X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=40fb513b158e3a5a2ec77730f56463bef87f48f4;hb=6398c0217546a4d6943f63f670c2684c7c7274be;hp=640bf455c3016429fe4b17b0461f0a971f3e95bc;hpb=fdda06e4e3b668fb08532ba9192c199bb57fb5bd;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 640bf45..40fb513 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -36,7 +36,7 @@ import jalview.schemes.NucleotideColourScheme; import jalview.schemes.ResidueProperties; import jalview.schemes.ZappoColourScheme; import jalview.util.Platform; -import jalview.util.QuickSort; +import jalview.workers.InformationThread; import java.awt.BasicStroke; import java.awt.Color; @@ -50,7 +50,6 @@ import java.awt.geom.AffineTransform; import java.awt.image.ImageObserver; import java.util.BitSet; import java.util.Hashtable; -import java.util.List; public class AnnotationRenderer { @@ -60,10 +59,6 @@ public class AnnotationRenderer private static final int CHAR_Z = 'Z'; // 90 - private static final int AMINO = 0; - - private static final int DNA = 1; - /** * flag indicating if timing and redraw parameter info should be output */ @@ -77,13 +72,19 @@ public class AnnotationRenderer 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; + + boolean av_renderProfile = true; + + boolean av_normaliseProfile = false; + + boolean av_infoHeight = false; ResidueShaderI profcolour = null; private ColumnSelection columnSelection; - + private HiddenColumns hiddenColumns; private ProfilesI hconsensus; @@ -94,6 +95,8 @@ public class AnnotationRenderer private boolean av_ignoreGapsConsensus; + private boolean av_ignoreBelowBackground; + /** * attributes set from AwtRenderPanelI */ @@ -169,7 +172,8 @@ public class AnnotationRenderer boolean validRes, boolean validEnd) { g.setColor(STEM_COLOUR); - int sCol = (lastSSX / charWidth) + startRes; + int sCol = (lastSSX / charWidth) + + hiddenColumns.visibleToAbsoluteColumn(startRes); int x1 = lastSSX; int x2 = (x * charWidth); @@ -193,8 +197,9 @@ public class AnnotationRenderer * display a backward arrow */ 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) @@ -211,8 +216,10 @@ public class AnnotationRenderer * 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); + g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, + new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, + 3); x2 -= 5; } if (diffupstream) @@ -232,7 +239,8 @@ 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); @@ -244,7 +252,8 @@ 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 && Rna.isClosingParenthesis(dc)) { @@ -254,8 +263,9 @@ 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) @@ -269,8 +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) @@ -332,7 +344,8 @@ public class AnnotationRenderer * the alignment has no colourscheme set * (would like to use user preference but n/a for applet) */ - ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme() + ColourSchemeI col = av.getAlignment().isNucleotide() + ? new NucleotideColourScheme() : new ZappoColourScheme(); profcolour = new ResidueShader(col); } @@ -342,96 +355,11 @@ public class AnnotationRenderer complementConsensus = av.getComplementConsensusHash(); hStrucConsensus = av.getRnaStructureConsensusHash(); av_ignoreGapsConsensus = av.isIgnoreGapsConsensus(); + av_ignoreBelowBackground = av.isIgnoreBelowBackground(); + av_infoHeight = av.isInfoLetterHeight(); } - public int[] getHMMProfileFor(AlignmentAnnotation aa, int column, - boolean removeBelowBackground) - { - - HiddenMarkovModel hmm; - hmm = aa.getHMM(); - int size = 0; - int alphabet = 0; - String alph = hmm.getAlphabetType(); - if (alph.equals("amino")) - { - size = 20; - alphabet = AMINO; - } - else if (alph.equals("DNA")) - { - size = 4; - alphabet = DNA; - } - - char symbols[] = new char[size]; - int values[] = new int[size]; - List charList = hmm.getSymbols(); - - int i = 0; - for (char character : charList) - { - symbols[i] = character; - i++; - } - - Integer totalCount = 0; - for (int j = 0; j < size; j++) - { - Double value; - char symbol = symbols[j]; - value = hmm.getMatchEmissionProbability(column, symbol); - double freq; - - if (alphabet == AMINO && removeBelowBackground) - { - freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol); - if (value < freq) - { - value = 0d; - } - } - else if (alphabet == DNA && removeBelowBackground) - { - freq = ResidueProperties.nucleotideBackgroundFrequencies - .get(symbol); - if (value < freq) - { - value = 0d; - } - } - value = value * 10000; - values[j] = value.intValue(); - totalCount += value.intValue(); - } - - QuickSort.sort(values, symbols); - - int[] profile = new int[3 + size * 2]; - - profile[0] = AlignmentAnnotation.SEQUENCE_PROFILE; - profile[1] = size; - profile[2] = totalCount; - - if (totalCount != 0) - { - int arrayPos = 3; - for (int k = size - 1; k >= 0; k--) - { - Double percentage; - Integer value = values[k]; - percentage = (value.doubleValue() / totalCount.doubleValue()) - * 100d; - profile[arrayPos] = symbols[k]; - profile[arrayPos + 1] = percentage.intValue(); - arrayPos += 2; - } - } - - return profile; - - } /** * Returns profile data; the first element is the profile type, the second is @@ -448,22 +376,25 @@ public class AnnotationRenderer // 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.label.startsWith("Information")) + if (InformationThread.HMM_CALC_ID.equals(aa.getCalcId())) { - return getHMMProfileFor(aa, column, true); + 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.get(column), - aa.groupRef.getIgnoreGapsConsensus()); + aa.groupRef.getConsensusData().get(column), + aa.groupRef.getIgnoreGapsConsensus()); } // TODO extend annotation row to enable dynamic and static profile data to // be stored @@ -471,13 +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.get(column), + return AAFrequency.extractProfile(hconsensus.get(column), av_ignoreGapsConsensus); } } @@ -563,7 +493,8 @@ hconsensus.get(column), .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 @@ -596,6 +527,21 @@ hconsensus.get(column), 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; @@ -614,8 +560,8 @@ hconsensus.get(column), 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) { @@ -655,8 +601,8 @@ hconsensus.get(column), { 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); @@ -693,7 +639,7 @@ hconsensus.get(column), { if (hasHiddenColumns) { - column = hiddenColumns.adjustForHiddenColumns(startRes + x); + column = hiddenColumns.visibleToAbsoluteColumn(startRes + x); if (column > row_annotations.length - 1) { break; @@ -714,7 +660,8 @@ hconsensus.get(column), { validRes = true; } - final String displayChar = validRes ? row_annotations[column].displayCharacter + final String displayChar = validRes + ? row_annotations[column].displayCharacter : null; if (x > -1) { @@ -784,17 +731,17 @@ hconsensus.get(column), 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); } @@ -858,7 +805,8 @@ hconsensus.get(column), { 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 @@ -952,8 +900,8 @@ hconsensus.get(column), 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; } @@ -1152,7 +1100,7 @@ hconsensus.get(column), { clipend = true; } - }// end if_in_visible_region + } // end if_in_visible_region if (row.graph > 0 && row.hasText) { y += charHeight; @@ -1169,13 +1117,13 @@ hconsensus.get(column), { 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 + ")"); } } ; @@ -1198,8 +1146,8 @@ hconsensus.get(column), private Color sdNOTCANONICAL_COLOUR; void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x, - int y, int iconOffset, int startRes, int column, - boolean validRes, boolean validEnd) + 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); @@ -1207,35 +1155,39 @@ hconsensus.get(column), 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); } } void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x, - int y, int iconOffset, int startRes, int column, - boolean validRes, boolean validEnd) + 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); @@ -1263,8 +1215,8 @@ hconsensus.get(column), 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); } @@ -1290,8 +1242,8 @@ hconsensus.get(column), } void drawLineGraph(Graphics g, AlignmentAnnotation _aa, - Annotation[] aa_annotations, int sRes, int eRes, int y, - float min, float max, int graphHeight) + Annotation[] aa_annotations, int sRes, int eRes, int y, float min, + float max, int graphHeight) { if (sRes > aa_annotations.length) { @@ -1335,7 +1287,7 @@ hconsensus.get(column), column = sRes + x; if (hasHiddenColumns) { - column = hiddenColumns.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } if (column > aaMax) @@ -1359,13 +1311,13 @@ hconsensus.get(column), 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++; } @@ -1374,7 +1326,8 @@ hconsensus.get(column), 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); @@ -1414,7 +1367,7 @@ hconsensus.get(column), column = sRes + x; if (hasHiddenColumns) { - column = hiddenColumns.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } if (column > aaMax) @@ -1436,8 +1389,8 @@ hconsensus.get(column), 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) { @@ -1511,10 +1464,10 @@ hconsensus.get(column), 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())); + 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); @@ -1542,8 +1495,8 @@ hconsensus.get(column), } 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++; @@ -1558,10 +1511,11 @@ hconsensus.get(column), 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()); }