X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=1b58dbc7c8b04d31439cf2ee44c3229ae979c805;hb=8d2724b83aca38ef75d68787cc5939d950467e63;hp=6ed2b9fc2b54cdef02ec22e4738ec9053ddce1f9;hpb=345f55c548098dd216a33cd5a71d5f632a276ac4;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 6ed2b9f..1b58dbc 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) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * @@ -14,6 +14,7 @@ * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.renderer; @@ -82,6 +83,7 @@ public class AnnotationRenderer // 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)) @@ -98,6 +100,7 @@ public class AnnotationRenderer } else { + // display a forward arrow if (diffdownstream) { @@ -170,7 +173,66 @@ public class AnnotationRenderer * master flag indicating if renderer should ever try to clip. not enabled for jalview 2.8.1 */ private boolean canClip=false; + + public 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) + { + //System.out.println(nonCanColor); + + g.setColor(nonCanColor); + int sCol = (lastSSX / charWidth) + 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; + + 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))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.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); + } // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI // av) public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel, @@ -240,7 +302,7 @@ public class AnnotationRenderer } // TODO extend annotation row to enable dynamic and static profile data to // be stored - if (aa.groupRef == null && aa.sequenceRef == null && av_renderProfile) + if (aa.groupRef == null && aa.sequenceRef == null) { return AAFrequency.extractProfile(hconsensus[column], av_ignoreGapsConsensus); @@ -262,7 +324,7 @@ public class AnnotationRenderer // to // be stored if (aa.groupRef == null && aa.sequenceRef == null - && av_renderProfile && hStrucConsensus != null + && hStrucConsensus != null && hStrucConsensus.length > column) { return StructureFrequency.extractProfile(hStrucConsensus[column], @@ -303,6 +365,7 @@ public class AnnotationRenderer updateFromAwtRenderPanel(annotPanel, av); fm = g.getFontMetrics(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); + int temp = 0; if (aa==null) { return false; @@ -318,6 +381,8 @@ public class AnnotationRenderer boolean centreColLabels, centreColLabelsDef = av .getCentreColumnLabels(); boolean scaleColLabel = false; + AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation(); + boolean renderHistogram = true, renderProfile = true, normaliseProfile = false; BitSet graphGroupDrawn = new BitSet(); int charOffset = 0; // offset for a label @@ -331,6 +396,26 @@ public class AnnotationRenderer for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; + { + // check if this is a consensus annotation row and set the display settings appropriately + // TODO: generalise this to have render styles for consensus/profile + // data + if (row.groupRef != null && row == row.groupRef.getConsensus()) + { + renderHistogram = row.groupRef.isShowConsensusHistogram(); + renderProfile = row.groupRef.isShowSequenceLogo(); + normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); + } + else if (row == consensusAnnot || row == structConsensusAnnot) + { + renderHistogram = av_renderHistogram; + renderProfile = av_renderProfile; + normaliseProfile = av_normaliseProfile; + } else { + renderHistogram = true; + // don't need to set render/normaliseProfile since they are not currently used in any other annotation track renderer + } + } Annotation[] row_annotations = row.annotations; if (!row.visible) { @@ -514,7 +599,8 @@ public class AnnotationRenderer .