X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=adca17e5a81152a2a1bc5b217b487527a7bb1b61;hb=2b618ede76f5a9d2f1be7db9aad8bb3a2b10e23b;hp=c1b1ab21250b9d210e8a064b228c03d41ffb8171;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index c1b1ab2..adca17e 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -22,13 +22,19 @@ package jalview.renderer; import jalview.analysis.AAFrequency; import jalview.analysis.CodingUtils; +import jalview.analysis.Rna; import jalview.analysis.StructureFrequency; 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.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; @@ -43,8 +49,6 @@ import java.awt.image.ImageObserver; import java.util.BitSet; import java.util.Hashtable; -import com.stevesoft.pat.Regex; - public class AnnotationRenderer { private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32 @@ -58,95 +62,24 @@ public class AnnotationRenderer */ private final boolean debugRedraw; - public AnnotationRenderer() - { - this(false); - } - - /** - * Create a new annotation Renderer - * - * @param debugRedraw - * flag indicating if timing and redraw parameter info should be - * output - */ - public AnnotationRenderer(boolean debugRedraw) - { - this.debugRedraw = debugRedraw; - } - - public 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) + startRes; - int x1 = lastSSX; - int x2 = (x * charWidth); - Regex closeparen = new Regex("(\\))"); - - char dc = (column == 0 || row_annotations[column - 1] == null) ? ' ' - : row_annotations[column - 1].secondaryStructure; - - boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null - || dc != row_annotations[sCol - 1].secondaryStructure; - boolean diffdownstream = !validRes || !validEnd - || row_annotations[column] == null - || dc != row_annotations[column].secondaryStructure; - // 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 && ResidueProperties.isCloseParenRNA(dc)) - { - - if (diffupstream) - // 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 }, - new int[] { y + iconOffset, y + 14 + iconOffset, - y + 8 + iconOffset }, 3); - x1 += 5; - } - if (diffdownstream) - { - x2 -= 1; - } - } - else - { - - // 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); - x2 -= 5; - } - if (diffupstream) - { - x1 += 1; - } - } - // draw arrow body - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); - } - private int charWidth, endRes, charHeight; private boolean validCharWidth, hasHiddenColumns; private FontMetrics fm; - private final boolean MAC = jalview.util.Platform.isAMac(); + private final boolean MAC = Platform.isAMac(); 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 ProfilesI hconsensus; private Hashtable[] complementConsensus; @@ -195,7 +128,100 @@ public class AnnotationRenderer */ private boolean canClip = false; - public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, + public AnnotationRenderer() + { + this(false); + } + + /** + * Create a new annotation Renderer + * + * @param debugRedraw + * flag indicating if timing and redraw parameter info should be + * output + */ + public AnnotationRenderer(boolean debugRedraw) + { + this.debugRedraw = debugRedraw; + } + + /** + * Remove any references and resources when this object is no longer required + */ + public void dispose() + { + hconsensus = null; + complementConsensus = null; + hStrucConsensus = null; + fadedImage = null; + annotationPanel = 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; + int x2 = (x * charWidth); + + char dc = (column == 0 || row_annotations[column - 1] == null) ? ' ' + : row_annotations[column - 1].secondaryStructure; + + boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null + || dc != row_annotations[sCol - 1].secondaryStructure; + boolean diffdownstream = !validRes || !validEnd + || row_annotations[column] == null + || dc != row_annotations[column].secondaryStructure; + + if (column > 0 && Rna.isClosingParenthesis(dc)) + { + if (diffupstream) + // if (validRes && column>1 && row_annotations[column-2]!=null && + // dc.equals(row_annotations[column-2].displayCharacter)) + { + /* + * 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 }, + new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, + 3); + x1 += 5; + } + if (diffdownstream) + { + x2 -= 1; + } + } + else + { + // display a forward arrow + if (diffdownstream) + { + /* + * 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); + x2 -= 5; + } + if (diffupstream) + { + x1 += 1; + } + } + // draw arrow body + g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); + } + + void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, Annotation[] row_annotations, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd) @@ -203,10 +229,10 @@ 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); - Regex closeparen = new Regex("}|]|<|[a-z]"); String dc = (column == 0 || row_annotations[column - 1] == null) ? "" : row_annotations[column - 1].displayCharacter; @@ -216,10 +242,10 @@ 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 && closeparen.search(dc))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc)) - // ) + if (column > 0 && Rna.isClosingParenthesis(dc)) { if (diffupstream) @@ -227,8 +253,9 @@ 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) @@ -242,8 +269,10 @@ 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) @@ -290,22 +319,28 @@ public class AnnotationRenderer 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(); @@ -321,15 +356,14 @@ public class AnnotationRenderer * @param column * @return */ - public int[] getProfileFor(AlignmentAnnotation aa, int column) + int[] getProfileFor(AlignmentAnnotation aa, int column) { // TODO : consider refactoring the global alignment calculation // 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 @@ -337,7 +371,7 @@ 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 @@ -346,12 +380,12 @@ 