X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=eb83f31945e3cc5f6f0f61a253cb8bd4dbd7ba1a;hb=fbfbbe26bee37143d5279fe4d254a5a89c96b021;hp=3fdcb3b7f548e080a804d25cee8de8d80f6dfaf1;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 3fdcb3b..eb83f31 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -28,8 +28,14 @@ import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.ProfilesI; +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; @@ -39,7 +45,6 @@ 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; @@ -64,20 +69,22 @@ public class AnnotationRenderer private FontMetrics fm; - private final boolean MAC = Platform.isAMac(); + private final boolean USE_FILL_ROUND_RECT = Platform.isAMacAndNotJS(); boolean av_renderHistogram = true, av_renderProfile = true, av_normaliseProfile = false; - ColourSchemeI profcolour = null; + ResidueShaderI profcolour = null; private ColumnSelection columnSelection; - private Hashtable[] hconsensus; + private HiddenColumns hiddenColumns; - private Hashtable[] complementConsensus; + private ProfilesI hconsensus; - private Hashtable[] hStrucConsensus; + private Hashtable[] complementConsensus; + + private Hashtable[] hStrucConsensus; private boolean av_ignoreGapsConsensus; @@ -144,11 +151,13 @@ 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, @@ -156,7 +165,8 @@ 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); @@ -180,8 +190,9 @@ public class AnnotationRenderer * display a backward arrow */ g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX }, - new int[] { y + iconOffset, y + 14 + iconOffset, - y + 8 + iconOffset }, 3); + new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, + 3); x1 += 5; } if (diffdownstream) @@ -198,8 +209,10 @@ 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 }, new int[] { - y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); + g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, + new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, + 3); x2 -= 5; } if (diffupstream) @@ -219,7 +232,8 @@ 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); @@ -231,7 +245,8 @@ 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+" down:"+diffdownstream); + // System.out.println("Column "+column+" diff up: "+diffupstream+" + // down:"+diffdownstream); // If a closing base pair half of the stem, display a backward arrow if (column > 0 && Rna.isClosingParenthesis(dc)) { @@ -241,8 +256,9 @@ public class AnnotationRenderer // dc.equals(row_annotations[column-2].displayCharacter)) { g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX }, - new int[] { y + iconOffset, y + 14 + iconOffset, - y + 8 + iconOffset }, 3); + new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, + 3); x1 += 5; } if (diffdownstream) @@ -256,8 +272,10 @@ public class AnnotationRenderer // display a forward arrow if (diffdownstream) { - g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] { - y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); + g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, + new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, + 3); x2 -= 5; } if (diffupstream) @@ -298,28 +316,35 @@ public class AnnotationRenderer useClip = false; } + rendererFactoryI = AnnotationRendererFactory.getRendererFactory(); updateFromAlignViewport(av); } public void updateFromAlignViewport(AlignViewportI av) { charWidth = av.getCharWidth(); - endRes = av.getEndRes(); + endRes = av.getRanges().getEndRes(); charHeight = av.getCharHeight(); hasHiddenColumns = av.hasHiddenColumns(); validCharWidth = av.isValidCharWidth(); av_renderHistogram = av.isShowConsensusHistogram(); av_renderProfile = av.isShowSequenceLogo(); av_normaliseProfile = av.isNormaliseSequenceLogo(); - profcolour = av.getGlobalColourScheme(); - if (profcolour == null) + profcolour = av.getResidueShading(); + if (profcolour == null || profcolour.getColourScheme() == null) { - // Set the default colour for sequence logo if the alignnent has no - // colourscheme set - profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme() - : new jalview.schemes.ZappoColourScheme(); + /* + * Use default colour for sequence logo if + * the alignment has no colourscheme set + * (would like to use user preference but n/a for applet) + */ + ColourSchemeI col = av.getAlignment().isNucleotide() + ? new NucleotideColourScheme() + : new ZappoColourScheme(); + profcolour = new ResidueShader(col); } columnSelection = av.getColumnSelection(); + hiddenColumns = av.getAlignment().getHiddenColumns(); hconsensus = av.getSequenceConsensusHash(); complementConsensus = av.getComplementConsensusHash(); hStrucConsensus = av.getRnaStructureConsensusHash(); @@ -341,9 +366,8 @@ public class AnnotationRenderer // properties/rendering attributes as a global 'alignment group' which holds // all vis settings for the alignment as a whole rather than a subset // - if (aa.autoCalculated - && (aa.label.startsWith("Consensus") || aa.label - .startsWith("cDNA Consensus"))) + if (aa.autoCalculated && (aa.label.startsWith("Consensus") + || aa.label.startsWith("cDNA Consensus"))) { boolean forComplement = aa.label.startsWith("cDNA Consensus"); if (aa.groupRef != null && aa.groupRef.consensusData != null @@ -351,7 +375,7 @@ public class AnnotationRenderer { // TODO? group consensus for cDNA complement return AAFrequency.extractProfile( - aa.groupRef.consensusData[column], + aa.groupRef.consensusData.get(column), aa.groupRef.getIgnoreGapsConsensus()); } // TODO extend annotation row to enable dynamic and static profile data to @@ -360,12 +384,12 @@ public class AnnotationRenderer { if (forComplement) { - return AAFrequency.extractCdnaProfile( - complementConsensus[column], av_ignoreGapsConsensus); + return AAFrequency.extractCdnaProfile(complementConsensus[column], + av_ignoreGapsConsensus); } else { - return AAFrequency.extractProfile(hconsensus[column], + return AAFrequency.extractProfile(hconsensus.get(column), av_ignoreGapsConsensus); } } @@ -399,6 +423,8 @@ public class AnnotationRenderer boolean rna = false; + private AnnotationRendererFactoryI rendererFactoryI; + /** * Render the annotation rows associated with an alignment. * @@ -429,7 +455,7 @@ public class AnnotationRenderer updateFromAwtRenderPanel(annotPanel, av); fm = g.getFontMetrics(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); - int temp = 0; + // int temp = 0; if (aa == null) { return false; @@ -442,8 +468,8 @@ 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(); @@ -451,13 +477,9 @@ public class AnnotationRenderer .getAlignmentStrucConsensusAnnotation(); final AlignmentAnnotation complementConsensusAnnot = av .getComplementConsensusAnnotation(); - boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna; 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; @@ -465,45 +487,42 @@ public class AnnotationRenderer for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; - isRNA = row.isRNA(); + boolean renderHistogram = true; + boolean renderProfile = false; + boolean normaliseProfile = false; + boolean isRNA = row.isRNA(); + + // check if this is a consensus annotation row and set the display + // settings appropriately + // TODO: generalise this to have render styles for consensus/profile + // data + if (row.groupRef != null && row == row.groupRef.getConsensus()) { - // check if this is a consensus annotation row and set the display - // settings appropriately - // TODO: generalise this to have render styles for consensus/profile - // data - if (row.groupRef != null && row == row.groupRef.getConsensus()) - { - renderHistogram = row.groupRef.isShowConsensusHistogram(); - renderProfile = row.groupRef.isShowSequenceLogo(); - normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); - } - else if (row == consensusAnnot || row == structConsensusAnnot - || row == complementConsensusAnnot) - { - renderHistogram = av_renderHistogram; - renderProfile = av_renderProfile; - normaliseProfile = av_normaliseProfile; - } - else - { - renderHistogram = true; - // don't need to set render/normaliseProfile since they are not - // currently used in any other annotation track renderer - } + renderHistogram = row.groupRef.isShowConsensusHistogram(); + renderProfile = row.groupRef.isShowSequenceLogo(); + normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); } + else if (row == consensusAnnot || row == structConsensusAnnot + || row == complementConsensusAnnot) + { + renderHistogram = av_renderHistogram; + renderProfile = av_renderProfile; + normaliseProfile = av_normaliseProfile; + } + Annotation[] row_annotations = row.annotations; if (!row.visible) { continue; } - centreColLabels = row.centreColLabels || centreColLabelsDef; + // centreColLabels = row.centreColLabels || centreColLabelsDef; labelAllCols = row.showAllColLabels; scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; - if (!useClip - || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset)) + if (!useClip || ((y - charHeight) < visHeight + && (y + row.height + charHeight * 2) >= sOffset)) {// if_in_visible_region if (!clipst) { @@ -543,8 +562,8 @@ public class AnnotationRenderer { y += charHeight; usedFaded = true; - g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y - - row.height, imgWidth, y, annotationPanel); + g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, + y - row.height, imgWidth, y, annotationPanel); g.setColor(Color.black); // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2); @@ -581,7 +600,7 @@ public class AnnotationRenderer { if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(startRes + x); + column = hiddenColumns.visibleToAbsoluteColumn(startRes + x); if (column > row_annotations.length - 1) { break; @@ -602,7 +621,8 @@ public class AnnotationRenderer { validRes = true; } - final String displayChar = validRes ? row_annotations[column].displayCharacter + final String displayChar = validRes + ? row_annotations[column].displayCharacter : null; if (x > -1) { @@ -631,60 +651,78 @@ public class AnnotationRenderer if (validCharWidth && validRes && displayChar != null && (displayChar.length() > 0)) { - - fmWidth = fm.charsWidth(displayChar.toCharArray(), 0, + Graphics2D gg = ((Graphics2D) g); + 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; + + /* + * translate to drawing position _before_ applying any scaling + */ + 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(row_annotations[column - 1].displayCharacter) || (displayChar - .length() < 2 && row_annotations[column].secondaryStructure == ' '))) + else if (row_annotations[column - 1] == null || (labelAllCols + || !displayChar.equals( + row_annotations[column - 1].displayCharacter) + || (displayChar.length() < 2 + && row_annotations[column].secondaryStructure == ' '))) { - g.drawString(displayChar, x * charWidth + charOffset, y - + iconOffset); + gg.drawString(displayChar, 0, 0); } - g.setFont(ofont); + if (scaledToFit) + { + /* + * undo scaling before translating back + * (restoring saved transform does NOT work in JS PDFGraphics!) + */ + gg.transform(AffineTransform + .getScaleInstance(1D / fmScaling, 1.0)); + } + gg.translate(-xPos, -yPos); } } if (row.hasIcons) @@ -745,15 +783,16 @@ public class AnnotationRenderer if (x > -1) { - int nb_annot = x - temp; - // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot); + // int nb_annot = x - temp; + // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre + // annot :"+nb_annot); switch (lastSS) { case '(': // Stem case for RNA secondary structure case ')': // and opposite direction drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); - temp = x; + // temp = x; break; case 'H': @@ -836,13 +875,13 @@ public class AnnotationRenderer drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); - temp = x; + // temp = x; break; default: g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - - lastSSX, 2); - temp = x; + g.fillRect(lastSSX, y + 6 + iconOffset, + (x * charWidth) - lastSSX, 2); + // temp = x; break; } } @@ -1032,6 +1071,32 @@ 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); + } + if (debugRedraw) + { + if (renderer == null) + { + System.err.println("No renderer found for " + + row.toString()); + } + else + { + System.err.println("rendered with " + + renderer.getClass().toString()); + } + } + + } } } else @@ -1040,7 +1105,7 @@ public class AnnotationRenderer { clipend = true; } - }// end if_in_visible_region + } // end if_in_visible_region if (row.graph > 0 && row.hasText) { y += charHeight; @@ -1057,13 +1122,13 @@ public class AnnotationRenderer { if (clipst) { - System.err.println("Start clip at : " + yfrom + " (index " + f_i - + ")"); + System.err.println( + "Start clip at : " + yfrom + " (index " + f_i + ")"); } if (clipend) { - System.err.println("End clip at : " + yto + " (index " + f_to - + ")"); + System.err.println( + "End clip at : " + yto + " (index " + f_to + ")"); } } ; @@ -1083,11 +1148,11 @@ public class AnnotationRenderer public static final Color STEM_COLOUR = Color.blue; - private Color sdNOTCANONICAL_COLOUR; + // 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) + int y, int iconOffset, int startRes, int column, boolean validRes, + boolean validEnd) { g.setColor(GLYPHLINE_COLOR); g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2); @@ -1095,39 +1160,43 @@ public class AnnotationRenderer void drawSheetAnnot(Graphics g, Annotation[] row, - int lastSSX, int x, int y, int iconOffset, int startRes, int column, - boolean validRes, boolean validEnd) + 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(new int[] { (x * charWidth) - 4, (x * charWidth) - 4, - (x * charWidth) }, new int[] { y + iconOffset, - y + 14 + iconOffset, y + 7 + iconOffset }, 3); + g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX - 4, + 7); + g.fillPolygon( + new int[] + { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) }, + new int[] + { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, + 