void draw(Graphics2D g) {
int endX, endY;
Block from = null;
if (fromId > -1) from = diag.blocks.get(new Integer(fromId));
Block to = null;
if (!endsAtLine && toId > -1) to = diag.blocks.get(new Integer(toId));
if (toX == -1) endX = diag.xa;
else endX = toX;
if (toY == -1) endY = diag.ya;
else endY = toY;
g.setColor(Color.GRAY);
Stroke stroke = g.getStroke();
ZigzagStroke zzstroke = new ZigzagStroke(stroke, 2, 4);
if (toX == -1) {
g.drawRect(fromX - 3, fromY - 3, 6, 6);
return;
}
if (from != null) {
if (fromSide == Side.TOP) fromY = from.cy - from.height / 2;
else if (fromSide == Side.BOTTOM) fromY = from.cy + from.height / 2;
else if (fromSide == Side.LEFT) fromX = from.cx - from.width / 2;
else if (fromSide == Side.RIGHT) fromX = from.cx + from.width / 2;
}
if (to != null) {
if (toSide == Side.TOP) toY = to.cy - to.height / 2;
else if (toSide == Side.BOTTOM) toY = to.cy + to.height / 2;
else if (toSide == Side.LEFT) toX = to.cx - to.width / 2;
else if (toSide == Side.RIGHT) toX = to.cx + to.width / 2;
}
if (driver.selArrowP == this) g.setColor(Color.BLUE);
else if ((from instanceof ComponentBlock
|| from instanceof ExtPortBlock
|| from instanceof Enclosure)
&& (to instanceof ComponentBlock
|| to instanceof ExtPortBlock
|| to instanceof Enclosure
|| endsAtLine))
if (checkStatus == Status.UNCHECKED) g.setColor(Color.BLACK);
else if (checkStatus == Status.COMPATIBLE) g.setColor(FOREST_GREEN);
else g.setColor(ORANGE_RED);
else if (from instanceof LegendBlock || to instanceof LegendBlock) g.setColor(Color.GRAY);
int fx, fy, tx, ty;
fx = fromX;
fy = fromY;
// tx = toX;
// ty = toY;
// int autoX = -1, autoY = -1; // only used for automatic ports
if (bends != null) {
for (Bend bend : bends) {
tx = bend.x;
ty = bend.y;
if (!dropOldest) g.drawLine(fx, fy, tx, ty);
else {
Shape shape = new Line2D.Double(fx, fy, tx, ty);
shape = zzstroke.createStrokedShape(shape);
g.draw(shape);
// g.setStroke(stroke);
}
if (bend.marked) {
Color col = g.getColor();
g.setColor(Color.RED);
g.drawOval(tx - 5, ty - 5, 10, 10);
g.setColor(col);
}
calcLimits(fx, tx, fy, ty);
fx = tx;
fy = ty;
}
}
tx = endX;
ty = endY;
int x = endX;
if (to != null && endsAtBlock && to.multiplex) {
String s = to.mpxfactor;
if (s == null) s = " ";
int i = s.length() * driver.fontWidth + 10;
x -= i;
}
if (headMarked) {
Color col = g.getColor();
g.setColor(Color.RED);
g.drawOval(x - 5, toY - 5, 10, 10);
g.setColor(col);
}
if (!dropOldest) g.drawLine(fx, fy, tx, ty);
else {
Shape shape = new Line2D.Double(fx, fy, tx, ty);
shape = zzstroke.createStrokedShape(shape);
g.draw(shape);
// g.setStroke(stroke);
}
if (tailMarked) {
Color col = g.getColor();
g.setColor(Color.RED);
g.drawOval(fromX - 5, fromY - 5, 10, 10);
g.setColor(col);
}
calcLimits(fx, x, fy, toY);
if (!endsAtBlock && !endsAtLine) {
g.drawRect(fromX - 3, fromY - 3, 6, 6);
g.drawRect(x - 3, toY - 3, 6, 6);
} else if (endsAtBlock) {
if ((from instanceof ComponentBlock
|| from instanceof ExtPortBlock
|| from instanceof Enclosure)
&& (to instanceof ComponentBlock
|| to instanceof ExtPortBlock
|| to instanceof Enclosure)) {
Arrowhead ah = new Arrowhead(fx, fy, toX, toY);
ah.draw(g);
}
} else if (endsAtLine) {
drawCircleTo(g, fx, fy, x, toY, Color.BLACK, 4);
// g.drawOval(toX - 2, toY - 2, 4, 4);
// g.fillOval(toX - 2, toY - 2, 4, 4);
}
if (toX != -1 && (endsAtBlock || endsAtLine)) {
if (upStreamPort != null && (from instanceof ComponentBlock || from instanceof Enclosure)) {
if (upStreamPort.equals("*")) {
drawCircleFrom(g, fromX, fromY, endX, endY, Color.BLUE, 8);
// g.setColor(Color.BLUE);