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); } } @@ -437,7 +471,8 @@ public class AnnotationRenderer .getAlignmentStrucConsensusAnnotation(); final AlignmentAnnotation complementConsensusAnnot = av .getComplementConsensusAnnotation(); - boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna; + boolean renderHistogram = true, renderProfile = true, + normaliseProfile = false, isRNA = rna; BitSet graphGroupDrawn = new BitSet(); int charOffset = 0; // offset for a label @@ -488,8 +523,8 @@ public class AnnotationRenderer 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) { @@ -529,8 +564,8 @@ 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); @@ -567,7 +602,7 @@ public class AnnotationRenderer { if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(startRes + x); + column = hiddenColumns.visibleToAbsoluteColumn(startRes + x); if (column > row_annotations.length - 1) { break; @@ -588,7 +623,8 @@ 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) { @@ -598,14 +634,9 @@ public class AnnotationRenderer if (columnSelection != null) { - for (int n = 0; n < columnSelection.size(); n++) + if (columnSelection.contains(column)) { - int v = columnSelection.columnAt(n); - - if (v == column) - { - g.fillRect(x * charWidth, y, charWidth, charHeight); - } + g.fillRect(x * charWidth, y, charWidth, charHeight); } } } @@ -663,17 +694,17 @@ public class AnnotationRenderer if (column == 0 || row.graph > 0) { - g.drawString(displayChar, (x * charWidth) + charOffset, y - + iconOffset); + g.drawString(displayChar, (x * charWidth) + charOffset, + y + iconOffset); } - 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); + g.drawString(displayChar, x * charWidth + charOffset, + y + iconOffset); } g.setFont(ofont); } @@ -737,7 +768,8 @@ public class AnnotationRenderer { int nb_annot = x - temp; - // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot); + // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre + // annot :"+nb_annot); switch (lastSS) { case '(': // Stem case for RNA secondary structure @@ -755,7 +787,7 @@ public class AnnotationRenderer validEnd); break; } - + // no break if isRNA - falls through to drawNotCanonicalAnnot! case 'E': if (!isRNA) { @@ -764,6 +796,7 @@ public class AnnotationRenderer validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '{': case '}': @@ -830,8 +863,8 @@ public class AnnotationRenderer break; default: g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - - lastSSX, 2); + g.fillRect(lastSSX, y + 6 + iconOffset, + (x * charWidth) - lastSSX, 2); temp = x; break; } @@ -871,7 +904,6 @@ public class AnnotationRenderer { validRes = true; } - // x ++; if (row.hasIcons) @@ -886,6 +918,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case 'E': if (!isRNA) @@ -894,6 +927,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '(': case ')': // Stem case for RNA secondary structure @@ -1029,7 +1063,7 @@ public class AnnotationRenderer { clipend = true; } - }// end if_in_visible_region + } // end if_in_visible_region if (row.graph > 0 && row.hasText) { y += charHeight; @@ -1046,13 +1080,13 @@ 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 + ")"); } } ; @@ -1074,45 +1108,49 @@ public class AnnotationRenderer private Color sdNOTCANONICAL_COLOUR; - public 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, Annotation[] row, int lastSSX, int x, + 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); } - public void drawSheetAnnot(Graphics g, Annotation[] row, + 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); } } - public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, - int x, int y, int iconOffset, int startRes, int column, - boolean validRes, boolean validEnd) + 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) + startRes; + int sCol = (lastSSX / charWidth) + + hiddenColumns.visibleToAbsoluteColumn(startRes); int x1 = lastSSX; int x2 = (x * charWidth); @@ -1140,8 +1178,8 @@ 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); } @@ -1166,9 +1204,9 @@ public class AnnotationRenderer g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); } - public void drawLineGraph(Graphics g, AlignmentAnnotation _aa, - Annotation[] aa_annotations, int sRes, int eRes, int y, - float min, float max, int graphHeight) + void drawLineGraph(Graphics g, AlignmentAnnotation _aa, + Annotation[] aa_annotations, int sRes, int eRes, int y, float min, + float max, int graphHeight) { if (sRes > aa_annotations.length) { @@ -1212,7 +1250,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } if (column > aaMax) @@ -1236,13 +1274,13 @@ 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++; } @@ -1251,7 +1289,8 @@ 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); @@ -1259,7 +1298,7 @@ public class AnnotationRenderer } } - public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, + void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, int eRes, float min, float max, int y, boolean renderHistogram, boolean renderProfile, boolean normaliseProfile) @@ -1291,7 +1330,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } if (column > aaMax) @@ -1313,8 +1352,8 @@ 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) { @@ -1388,10 +1427,11 @@ public class AnnotationRenderer 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()); - g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( - wdth, scl / lm.getAscent()))); + 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 @@ -1418,8 +1458,8 @@ public class AnnotationRenderer } g.setColor(colour == Color.white ? Color.lightGray : colour); - hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm - .getBaselineIndex()])); + hght = (ht + (scl - lm.getDescent() + - lm.getBaselineOffsets()[lm.getBaselineIndex()])); g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght); valuesProcessed++; @@ -1434,10 +1474,11 @@ 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()); }