3); } else { - g.fillRect(lastSSX, y + 4 + iconOffset, - (x + 1) * charWidth - lastSSX, 7); + g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth - lastSSX, + 7); } } void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x, - int y, int iconOffset, int startRes, int column, - boolean validRes, boolean validEnd) + int y, int iconOffset, int startRes, int column, boolean validRes, + boolean validEnd) { g.setColor(HELIX_COLOUR); - int sCol = (lastSSX / charWidth) + startRes; + int sCol = (lastSSX / charWidth) + + hiddenColumns.visibleToAbsoluteColumn(startRes); int x1 = lastSSX; int x2 = (x * charWidth); - if (MAC) + if (USE_FILL_ROUND_RECT) { int ofs = charWidth / 2; // Off by 1 offset when drawing rects and ovals @@ -1151,8 +1220,8 @@ public class AnnotationRenderer else { // g.setColor(Color.magenta); - g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs - + 1, 8, 0, 0); + g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, + x2 - x1 - ofs + 1, 8, 0, 0); } @@ -1178,8 +1247,8 @@ public class AnnotationRenderer } void drawLineGraph(Graphics g, AlignmentAnnotation _aa, - Annotation[] aa_annotations, int sRes, int eRes, int y, - float min, float max, int graphHeight) + Annotation[] aa_annotations, int sRes, int eRes, int y, float min, + float max, int graphHeight) { if (sRes > aa_annotations.length) { @@ -1223,7 +1292,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } if (column > aaMax) @@ -1247,13 +1316,13 @@ public class AnnotationRenderer g.setColor(aa_annotations[column].colour); } - y1 = y - - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight); - y2 = y - - (int) (((aa_annotations[column].value - min) / range) * graphHeight); + y1 = y - (int) (((aa_annotations[column - 1].value - min) / range) + * graphHeight); + y2 = y - (int) (((aa_annotations[column].value - min) / range) + * graphHeight); - g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth - + charWidth / 2, y2); + g.drawLine(x * charWidth - charWidth / 2, y1, + x * charWidth + charWidth / 2, y2); x++; } @@ -1262,7 +1331,8 @@ 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)); + 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); @@ -1270,6 +1340,7 @@ 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, @@ -1302,7 +1373,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } if (column > aaMax) @@ -1324,8 +1395,8 @@ public class AnnotationRenderer g.setColor(aa_annotations[column].colour); } - y1 = y - - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight); + y1 = y - (int) (((aa_annotations[column].value - min) / (range)) + * _aa.graphHeight); if (renderHistogram) { @@ -1353,64 +1424,66 @@ public class AnnotationRenderer boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE; 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; + final double normaliseFactor = normaliseProfile ? _aa.graphHeight + : (y2 - y1); /** * 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()); + int percent = profl[c++]; + if (percent == 0) + { + // failsafe in case a count rounds down to 0% + continue; + } + double newHeight = normaliseFactor * scale * percent; /* * Set character colour as per alignment colour scheme; use the @@ -1420,7 +1493,7 @@ public class AnnotationRenderer if (isCdnaProfile) { final String codonTranslation = ResidueProperties - .codonTranslate(new String(dc)); + .codonTranslate(s); colour = profcolour.findColour(codonTranslation.charAt(0), column, null); } @@ -1430,13 +1503,58 @@ 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()); + + 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 (Platform.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; + int xShift = (int) Math.round(x * charWidth / sx); + int yShift = (int) Math.round(hght / sy); + gg.transform(AffineTransform.getScaleInstance(sx, sy)); + gg.drawString(s, xShift, yShift); + gg.transform( + AffineTransform.getScaleInstance(1D / sx, 1D / sy)); + ht2 += newHeight; + } + else + /** + * Java only + * + * @j2sIgnore + */ + { + // Java ('normal') method is to scale the font to fit - g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght); - valuesProcessed++; + 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); + g.setFont(ofont); + + ht += newHeight; + } } - g.setFont(ofont); } } x++; @@ -1446,10 +1564,11 @@ 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)); + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); - y2 = (int) (y - ((_aa.threshold.value - min) / range) - * _aa.graphHeight); + y2 = (int) (y + - ((_aa.threshold.value - min) / range) * _aa.graphHeight); g.drawLine(0, y2, (eRes - sRes) * charWidth, y2); g2.setStroke(new BasicStroke()); }