int yShift = (int) (hght / sy); + gg.transform(AffineTransform.getScaleInstance(sx, sy)); + gg.drawString(s, xShift, yShift); + gg.dispose(); + ht2 += newHeight; + } + else + { + final int hght = (int) (ht + (newAsc - newDec)); + Font font = ofont + .deriveFont(AffineTransform.getScaleInstance(sx, sy)); + g.setFont(font); + g.drawChars(dc, 0, dc.length, x * charWidth, hght); + ht += newHeight; + } } g.setFont(ofont); } @@ -1472,7 +1512,7 @@ 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);