X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=1d1010fcd3f868fd28fac84c9244175e31c90036;hb=15f308b25f41681924975f6e4c7d564ebe31263e;hp=4c3711d5c5cae6f7d60cdb92451d344631846f4b;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 4c3711d..1d1010f 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -21,12 +21,14 @@ package jalview.renderer; import jalview.analysis.AAFrequency; +import jalview.analysis.CodingUtils; import jalview.analysis.StructureFrequency; import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; import jalview.schemes.ColourSchemeI; +import jalview.schemes.ResidueProperties; import java.awt.BasicStroke; import java.awt.Color; @@ -77,17 +79,17 @@ public class AnnotationRenderer int x2 = (x * charWidth); Regex closeparen = new Regex("(\\))"); - String dc = (column == 0 || row_annotations[column - 1] == null) ? "" - : row_annotations[column - 1].displayCharacter; + char dc = (column == 0 || row_annotations[column - 1] == null) ? ' ' + : row_annotations[column - 1].secondaryStructure; boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null - || !dc.equals(row_annotations[sCol - 1].displayCharacter); + || dc != row_annotations[sCol - 1].secondaryStructure; boolean diffdownstream = !validRes || !validEnd || row_annotations[column] == null - || !dc.equals(row_annotations[column].displayCharacter); + || 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 && closeparen.search(dc)) + if (column > 0 && ResidueProperties.isCloseParenRNA(dc)) { if (diffupstream) @@ -141,6 +143,8 @@ public class AnnotationRenderer private Hashtable[] hconsensus; + private Hashtable[] complementConsensus; + private Hashtable[] hStrucConsensus; private boolean av_ignoreGapsConsensus; @@ -298,22 +302,36 @@ public class AnnotationRenderer : new jalview.schemes.ZappoColourScheme(); } 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()); @@ -322,8 +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 @@ -353,6 +379,8 @@ public class AnnotationRenderer return null; } + boolean rna = false; + /** * Render the annotation rows associated with an alignment. * @@ -396,13 +424,16 @@ 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; + 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 @@ -416,6 +447,7 @@ public class AnnotationRenderer for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; + isRNA = row.isRNA(); { // check if this is a consensus annotation row and set the display // settings appropriately @@ -427,7 +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; @@ -551,6 +584,8 @@ public class AnnotationRenderer { validRes = true; } + final String displayChar = validRes ? row_annotations[column].displayCharacter + : null; if (x > -1) { if (activeRow == i) @@ -570,27 +605,29 @@ public class AnnotationRenderer } } } - 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) { @@ -602,34 +639,37 @@ 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) + { 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 + || !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); } @@ -642,7 +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 = ')'; @@ -651,7 +691,7 @@ public class AnnotationRenderer } if (ss == '[') { - if ((row_annotations[column].displayCharacter.indexOf(']') > -1)) + if ((displayChar.indexOf(']') > -1)) { ss = ']'; @@ -660,7 +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 = '}'; @@ -669,7 +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 = '>'; @@ -678,7 +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); @@ -696,23 +736,31 @@ public class AnnotationRenderer // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot); switch (lastSS) { - - case '$': - drawHelixAnnot(g, row_annotations, lastSSX, x, y, - iconOffset, startRes, column, validRes, validEnd); - break; - - case '�': - drawSheetAnnot(g, row_annotations, lastSSX, x, y, - iconOffset, startRes, column, validRes, validEnd); - break; - case '(': // Stem case for RNA secondary structure case ')': // and opposite direction drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); temp = x; break; + + case 'H': + if (!isRNA) + { + drawHelixAnnot(g, row_annotations, lastSSX, x, y, + iconOffset, startRes, column, validRes, + validEnd); + break; + } + + case 'E': + if (!isRNA) + { + drawSheetAnnot(g, row_annotations, lastSSX, x, y, + iconOffset, startRes, column, validRes, + validEnd); + break; + } + case '{': case '}': case '[': @@ -727,13 +775,11 @@ public class AnnotationRenderer case 'c': case 'D': case 'd': - case 'E': case 'e': case 'F': case 'f': case 'G': case 'g': - case 'H': case 'h': case 'I': case 'i': @@ -828,17 +874,25 @@ public class AnnotationRenderer { switch (lastSS) { - case '$': - drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, - startRes, column, validRes, validEnd); - break; - case '�': - drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, - startRes, column, validRes, validEnd); - break; - case 's': - case 'S': // Stem case for RNA secondary structure + case 'H': + if (!isRNA) + { + drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, + startRes, column, validRes, validEnd); + break; + } + + case 'E': + if (!isRNA) + { + drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, + startRes, column, validRes, validEnd); + break; + } + + case '(': + case ')': // Stem case for RNA secondary structure drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); @@ -858,13 +912,11 @@ public class AnnotationRenderer case 'c': case 'D': case 'd': - case 'E': case 'e': case 'F': case 'f': case 'G': case 'g': - case 'H': case 'h': case 'I': case 'i': @@ -1008,13 +1060,13 @@ public class AnnotationRenderer return !usedFaded; } - private final Color GLYPHLINE_COLOR = Color.gray; + public static final Color GLYPHLINE_COLOR = Color.gray; - private final Color SHEET_COLOUR = Color.green; + public static final Color SHEET_COLOUR = Color.green; - private final Color HELIX_COLOUR = Color.red; + public static final Color HELIX_COLOUR = Color.red; - private final Color STEM_COLOUR = Color.blue; + public static final Color STEM_COLOUR = Color.blue; private Color sdNOTCANONICAL_COLOUR; @@ -1174,9 +1226,13 @@ 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); @@ -1248,9 +1304,13 @@ 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); @@ -1270,10 +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; @@ -1282,55 +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) + { + final String codonTranslation = ResidueProperties + .codonTranslate(new String(dc)); + colour = profcolour.findColour(codonTranslation.charAt(0), + column, null); + } + else { - 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); + 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); } @@ -1368,9 +1459,13 @@ 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)