// g.drawOval(fromX, fromY - 4, 8, 8);
// g.fillOval(fromX, fromY - 4, 8, 8);
} else if (from.visible) {
g.setColor(Color.BLUE);
int y = fromY + driver.fontHeight;
int x2 = fromX + driver.fontWidth;
g.drawString(upStreamPort, x2, y);
}
g.setColor(Color.BLACK);
}
if (downStreamPort != null
&& !endsAtLine
&& to != null
&& (to instanceof ComponentBlock || to instanceof Enclosure)) {
if (downStreamPort.equals("*")) {
drawCircleTo(g, fx, fy, toX, toY, Color.BLUE, 8);
// g.setColor(Color.BLUE);
// g.drawOval(x - 8, toY - 4, 8, 8);
// g.fillOval(x - 8, toY - 4, 8, 8);
} else if (to.visible) {
g.setColor(Color.BLUE);
int y = toY - driver.fontHeight / 2;
x = toX - driver.fontWidth * (downStreamPort.length() + 1);
if (!endsAtLine && to != null && to.multiplex) x -= 20;
g.drawString(downStreamPort, x, y);
}
g.setColor(Color.BLACK);
}
}
if (extraArrowhead != null) extraArrowhead.draw(g);
}
/**
* Factory for command line tools to call different functions
*
* @author Muhammad Shamim
* @since 1/30/2015
*/
public class CLTFactory {
// Commenting some out because we're not going to release all these when we release CLT
private static final String[] commandLineToolUsages = {
// "addGWNorm", "addGWNorm <input_HiC_file> <min resolution>",
// "addNorm", "addNorm <input_HiC_file> [0 for no frag, 1 for no single frag]",
// "bigWig", "bigWig <bigWig path or URL> <window size in bp> [chr] [start base]
// [end base]",
// "binToPairs", "binToPairs <input_HiC_file> <output_HiC_file>",
// "bpToFrag", "bpToFrag <fragmentFile> <inputBedFile> <outputFile>",
// "calcKR", "calcKR <input_HiC_file>",
// "fragmentToBed","fragmentToBed <fragmentFile>",
// "pairsToBin", "pairsToBin <input_HiC_file> <output_HiC_file> <genomeID>",
// "db", "db <frag|annot|update> [items]",
Dump.getUsage(),
PreProcessing.getBasicUsage(),
APA.getBasicUsage(),
Arrowhead.getBasicUsage(),
HiCCUPS.getBasicUsage(),
HiCCUPSDiff.getBasicUsage(),
ValidateFile.getUsage()
};
public static void generalUsage() {
System.out.println("Juicebox and Juicer Command Line Tools Usage:");
for (String usage : commandLineToolUsages) {
System.out.println("\t\t" + usage);
}
System.out.println("Type juicebox <commandName> for more detailed usage instructions");
}
public static JuiceboxCLT getCLTCommand(String cmd) {
cmd = cmd.toLowerCase();
if (cmd.equals("pre")) {
return new PreProcessing();
} else if (cmd.equals("dump")) {
return new Dump();
} else if (cmd.equals("validate")) {
return new ValidateFile();
} else if (cmd.equals("addGWNorm".toLowerCase())) {
return new AddGWNorm();
} else if (cmd.equals("addNorm".toLowerCase())) {
return new AddNorm();
} else if (cmd.equals("apa")) {
return new APA();
} else if (cmd.equals("compare")) {
return new CompareLists();
} else if (cmd.equals("arrowhead")) {
return new Arrowhead();
} else if (cmd.equals("bigWig".toLowerCase())) {
return new BigWig();
} else if (cmd.equals("binToPairs".toLowerCase())) {
return new BinToPairs();
} else if (cmd.equals("bpToFrag".toLowerCase())) {
return new BPToFragment();
} else if (cmd.equals("calcKR".toLowerCase())) {
return new CalcKR();
} else if (cmd.equals("fragmentToBed".toLowerCase())) {
return new FragmentToBed();
} else if (cmd.equals("hiccups")) {
return new HiCCUPS();
} else if (cmd.equals("motifs")) {
return new MotifFinder();
} else if (cmd.equals("pairsToBin".toLowerCase())) {
return new PairsToBin();
} else if (cmd.equals("db")) {
return new SQLDatabase();
} else if (cmd.equals("hiccupsdiff")) {
return new HiCCUPSDiff();
} else if (cmd.equals("ab_compdiff")) {
return new ABCompartmentsDiff();
}
return null;
}
}
