From: Jim Procter Date: Thu, 11 Jul 2013 12:58:09 +0000 (+0100) Subject: Merge branch 'JAL-1347' into develop X-Git-Tag: Jalview_2_9~226 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=60403f610c291791bf7c58f9c7232206469687cd;hp=-c;p=jalview.git Merge branch 'JAL-1347' into develop --- 60403f610c291791bf7c58f9c7232206469687cd diff --combined src/jalview/renderer/AnnotationRenderer.java index 23726df,8f25e77..e360ba4 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@@ -82,7 -82,6 +82,7 @@@ public class AnnotationRendere // 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)) @@@ -99,7 -98,6 +99,7 @@@ } else { + // display a forward arrow if (diffdownstream) { @@@ -172,66 -170,7 +172,66 @@@ * 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|b|c|d|e|f|g|h|i|j|k|l|m|n|o|p|q|r|s|t|u|v|w|x|y|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, @@@ -379,6 -318,8 +379,8 @@@ boolean centreColLabels, centreColLabelsDef = av .getCentreColumnLabels(); boolean scaleColLabel = false; + AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(); + boolean renderHistogram = true, renderProfile = true, normaliseProfile = false; BitSet graphGroupDrawn = new BitSet(); int charOffset = 0; // offset for a label @@@ -392,6 -333,26 +394,26 @@@ 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) + { + 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) { @@@ -575,8 -536,7 +597,8 @@@ .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); @@@ -585,284 -545,15 +607,284 @@@ 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 (ss == '[') + { + 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 == 'A') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('a') > -1) + { + ss = 'a'; + + + } + } + + if (ss == 'B') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('b') > -1) + { + ss = 'b'; + + } + } + + if (ss == 'C') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('c') > -1) + { + ss = 'c'; + + } + } + if (ss == 'D') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('d') > -1) + { + ss = 'd'; + + } + } + if (ss == '1') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('e') > -1) + { + ss = 'e'; + + } + } + if (ss == 'F') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('f') > -1) + { + ss = 'f'; + + } + } + if (ss == 'G') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('g') > -1) + { + ss = 'g'; + + } + } + if (ss == '2') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('h') > -1) + { + ss = 'h'; + + } + } + if (ss == 'I') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('i') > -1) + { + ss = 'i'; + + } + } + if (ss == 'J') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('j') > -1) + { + ss = 'j'; + + } + } + if (ss == 'K') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('k') > -1) + { + ss = 'k'; + + } + } + if (ss == 'L') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('l') > -1) + { + ss = 'l'; + + } + } + if (ss == 'M') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('m') > -1) + { + ss = 'm'; + + } + } + if (ss == 'N') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('n') > -1) + { + ss = 'n'; + + } + } + if (ss == 'O') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('o') > -1) + { + ss = 'o'; + + } + } + if (ss == 'P') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('p') > -1) + { + ss = 'p'; + + } + } + if (ss == 'Q') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('q') > -1) + { + ss = 'q'; + + } + } + if (ss == 'R') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('r') > -1) + { + ss = 'r'; + + } + } + if (ss == 'S') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('s') > -1) + { + ss = 's'; + + } + } + if (ss == 'T') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('t') > -1) + { + ss = 't'; + + } + } + if (ss == 'U') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('u') > -1) + { + ss = 'u'; + + } + } + if (ss == 'V') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('v') > -1) + { + ss = 'v'; + + } + } + if (ss == 'W') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('w') > -1) + { + ss = 'w'; + + } + } + if (ss == 'X') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('x') > -1) + { + ss = 'x'; + + } + } + if (ss == 'Y') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('y') > -1) + { + ss = 'y'; + + } + } + if (ss == 'Z') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('z') > -1) + { + ss = 'z'; + + } + } if (!validRes || (ss != lastSS)) { if (x > -1) @@@ -879,78 -570,12 +901,78 @@@ 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); +// 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); break; - + case '{': + case '}': + case '[': + case ']': + case '>': + case '<': + case 'A': + case 'a': + case 'B': + case 'b': + case 'C': + case 'c': + case 'D': + case 'd': + case '1': + case 'e': + case 'F': + case 'f': + case 'G': + case 'g': + case '2': + 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': + //System.out.println(lastSS); + Color nonCanColor= getNotCanonicalColor(lastSS); + drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + break; default: g.setColor(Color.gray); g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) @@@ -1015,67 -640,6 +1037,67 @@@ 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 '1': + case 'e': + case 'F': + case 'f': + case 'G': + case 'g': + case '2': + 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); @@@ -1132,7 -696,7 +1154,7 @@@ 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 { @@@ -1182,8 -746,6 +1204,8 @@@ 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, @@@ -1370,7 -932,7 +1392,7 @@@ 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) { @@@ -1394,23 -956,6 +1416,6 @@@ 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; @@@ -1565,135 -1110,4 +1570,135 @@@ x += charWidth; } } + + + Color getNotCanonicalColor(char lastss) + { + switch (lastss) + { + case '{': + case '}': + return Color.cyan; + + case '[': + case ']': + return Color.green; + + case '>': + case '<': + return Color.magenta; + + case 'A': + case 'a': + return Color.orange; + + case 'B': + case 'b': + return Color.pink; + + case 'C': + case 'c': + return Color.red; + + case 'D': + case 'd': + return Color.yellow; + + case '1': + case 'e': + return Color.black; + + case 'F': + case 'f': + return Color.darkGray; + + case 'G': + case 'g': + return Color.gray; + + case '2': + case 'h': + return Color.lightGray; + + case 'I': + case 'i': + return Color.white; + + case 'J': + case 'j': + return Color.cyan; + + case 'K': + case 'k': + return Color.magenta; + + case 'L': + case 'l': + return Color.orange; + + case 'M': + case 'm': + return Color.red; + + case 'N': + case 'n': + return Color.yellow; + + case 'O': + case 'o': + return Color.pink; + + case 'P': + case 'p': + return Color.black; + + case 'Q': + case 'q': + return Color.blue; + + case 'R': + case 'r': + return Color.cyan; + + case 'S': + case 's': + return Color.magenta; + + case 'T': + case 't': + return Color.darkGray; + + case 'U': + case 'u': + return Color.yellow; + + case 'V': + case 'v': + return Color.blue; + + case 'W': + case 'w': + return Color.orange; + + case 'X': + case 'x': + return Color.magenta; + + case 'Y': + case 'y': + return Color.blue; + + case 'Z': + case 'z': + return Color.blue; + + default : + System.out.println("This is not a interaction"); + return null; + + } + } } + + +