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter .length() < 2 && row_annotations[column].secondaryStructure == ' '))) { - g.drawString(row_annotations[column].displayCharacter, x + g.drawString(row_annotations[column].displayCharacter + , x * charWidth + charOffset, y + iconOffset); } g.setFont(ofont); @@ -523,42 +609,158 @@ public class AnnotationRenderer if (row.hasIcons) { char ss = validRes ? row_annotations[column].secondaryStructure - : ' '; - if (ss == 'S') + : '-'; + + if (ss == '(') { // distinguish between forward/backward base-pairing if (row_annotations[column].displayCharacter.indexOf(')') > -1) { - ss = 's'; + + ss = ')'; + } } - if (!validRes || (ss != lastSS)) + if (ss == '[') { - if (x > -1) + if ((row_annotations[column].displayCharacter.indexOf(']') > -1)) { + ss = ']'; + + + } + } + if (ss == '{') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('}') > -1) + { + ss = '}'; + + + } + } + if (ss == '<') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('<') > -1) + { + ss = '>'; + + + } + } + if (ss >=65) + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf(ss+32) > -1) + { + + ss = (char) (ss+32); + + + } + } + + + if (!validRes || (ss != lastSS)) + { + + + if (x > -1) + { + + + int nb_annot=x-temp; + //System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot); switch (lastSS) - { - case 'H': - drawHelixAnnot(g, row_annotations, lastSSX, x, y, - iconOffset, startRes, column, validRes, validEnd); + { + + case '$': + drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; - case 'E': - drawSheetAnnot(g, row_annotations, lastSSX, x, y, - iconOffset, startRes, column, validRes, validEnd); + case 'µ': + drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; - case 'S': // Stem case for RNA secondary structure - case 's': // and opposite direction - drawStemAnnot(g, row_annotations, lastSSX, x, y, - iconOffset, startRes, column, validRes, validEnd); + case '(': // Stem case for RNA secondary structure + case ')': // and opposite direction + drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + temp=x; break; - + case '{': + case '}': + case '[': + case ']': + case '>': + case '<': + case 'A': + case 'a': + case 'B': + case 'b': + case 'C': + case 'c': + case 'D': + case 'd': + case 'E': + case 'e': + case 'F': + case 'f': + case 'G': + case 'g': + case 'H': + case 'h': + case 'I': + case 'i': + case 'J': + case 'j': + case 'K': + case 'k': + case 'L': + case 'l': + case 'M': + case 'm': + case 'N': + case 'n': + case 'O': + case 'o': + case 'P': + case 'p': + case 'Q': + case 'q': + case 'R': + case 'r': + case 'S': + case 's': + case 'T': + case 't': + case 'U': + case 'u': + case 'V': + case 'v': + case 'W': + case 'w': + case 'X': + case 'x': + case 'Y': + case 'y': + case 'Z': + case 'z': + + Color nonCanColor= getNotCanonicalColor(lastSS); + drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + temp=x; + break; default: g.setColor(Color.gray); g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2); - + temp=x; break; } } @@ -604,23 +806,86 @@ public class AnnotationRenderer { switch (lastSS) { - case 'H': - drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, - startRes, column, validRes, validEnd); + case '$': + drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; - case 'E': - drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, - startRes, column, validRes, validEnd); + case 'µ': + drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; case 's': case 'S': // Stem case for RNA secondary structure - drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, - startRes, column, validRes, validEnd); + + drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + break; + case '{': + case '}': + case '[': + case ']': + case '>': + case '<': + case 'A': + case 'a': + case 'B': + case 'b': + case 'C': + 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': + case 'J': + case 'j': + case 'K': + case 'k': + case 'L': + case 'l': + case 'M': + case 'm': + case 'N': + case 'n': + case 'O': + case 'o': + case 'P': + case 'p': + case 'Q': + case 'q': + case 'R': + case 'r': + case 'T': + case 't': + case 'U': + case 'u': + case 'V': + case 'v': + case 'W': + case 'w': + case 'X': + case 'x': + case 'Y': + case 'y': + case 'Z': + case 'z': + //System.out.println(lastSS); + Color nonCanColor = getNotCanonicalColor(lastSS); + drawNotCanonicalAnnot(g,nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + break; default: - drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, - startRes, column, validRes, validEnd); + drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; } } @@ -658,8 +923,8 @@ public class AnnotationRenderer { if (aa[gg].graphGroup == row.graphGroup) { - drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, - endRes, y, groupmin, groupmax, row.graphHeight); + drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin, + groupmax, row.graphHeight); } } @@ -667,14 +932,14 @@ public class AnnotationRenderer } else { - drawLineGraph(g, row, row_annotations, startRes, endRes, y, - row.graphMin, row.graphMax, row.graphHeight); + drawLineGraph(g, row, row_annotations, startRes, endRes, y, row.graphMin, + row.graphMax, row.graphHeight); } } else if (row.graph == AlignmentAnnotation.BAR_GRAPH) { drawBarGraph(g, row, row_annotations, startRes, endRes, - row.graphMin, row.graphMax, y); + row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile); } } } else { @@ -724,18 +989,21 @@ public class AnnotationRenderer private final Color HELIX_COLOUR = Color.red; private final Color STEM_COLOUR = Color.blue; + + 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) + public 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, int lastSSX, - int x, int y, int iconOffset, int startRes, int column, - boolean validRes, boolean validEnd) + public void drawSheetAnnot(Graphics g, Annotation[] row, + + int lastSSX, int x, int y, int iconOffset, int startRes, + int column, boolean validRes, boolean validEnd) { g.setColor(SHEET_COLOUR); @@ -910,7 +1178,7 @@ public class AnnotationRenderer public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, int eRes, float min, - float max, int y) + float max, int y, boolean renderHistogram,boolean renderProfile,boolean normaliseProfile) { if (sRes > aa_annotations.length) { @@ -934,23 +1202,6 @@ public class AnnotationRenderer int column; int aaMax = aa_annotations.length - 1; - boolean renderHistogram = true, renderProfile = true, normaliseProfile = false; - // if (aa.autoCalculated && aa.label.startsWith("Consensus")) - { - // TODO: generalise this to have render styles for consensus/profile data - if (_aa.groupRef != null) - { - renderHistogram = _aa.groupRef.isShowConsensusHistogram(); - renderProfile = _aa.groupRef.isShowSequenceLogo(); - normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo(); - } - else - { - renderHistogram = av_renderHistogram; - renderProfile = av_renderProfile; - normaliseProfile = av_normaliseProfile; - } - } while (x < eRes - sRes) { column = sRes + x; @@ -1105,4 +1356,135 @@ public class AnnotationRenderer x += charWidth; } } + + + Color getNotCanonicalColor(char lastss) + { + switch (lastss) + { + case '{': + case '}': + return new Color(255,125,5); + + case '[': + case ']': + return new Color(245,115,10); + + case '>': + case '<': + return new Color(235,135,15); + + case 'A': + case 'a': + return new Color(225,105,20); + + case 'B': + case 'b': + return new Color(215,145,30); + + case 'C': + case 'c': + return new Color(205,95,35); + + case 'D': + case 'd': + return new Color(195,155,45); + + case 'E': + case 'e': + return new Color(185,85,55); + + case 'F': + case 'f': + return new Color(175,165,65); + + case 'G': + case 'g': + return new Color(170,75,75); + + case 'H': + case 'h': + return new Color(160,175,85); + + case 'I': + case 'i': + return new Color(150,65,95); + + case 'J': + case 'j': + return new Color(140,185,105); + + case 'K': + case 'k': + return new Color(130,55,110); + + case 'L': + case 'l': + return new Color(120,195,120); + + case 'M': + case 'm': + return new Color(110,45,130); + + case 'N': + case 'n': + return new Color(100,205,140); + + case 'O': + case 'o': + return new Color(90,35,150); + + case 'P': + case 'p': + return new Color(85,215,160); + + case 'Q': + case 'q': + return new Color(75,25,170); + + case 'R': + case 'r': + return new Color(65,225,180); + + case 'S': + case 's': + return new Color(55,15,185); + + case 'T': + case 't': + return new Color(45,235,195); + + case 'U': + case 'u': + return new Color(35,5,205); + + case 'V': + case 'v': + return new Color(25,245,215); + + case 'W': + case 'w': + return new Color(15,0,225); + + case 'X': + case 'x': + return new Color(10,255,235); + + case 'Y': + case 'y': + return new Color(5,150,245); + + case 'Z': + case 'z': + return new Color(0,80,255); + + default : + System.out.println("This is not a interaction : "+lastss); + return null; + + } + } } + + +