private boolean isSequenceRecognized(final String sequence) {
return (sequenceDictionary.getSequence(sequence) != null);
}
@Override
public int doWork(String[] args) {
com.github.lindenb.jvarkit.util.cli.GetOpt opt =
new com.github.lindenb.jvarkit.util.cli.GetOpt();
int c;
while ((c = opt.getopt(args, getGetOptDefault() + "k:")) != -1) {
switch (c) {
case 'k':
this.ucscKnownGene = opt.getOptArg();
break;
default:
{
switch (handleOtherOptions(c, opt, null)) {
case EXIT_FAILURE:
return -1;
case EXIT_SUCCESS:
return 0;
default:
break;
}
}
}
}
VcfIterator iter = null;
BufferedReader r = null;
try {
if (opt.getOptInd() == args.length) {
info("Reading from stdin");
iter = new VcfIterator(System.in);
} else if (opt.getOptInd() + 1 == args.length) {
String uri = args[opt.getOptInd()];
info("Reading from " + uri);
iter = new VcfIterator(IOUtils.openURIForReading(uri));
} else {
error("Illegal number of arguments.");
return -1;
}
info("Reading " + this.ucscKnownGene);
SAMSequenceDictionary dict = iter.getHeader().getSequenceDictionary();
int nKG = 0;
r = IOUtils.openURIForBufferedReading(ucscKnownGene);
Pattern tab = Pattern.compile("[\t]");
String line;
while ((line = r.readLine()) != null) {
String tokens[] = tab.split(line);
KnownGene g = new KnownGene(tokens);
if (dict != null && dict.getSequence(g.getChr()) == null) continue;
List<KnownGene> kg = this.chrom2knownGenes.get(g.getChr());
if (kg == null) {
kg = new ArrayList<KnownGene>();
this.chrom2knownGenes.put(g.getChr(), kg);
}
kg.add(g);
++nKG;
}
r.close();
info("Done Reading knownGenes. N=" + nKG);
final double ticksH = (fHeight / 2.0f) * 0.6f;
final double ticksx = 20;
System.out.print(
"%!PS\n"
+ "%%Creator: Pierre Lindenbaum PhD [email protected] http://plindenbaum.blogspot.com\n"
+ "%%Title: "
+ getClass().getSimpleName()
+ "\n"
+ "%%CreationDate: "
+ new Date()
+ "\n"
+ "%%EndComments\n"
+ "%%BoundingBox: 0 0 "
+ (this.pageDef.width + margin.left + margin.right)
+ " "
+ (this.pageDef.height + margin.top + margin.bottom)
+ "\n"
+ "/Courier findfont 9 scalefont setfont\n"
+ "/circle { 10 0 360 arc} bind def\n"
+ "/ticksF {\n"
+ (-ticksH)
+ " "
+ (ticksH)
+ " rmoveto\n"
+ ticksH
+ " "
+ (-ticksH)
+ " rlineto\n"
+ (-ticksH)
+ " "
+ (-ticksH)
+ " rlineto\n"
+ ticksH
+ " "
+ ticksH
+ " rmoveto\n"
+ "} bind def\n"
+ "/ticksR {\n"
+ (ticksH)
+ " "
+ (ticksH)
+ " rmoveto\n"
+ (-ticksH)
+ " "
+ (-ticksH)
+ " rlineto\n"
+ (ticksH)
+ " "
+ (-ticksH)
+ " rlineto\n"
+ (-ticksH)
+ " "
+ (ticksH)
+ " rmoveto\n"
+ "} bind def\n"
+ "/forticksF {2 dict begin\n"
+ "/x2 exch def\n"
+ "/x1 exch def\n"
+ "0 1 x2 x1 sub "
+ ticksx
+ " div {\n"
+ "ticksF "
+ ticksx
+ " 0 rmoveto\n"
+ "}for\n"
+ "} bind def\n"
+ "/forticksR {2 dict begin\n"
+ "/x2 exch def\n"
+ "/x1 exch def\n"
+ "0 1 x2 x1 sub "
+ ticksx
+ " div {\n"
+ " ticksR "
+ ticksx
+ " 0 rmoveto\n"
+ "}for\n"
+ "} bind def\n"
+ "/box\n"
+ "{\n"
+ "4 dict begin\n"
+ "/height exch def\n"
+ "/width exch def\n"
+ "/y exch def\n"
+ "/x exch def\n"
+ "x y moveto\n"
+ "width 0 rlineto\n"
+ "0 height rlineto\n"
+ "width -1 mul 0 rlineto\n"
+ "0 height -1 mul rlineto\n"
+ "end\n"
+ "} bind def\n"
+ "/gradient\n"
+ "{\n"
+ "4 dict begin\n"
+ "/height exch def\n"
+ "/width exch def\n"
+ "/y exch def\n"
+ "/x exch def\n"
+ "/i 0 def\n"
+ "height 2 div /i exch def\n"
+ "\n"
+ "0 1 height 2 div {\n"
+ " 1 i height 2.0 div div sub setgray\n"
+ " newpath\n"
+ " x \n"
+ " y height 2 div i sub add\n"
+ " width\n"
+ " i 2 mul\n"
+ " box\n"
+ " closepath\n"
+ " fill\n"
+ " i 1 sub /i exch def\n"
+ " }for\n"
+ "newpath\n"
+ "0 setgray\n"
+ "0.4 setlinewidth\n"
+ "x y width height box\n"
+ "closepath\n"
+ "stroke\n"
+ "end\n"
+ "} bind def\n");
run(iter);
System.out.print("\n%%Trailer\n%%EOF\n");
return 0;
} catch (Exception err) {
error(err);
return -1;
} finally {
CloserUtil.close(r);
CloserUtil.close(iter);
}
}