protected void calcSimilarity() {
Map<String, Double> idMap = AFPAlignmentDisplay.calcIdSimilarity(alnseq1, alnseq2, alnLength);
// probability = idMap.get("probability");
similarity = idMap.get("similarity");
identity = idMap.get("identity");
}
public void paintComponent(Graphics g) {
super.paintComponent(g);
Graphics2D g2D = (Graphics2D) g;
g2D.setRenderingHint(
RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
// only draw within the ranges of the Clip
// Rectangle drawHere = g2D.getClipBounds();
// int startpos = coordManager.getSeqPos(0,drawHere.x);
// int endpos = coordManager.getSeqPos(0,drawHere.x+drawHere.width-2);
char[] seq1 = afpChain.getAlnseq1();
char[] seq2 = afpChain.getAlnseq2();
char[] symb = afpChain.getAlnsymb();
int startpos = 0;
int endpos = afpChain.getAlnLength();
String summary = afpChain.toString();
g2D.drawString(summary, 20, coordManager.getSummaryPos());
Color significantCol = Color.red;
if (afpChain.isSignificantResult()) significantCol = Color.green;
g2D.setPaint(significantCol);
// draw a darker backgroun
Rectangle sig = new Rectangle(10, 10, 10, 10);
g2D.fill(sig);
boolean isFATCAT = false;
if (afpChain.getAlgorithmName().startsWith("jFatCat")) {
isFATCAT = true;
}
for (int i = startpos; ((i <= endpos) && (i < afpChain.getAlnLength())); i++) {
// TODO:
// color amino acids by hydrophobicity
char c1 = seq1[i];
char c2 = seq2[i];
boolean isGapped = false;
g2D.setFont(seqFont);
List<Integer> alignedPos = null;
if (colorByAlignmentBlock) {
alignedPos = DisplayAFP.getEQRAlignmentPos(afpChain);
}
if (isFATCAT) {
char s = symb[i];
if (s != ' ') {
isGapped = false;
g2D.setFont(eqFont);
} else isGapped = true;
} else {
if (c1 != '-' && c2 != '-') {
// no gap
g2D.setFont(eqFont);
} else {
isGapped = true;
}
}
Point p1 = coordManager.getPanelPos(0, i);
int xpos1 = p1.x;
int ypos1 = p1.y;
Point p2 = coordManager.getPanelPos(1, i);
int xpos2 = p2.x;
int ypos2 = p2.y;
int blockNum = afpChain.getBlockNum();
if (!isGapped) {
Color bg = Color.white;
Color bg2 = Color.white;
Color end1 = ColorUtils.rotateHue(ColorUtils.orange, (1.0f / 24.0f) * blockNum);
Color end2 = ColorUtils.rotateHue(ColorUtils.cyan, (1.0f / 24.0f) * (blockNum + 1));
if (colorByAlignmentBlock) {
if (!alignedPos.contains(i)) {
// unaligned!
