/* Note: low and high are relative coordinates */
protected String getResiduesFromSourceImpl(int low, int high) {
int realStart = low; // + getRange().getStart();
int realEnd = high; // + getRange().getStart();
Hashtable var = new Hashtable();
// var.put("bp_start",String.valueOf(new Integer(realStart)));
// var.put("bp_end", String.valueOf(new Integer(realEnd)));
// var.put("chr",getRange().getName());
// var.put("type","basepairs");
// var.put("format","fasta");
// var.put("region","1");
// var.put("btnsubmit","Export");
// var.put("tab","fasta");
// http://dev.ensembl.org:80/perl/exportview?tab=fasta&btnsubmit=Export&format=fasta®ion=1&type=basepairs&chr=2&bp_start=123&bp_end=100000
var.put("vc_start", String.valueOf(new Integer(realStart)));
var.put("vc_end", String.valueOf(new Integer(realEnd)));
var.put("chr", getRange().getName());
var.put("seqonly", "1");
// http://dev.ensembl.org:80/perl/exportview?tab=fasta&btnsubmit=Export&format=fasta®ion=1&type=basepairs&chr=2&bp_start=123&bp_end=100000
String host = server;
int port = Config.getCGIPort();
String cgistr = "perl/apolloview";
// String cgistr = "perl/exportview";
CGI cgi = new CGI(host, port, cgistr, var, System.out);
cgi.run();
FastaFile fa = new FastaFile(cgi.getInput(), false);
Vector seqs = fa.getSeqs();
if (seqs.size() == 1) {
System.out.println("Returning sequence");
return ((SequenceI) seqs.elementAt(0)).getResidues();
} else {
System.out.println("Returning null");
return null;
}
}
