X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=1d1010fcd3f868fd28fac84c9244175e31c90036;hb=15f308b25f41681924975f6e4c7d564ebe31263e;hp=d5b2f492e7a7c1c241c7d90420d56f004a8bb616;hpb=9bc6fd9d86db21bda68daa57376d2c879e395f6c;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index d5b2f49..1d1010f 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -21,6 +21,7 @@ package jalview.renderer; import jalview.analysis.AAFrequency; +import jalview.analysis.CodingUtils; import jalview.analysis.StructureFrequency; import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; @@ -142,6 +143,8 @@ public class AnnotationRenderer private Hashtable[] hconsensus; + private Hashtable[] complementConsensus; + private Hashtable[] hStrucConsensus; private boolean av_ignoreGapsConsensus; @@ -298,24 +301,37 @@ public class AnnotationRenderer profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme() : new jalview.schemes.ZappoColourScheme(); } - boolean rna = av.getAlignment().isNucleotide(); columnSelection = av.getColumnSelection(); - hconsensus = av.getSequenceConsensusHash();// hconsensus; - hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus; - av_ignoreGapsConsensus = av.getIgnoreGapsConsensus(); + hconsensus = av.getSequenceConsensusHash(); + complementConsensus = av.getComplementConsensusHash(); + hStrucConsensus = av.getRnaStructureConsensusHash(); + av_ignoreGapsConsensus = av.isIgnoreGapsConsensus(); } + /** + * 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 + */ public 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.getIgnoreGapsConsensus()); @@ -324,8 +340,16 @@ public class AnnotationRenderer // 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[column], + av_ignoreGapsConsensus); + } } } else @@ -400,12 +424,15 @@ 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(); + final AlignmentAnnotation complementConsensusAnnot = av + .getComplementConsensusAnnotation(); boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna; BitSet graphGroupDrawn = new BitSet(); @@ -432,7 +459,8 @@ 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; @@ -556,6 +584,8 @@ public class AnnotationRenderer { validRes = true; } + final String displayChar = validRes ? row_annotations[column].displayCharacter + : null; if (x > -1) { if (activeRow == i) @@ -585,21 +615,19 @@ public class AnnotationRenderer g.setColor(Color.orange.darker()); g.fillRect(x * charWidth, y, charWidth, charHeight); } - if (validCharWidth - && validRes - && row_annotations[column].displayCharacter != null - && (row_annotations[column].displayCharacter.length() > 0)) + 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) { @@ -611,14 +639,13 @@ public class AnnotationRenderer // 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) @@ -632,17 +659,17 @@ public class AnnotationRenderer 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 + || !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); } @@ -655,7 +682,7 @@ public class AnnotationRenderer if (ss == '(') { // distinguish between forward/backward base-pairing - if (row_annotations[column].displayCharacter.indexOf(')') > -1) + if (displayChar.indexOf(')') > -1) { ss = ')'; @@ -664,7 +691,7 @@ public class AnnotationRenderer } if (ss == '[') { - if ((row_annotations[column].displayCharacter.indexOf(']') > -1)) + if ((displayChar.indexOf(']') > -1)) { ss = ']'; @@ -673,7 +700,7 @@ public class AnnotationRenderer if (ss == '{') { // distinguish between forward/backward base-pairing - if (row_annotations[column].displayCharacter.indexOf('}') > -1) + if (displayChar.indexOf('}') > -1) { ss = '}'; @@ -682,7 +709,7 @@ public class AnnotationRenderer if (ss == '<') { // distinguish between forward/backward base-pairing - if (row_annotations[column].displayCharacter.indexOf('<') > -1) + if (displayChar.indexOf('<') > -1) { ss = '>'; @@ -691,7 +718,7 @@ public class AnnotationRenderer if (ss >= 65) { // distinguish between forward/backward base-pairing - if (row_annotations[column].displayCharacter.indexOf(ss + 32) > -1) + if (displayChar.indexOf(ss + 32) > -1) { ss = (char) (ss + 32); @@ -1303,10 +1330,16 @@ 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; @@ -1315,55 +1348,80 @@ 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()); + 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()); + + /* + * 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); }