X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=f1f5fa8170040fcee33096563bf0655436b04625;hb=b7dcfba58fd94e7a413342fce5c69bfc02a4f9c3;hp=33596788d2bfe4c5e491372f21d02d74712ce8d2;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 3359678..f1f5fa8 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -22,13 +22,21 @@ 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.HiddenMarkovModel; +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 jalview.workers.InformationThread; import java.awt.BasicStroke; import java.awt.Color; @@ -43,88 +51,18 @@ import java.awt.image.ImageObserver; import java.util.BitSet; import java.util.Hashtable; -import com.stevesoft.pat.Regex; - public class AnnotationRenderer { - /** - * flag indicating if timing and redraw parameter info should be output - */ - private final boolean debugRedraw; + private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32 - public AnnotationRenderer() - { - this(false); - } + private static final int CHAR_A = 'A'; // 65 + + private static final int CHAR_Z = 'Z'; // 90 /** - * Create a new annotation Renderer - * - * @param debugRedraw - * flag indicating if timing and redraw parameter info should be - * output + * 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 final boolean debugRedraw; private int charWidth, endRes, charHeight; @@ -132,16 +70,24 @@ public class AnnotationRenderer 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; + // todo remove these flags, read from group/viewport where needed + boolean av_renderHistogram = true; - ColourSchemeI profcolour = null; + boolean av_renderProfile = true; + + boolean av_normaliseProfile = false; + + boolean av_infoHeight = false; + + ResidueShaderI profcolour = null; private ColumnSelection columnSelection; - private Hashtable[] hconsensus; + private HiddenColumns hiddenColumns; + + private ProfilesI hconsensus; private Hashtable[] complementConsensus; @@ -149,6 +95,8 @@ public class AnnotationRenderer private boolean av_ignoreGapsConsensus; + private boolean av_ignoreBelowBackground; + /** * attributes set from AwtRenderPanelI */ @@ -190,7 +138,100 @@ 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) @@ -198,10 +239,10 @@ 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; @@ -211,19 +252,20 @@ 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) // 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); + g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX }, + new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, + 3); x1 += 5; } if (diffdownstream) @@ -237,9 +279,10 @@ 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) @@ -286,28 +329,38 @@ 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(); av_ignoreGapsConsensus = av.isIgnoreGapsConsensus(); + av_ignoreBelowBackground = av.isIgnoreBelowBackground(); + av_infoHeight = av.isInfoLetterHeight(); } + + /** * Returns profile data; the first element is the profile type, the second is * the number of distinct values, the third the total count, and the remainder @@ -317,24 +370,31 @@ 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 (InformationThread.HMM_CALC_ID.equals(aa.getCalcId())) + { + HiddenMarkovModel hmm = aa.sequenceRef.getHMM(); + return AAFrequency.extractHMMProfile(hmm, column, + av_ignoreBelowBackground, av_infoHeight); // TODO check if this follows standard + // pipeline + } 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 + if (aa.groupRef != null && aa.groupRef.getConsensusData() != null && aa.groupRef.isShowSequenceLogo()) { // TODO? group consensus for cDNA complement return AAFrequency.extractProfile( - aa.groupRef.consensusData[column], - aa.groupRef.getIgnoreGapsConsensus()); + aa.groupRef.getConsensusData().get(column), + aa.groupRef.isIgnoreGapsConsensus()); } // TODO extend annotation row to enable dynamic and static profile data to // be stored @@ -342,12 +402,12 @@ 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); } } @@ -433,7 +493,8 @@ 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 @@ -466,6 +527,21 @@ public class AnnotationRenderer renderProfile = av_renderProfile; normaliseProfile = av_normaliseProfile; } + else if (InformationThread.HMM_CALC_ID.equals(row.getCalcId())) + { + if (row.groupRef != null) + { + renderHistogram = row.groupRef.isShowInformationHistogram(); + renderProfile = row.groupRef.isShowHMMSequenceLogo(); + normaliseProfile = row.groupRef.isNormaliseHMMSequenceLogo(); + } + else + { + renderHistogram = av.isShowInformationHistogram(); + renderProfile = av.isShowHMMSequenceLogo(); + normaliseProfile = av.isNormaliseHMMSequenceLogo(); + } + } else { renderHistogram = true; @@ -484,8 +560,8 @@ 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) { @@ -525,8 +601,8 @@ 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); @@ -563,7 +639,7 @@ public class AnnotationRenderer { if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(startRes + x); + column = hiddenColumns.visibleToAbsoluteColumn(startRes + x); if (column > row_annotations.length - 1) { break; @@ -584,7 +660,8 @@ 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) { @@ -594,14 +671,9 @@ 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); } } } @@ -628,17 +700,17 @@ public class AnnotationRenderer // // 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; - } + // 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; + } // } } // TODO is it ok to use width of / show all characters here? @@ -659,17 +731,17 @@ 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); } @@ -715,14 +787,14 @@ public class AnnotationRenderer } } - if (ss >= 65) + if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z)) { // distinguish between forward/backward base-pairing - if (displayChar.indexOf(ss + 32) > -1) + int ssLowerCase = ss + UPPER_TO_LOWER; + // TODO would .equals() be safer here? or charAt(0)? + if (displayChar.indexOf(ssLowerCase) > -1) { - - ss = (char) (ss + 32); - + ss = (char) ssLowerCase; } } @@ -733,7 +805,8 @@ 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 @@ -751,7 +824,7 @@ public class AnnotationRenderer validEnd); break; } - + // no break if isRNA - falls through to drawNotCanonicalAnnot! case 'E': if (!isRNA) { @@ -760,6 +833,7 @@ public class AnnotationRenderer validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '{': case '}': @@ -826,8 +900,8 @@ 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; } @@ -867,7 +941,6 @@ public class AnnotationRenderer { validRes = true; } - // x ++; if (row.hasIcons) @@ -882,6 +955,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case 'E': if (!isRNA) @@ -890,6 +964,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '(': case ')': // Stem case for RNA secondary structure @@ -1025,7 +1100,7 @@ public class AnnotationRenderer { clipend = true; } - }// end if_in_visible_region + } // end if_in_visible_region if (row.graph > 0 && row.hasText) { y += charHeight; @@ -1042,13 +1117,13 @@ 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 + ")"); } } ; @@ -1070,47 +1145,49 @@ 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) }, + 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); @@ -1138,8 +1215,8 @@ 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); } @@ -1164,9 +1241,9 @@ 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) { @@ -1210,7 +1287,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } if (column > aaMax) @@ -1234,13 +1311,13 @@ 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++; } @@ -1258,7 +1335,7 @@ 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) @@ -1290,7 +1367,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } if (column > aaMax) @@ -1312,8 +1389,8 @@ 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) { @@ -1387,10 +1464,11 @@ 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 @@ -1417,8 +1495,8 @@ 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++; @@ -1436,8 +1514,8 @@ public class AnnotationRenderer 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()); }