X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=e360ba4fc109928930984bc1ce1a0a4a6e4bf7b8;hb=60403f610c291791bf7c58f9c7232206469687cd;hp=8f25e7771f2c9e5eecd0006d1dee40b4a06c4952;hpb=e66bdc1c0086ab56c56979d9dc6635e81503eb84;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 8f25e77..e360ba4 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -82,6 +82,7 @@ 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 +99,7 @@ public class AnnotationRenderer } else { + // display a forward arrow if (diffdownstream) { @@ -170,7 +172,66 @@ 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|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, @@ -536,7 +597,8 @@ 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); @@ -545,15 +607,284 @@ 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 (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) @@ -570,12 +901,78 @@ public class AnnotationRenderer 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) @@ -640,6 +1037,67 @@ public class AnnotationRenderer 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); @@ -746,6 +1204,8 @@ 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, @@ -1110,4 +1570,135 @@ public class AnnotationRenderer 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; + + } + } } + + +