X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=671bf6b799c8d58e305fc558015e51a307b90cb4;hb=f6d3b491c392914981b65fee21df51b530ee80f7;hp=e7319106ed016fa1586b01595aca924dc0966627;hpb=cce26350d1d8106b82701deab38a8b20022b4737;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index e731910..671bf6b 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 2.8.2) - * Copyright (C) 2014 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. * @@ -21,12 +21,20 @@ 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; @@ -41,88 +49,18 @@ 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("(\\))"); - - String dc = (column == 0 || row_annotations[column - 1] == null) ? "" - : row_annotations[column - 1].displayCharacter; - - boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null - || !dc.equals(row_annotations[sCol - 1].displayCharacter); - boolean diffdownstream = !validRes || !validEnd - || row_annotations[column] == null - || !dc.equals(row_annotations[column].displayCharacter); - // 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)) - { - - 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; @@ -130,16 +68,20 @@ public class AnnotationRenderer private FontMetrics fm; - private final boolean MAC = new 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; private Hashtable[] hStrucConsensus; @@ -186,7 +128,101 @@ 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() + { + hiddenColumns = null; + 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) @@ -194,10 +230,10 @@ 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; @@ -207,19 +243,20 @@ 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) @@ -233,9 +270,10 @@ 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) @@ -282,49 +320,75 @@ 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); } - boolean rna = av.getAlignment().isNucleotide(); columnSelection = av.getColumnSelection(); - hconsensus = av.getSequenceConsensusHash();// hconsensus; - hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus; - av_ignoreGapsConsensus = av.getIgnoreGapsConsensus(); + hiddenColumns = av.getAlignment().getHiddenColumns(); + hconsensus = av.getSequenceConsensusHash(); + complementConsensus = av.getComplementConsensusHash(); + hStrucConsensus = av.getRnaStructureConsensusHash(); + av_ignoreGapsConsensus = av.isIgnoreGapsConsensus(); } - public int[] getProfileFor(AlignmentAnnotation aa, int column) + /** + * 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 + * depend on the profile type. + * + * @param aa + * @param column + * @return + */ + 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")) + 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 && aa.groupRef.isShowSequenceLogo()) { + // 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 // be stored if (aa.groupRef == null && aa.sequenceRef == null) { - return AAFrequency.extractProfile(hconsensus[column], - av_ignoreGapsConsensus); + if (forComplement) + { + return AAFrequency.extractCdnaProfile(complementConsensus[column], + av_ignoreGapsConsensus); + } + else + { + return AAFrequency.extractProfile(hconsensus.get(column), + av_ignoreGapsConsensus); + } } } else @@ -399,13 +463,17 @@ public class AnnotationRenderer boolean validRes = false; boolean validEnd = false; boolean labelAllCols = false; - boolean centreColLabels, centreColLabelsDef = av - .getCentreColumnLabels(); + boolean centreColLabels; + boolean centreColLabelsDef = av.isCentreColumnLabels(); boolean scaleColLabel = false; - AlignmentAnnotation consensusAnnot = av - .getAlignmentConsensusAnnotation(), structConsensusAnnot = av + final AlignmentAnnotation consensusAnnot = av + .getAlignmentConsensusAnnotation(); + final AlignmentAnnotation structConsensusAnnot = av .getAlignmentStrucConsensusAnnotation(); - boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna; + 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 @@ -431,7 +499,8 @@ public class AnnotationRenderer renderProfile = row.groupRef.isShowSequenceLogo(); normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); } - else if (row == consensusAnnot || row == structConsensusAnnot) + else if (row == consensusAnnot || row == structConsensusAnnot + || row == complementConsensusAnnot) { renderHistogram = av_renderHistogram; renderProfile = av_renderProfile; @@ -455,8 +524,8 @@ 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) { @@ -496,8 +565,8 @@ 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); @@ -534,7 +603,7 @@ public class AnnotationRenderer { if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(startRes + x); + column = hiddenColumns.visibleToAbsoluteColumn(startRes + x); if (column > row_annotations.length - 1) { break; @@ -555,6 +624,9 @@ public class AnnotationRenderer { validRes = true; } + final String displayChar = validRes + ? row_annotations[column].displayCharacter + : null; if (x > -1) { if (activeRow == i) @@ -563,77 +635,77 @@ 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); } } } - if (!row.isValidStruc()) + if (row.getInvalidStrucPos() > x) { g.setColor(Color.orange); - g.fillRect((int) row.getInvalidStrucPos() * charWidth, y, - charWidth, charHeight); + g.fillRect(x * charWidth, y, charWidth, charHeight); } - if (validCharWidth - && validRes - && row_annotations[column].displayCharacter != null - && (row_annotations[column].displayCharacter.length() > 0)) + else if (row.getInvalidStrucPos() == x) + { + g.setColor(Color.orange.darker()); + g.fillRect(x * charWidth, y, charWidth, charHeight); + } + if (validCharWidth && validRes && displayChar != null + && (displayChar.length() > 0)) { - if (centreColLabels || scaleColLabel) + fmWidth = fm.charsWidth(displayChar.toCharArray(), 0, + displayChar.length()); + if (/* centreColLabels || */scaleColLabel) { - fmWidth = fm.charsWidth( - row_annotations[column].displayCharacter - .toCharArray(), 0, - row_annotations[column].displayCharacter.length()); - - if (scaleColLabel) + // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0, + // displayChar.length()); + // + // if (scaleColLabel) + // { + // justify the label and scale to fit in column + if (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; - } + // 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; } + // } } - else - { - fmWidth = fm - .charWidth(row_annotations[column].displayCharacter - .charAt(0)); - } + // 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); + } else + { g.setColor(row_annotations[column].colour); + } if (column == 0 || row.graph > 0) { - g.drawString(row_annotations[column].displayCharacter, - (x * charWidth) + charOffset, y + iconOffset); + g.drawString(displayChar, (x * charWidth) + charOffset, + y + iconOffset); } - else if (row_annotations[column - 1] == null - || (labelAllCols - || !row_annotations[column].displayCharacter - .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter - .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(row_annotations[column].displayCharacter, x - * charWidth + charOffset, y + iconOffset); + g.drawString(displayChar, x * charWidth + charOffset, + y + iconOffset); } g.setFont(ofont); } @@ -646,7 +718,7 @@ public class AnnotationRenderer if (ss == '(') { // distinguish between forward/backward base-pairing - if (row_annotations[column].displayCharacter.indexOf(')') > -1) + if (displayChar.indexOf(')') > -1) { ss = ')'; @@ -655,7 +727,7 @@ public class AnnotationRenderer } if (ss == '[') { - if ((row_annotations[column].displayCharacter.indexOf(']') > -1)) + if ((displayChar.indexOf(']') > -1)) { ss = ']'; @@ -664,7 +736,7 @@ public class AnnotationRenderer if (ss == '{') { // distinguish between forward/backward base-pairing - if (row_annotations[column].displayCharacter.indexOf('}') > -1) + if (displayChar.indexOf('}') > -1) { ss = '}'; @@ -673,20 +745,20 @@ public class AnnotationRenderer if (ss == '<') { // distinguish between forward/backward base-pairing - if (row_annotations[column].displayCharacter.indexOf('<') > -1) + if (displayChar.indexOf('<') > -1) { ss = '>'; } } - if (ss >= 65) + if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z)) { // distinguish between forward/backward base-pairing - if (row_annotations[column].displayCharacter.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; } } @@ -697,7 +769,8 @@ 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 @@ -715,7 +788,7 @@ public class AnnotationRenderer validEnd); break; } - + // no break if isRNA - falls through to drawNotCanonicalAnnot! case 'E': if (!isRNA) { @@ -724,6 +797,7 @@ public class AnnotationRenderer validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '{': case '}': @@ -790,8 +864,8 @@ 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; } @@ -831,7 +905,6 @@ public class AnnotationRenderer { validRes = true; } - // x ++; if (row.hasIcons) @@ -846,6 +919,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case 'E': if (!isRNA) @@ -854,6 +928,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '(': case ')': // Stem case for RNA secondary structure @@ -989,7 +1064,7 @@ public class AnnotationRenderer { clipend = true; } - }// end if_in_visible_region + } // end if_in_visible_region if (row.graph > 0 && row.hasText) { y += charHeight; @@ -1006,13 +1081,13 @@ 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 + ")"); } } ; @@ -1034,47 +1109,49 @@ 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); @@ -1102,8 +1179,8 @@ 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); } @@ -1128,9 +1205,9 @@ 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) { @@ -1174,7 +1251,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } if (column > aaMax) @@ -1190,17 +1267,21 @@ public class AnnotationRenderer } if (aa_annotations[column].colour == null) + { g.setColor(Color.black); + } else + { 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++; } @@ -1218,7 +1299,7 @@ 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) @@ -1250,7 +1331,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } if (column > aaMax) @@ -1264,12 +1345,16 @@ public class AnnotationRenderer continue; } if (aa_annotations[column].colour == null) + { g.setColor(Color.black); + } else + { 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) { @@ -1286,10 +1371,16 @@ public class AnnotationRenderer if (renderProfile) { + /* + * {profile type, #values, total count, char1, pct1, char2, pct2...} + */ int profl[] = getProfileFor(_aa, column); + // just try to draw the logo if profl is not null - if (profl != null && profl[1] != 0) + if (profl != null && profl[2] != 0) { + 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; @@ -1298,55 +1389,81 @@ public class AnnotationRenderer char[] dc; /** - * profl.length == 74 indicates that the profile of a secondary - * structure conservation row was accesed. Therefore dc gets length 2, - * to have space for a basepair instead of just a single nucleotide + * Render a single base for a sequence profile, a base pair for + * structure profile, and a triplet for a cdna profile */ - if (profl.length == 74) - { - dc = new char[2]; - } - else - { - dc = new char[1]; - } + dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)]; + LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g); - double scale = 1f / (normaliseProfile ? profl[1] : 100f); + double scale = 1f / (normaliseProfile ? profl[2] : 100f); float ofontHeight = 1f / lm.getAscent();// magnify to fill box double scl = 0.0; - for (int c = 2; c < profl[0];) - { - dc[0] = (char) profl[c++]; - if (_aa.label.startsWith("StrucConsensus")) + /* + * Traverse the character(s)/percentage data in the array + */ + int c = 3; + int valuesProcessed = 0; + // profl[1] is the number of values in the profile + while (valuesProcessed < profl[1]) + { + if (isStructureProfile) { + // todo can we encode a structure pair as an int, like codons? + dc[0] = (char) profl[c++]; dc[1] = (char) profl[c++]; } + else if (isCdnaProfile) + { + dc = CodingUtils.decodeCodon(profl[c++]); + } + else + { + dc[0] = (char) profl[c++]; + } 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()); + + /* + * Set character colour as per alignment colour scheme; use the + * codon translation if a cDNA profile + */ + Color colour = null; + if (isCdnaProfile) { - 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 = 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()); - g.setColor(profcolour.findColour(dc[0], column, null)); - - hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm - .getBaselineIndex()])); - - g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght); + final String codonTranslation = ResidueProperties + .codonTranslate(new String(dc)); + colour = profcolour.findColour(codonTranslation.charAt(0), + column, null); } + else + { + colour = profcolour.findColour(dc[0], column, null); + } + g.setColor(colour == Color.white ? Color.lightGray : colour); + + hght = (ht + (scl - lm.getDescent() + - lm.getBaselineOffsets()[lm.getBaselineIndex()])); + + g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght); + valuesProcessed++; } g.setFont(ofont); } @@ -1361,8 +1478,8 @@ 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()); } @@ -1384,9 +1501,13 @@ public class AnnotationRenderer if (aa_annotations[j] != null) { if (aa_annotations[j].colour == null) + { g.setColor(Color.black); + } else + { g.setColor(aa_annotations[j].colour); + } height = (int) ((aa_annotations[j].value / _aa.graphMax) * y); if (height > y)