bg = Color.white;
bg2 = Color.white;
} else {
int colorPos = 0;
if (isFATCAT) {
int block = 0;
char s = symb[i];
try {
block = Integer.parseInt(s + "") - 1;
bg = ColorUtils.getIntermediate(ColorUtils.orange, end1, blockNum, block);
bg2 = ColorUtils.getIntermediate(ColorUtils.cyan, end2, blockNum, block);
// bg = ColorUtils.rotateHue(ColorUtils.orange, (1.0f / 24.0f) * block );
// bg2 = ColorUtils.rotateHue(ColorUtils.cyan, (1.0f / 16.0f) * block );
} catch (Exception e) {
}
if (colorPos > ColorUtils.colorWheel.length) {
colorPos = ColorUtils.colorWheel.length % colorPos;
}
} else {
colorPos = DisplayAFP.getBlockNrForAlignPos(afpChain, i);
bg = ColorUtils.getIntermediate(ColorUtils.orange, end1, blockNum, colorPos);
bg2 = ColorUtils.getIntermediate(ColorUtils.cyan, end2, blockNum, colorPos);
// bg = ColorUtils.rotateHue(ColorUtils.orange, (1.0f / 24.0f) * colorPos );
// bg2 = ColorUtils.rotateHue(ColorUtils.cyan, (1.0f / 16.0f) * colorPos);
}
}
} else {
bg = Color.LIGHT_GRAY;
bg2 = Color.LIGHT_GRAY;
}
// draw a darker background
g2D.setPaint(bg);
Rectangle rec = new Rectangle(p1.x - 1, p1.y - 11, (p2.x - p1.x) + 12, (p2.y - p1.y) + 1);
g2D.fill(rec);
g2D.setPaint(bg2);
Rectangle rec2 = new Rectangle(p1.x - 1, p1.y + 4, (p2.x - p1.x) + 12, (p2.y - p1.y) - 3);
g2D.fill(rec2);
// g2D.setPaint(Color.black);
// g2D.draw(rec);
}
if (colorBySimilarity) {
if (c1 == c2) {
Color bg = Color.red;
g2D.setPaint(bg);
Rectangle rec =
new Rectangle(p1.x - 1, p1.y - 11, (p2.x - p1.x) + 12, (p2.y - p1.y) + 12);
g2D.fill(rec);
} else if (AFPAlignmentDisplay.aaScore(c1, c2) > 0) {
Color bg = Color.orange;
g2D.setPaint(bg);
Rectangle rec =
new Rectangle(p1.x - 1, p1.y - 11, (p2.x - p1.x) + 12, (p2.y - p1.y) + 12);
g2D.fill(rec);
}
}
// if ( selectionStart != null && selectionEnd != null){
// if ( i >= selectionStart.getPos1() && i <= selectionEnd.getPos1()) {
if (isSelected(i)) {
// draw selection
Color bg = Color.YELLOW;
g2D.setPaint(bg);
// draw a darker backgroun
Rectangle rec = new Rectangle(p1.x - 1, p1.y - 11, (p2.x - p1.x) + 12, (p2.y - p1.y) + 12);
g2D.fill(rec);
// }
}
// draw the AA sequence
g2D.setColor(Color.black);
g2D.drawString(c1 + "", xpos1, ypos1);
g2D.drawString(c2 + "", xpos2, ypos2);
// System.out.println(seq1[i] + " " + xpos1 + " " + ypos1 + " " + seq2[i] + xpos2 + " " +
// ypos2);
}
int nrLines = (afpChain.getAlnLength() - 1) / AFPChainCoordManager.DEFAULT_LINE_LENGTH;
for (int i = 0; i <= nrLines; i++) {
try {
// draw legend at i
Point p1 = coordManager.getLegendPosition(i, 0);
Point p2 = coordManager.getLegendPosition(i, 1);
int aligPos = i * AFPChainCoordManager.DEFAULT_LINE_LENGTH;
Atom a1 = DisplayAFP.getAtomForAligPos(afpChain, 0, aligPos, ca1, false);
Atom a2 = DisplayAFP.getAtomForAligPos(afpChain, 1, aligPos, ca2, false);
String label1 = JmolTools.getPdbInfo(a1, false);
String label2 = JmolTools.getPdbInfo(a2, false);
g2D.drawString(label1, p1.x, p1.y);
g2D.drawString(label2, p2.x, p2.y);
Point p3 = coordManager.getEndLegendPosition(i, 0);
Point p4 = coordManager.getEndLegendPosition(i, 1);
aligPos =
i * AFPChainCoordManager.DEFAULT_LINE_LENGTH
+ AFPChainCoordManager.DEFAULT_LINE_LENGTH
- 1;
if (aligPos > afpChain.getAlnLength()) aligPos = afpChain.getAlnLength() - 1;
Atom a3 = DisplayAFP.getAtomForAligPos(afpChain, 0, aligPos, ca1, true);
Atom a4 = DisplayAFP.getAtomForAligPos(afpChain, 1, aligPos, ca2, true);
String label3 = JmolTools.getPdbInfo(a3, false);
String label4 = JmolTools.getPdbInfo(a4, false);
g2D.drawString(label3, p3.x, p3.y);
g2D.drawString(label4, p4.x, p4.y);
} catch (StructureException e) {
e.printStackTrace();
}
}
}