public static void main(String[] argv) throws Exception {
DriverManager.load(
"org/ensembl/conf/current_driver.conf:org/ensembl/conf/kaka_mysql_server.conf");
Controller c = new Controller();
EnsJSequence seq =
new EnsJSequence("Dummy", c, new AssemblyLocation("22", 20000000, 20100000, 0), "current");
SequenceAdaptor sa = (SequenceAdaptor) DriverManager.get("current").getAdaptor("sequence");
seq.getCacher().setMinChunkSize(100);
System.out.println("Have sequence. Dumping regions");
String processedSeq = seq.getResidues(1, 10);
String rawSeq = sa.fetch(new AssemblyLocation("22", 20000000, 20000009, 0)).getString();
String diff =
(rawSeq.equals(processedSeq))
? "SAME"
: "protected = " + processedSeq + "\nraw = " + rawSeq;
System.out.println("Sequence first 10 = " + diff);
processedSeq = seq.getResidues(100, 110);
rawSeq = sa.fetch(new AssemblyLocation("22", 20000099, 20000109, 0)).getString();
diff =
(rawSeq.equals(processedSeq))
? "SAME"
: "protected = " + processedSeq + "\nraw = " + rawSeq;
System.out.println("Sequence 100-110 = " + diff);
processedSeq = seq.getResidues(10000, 11010);
rawSeq = sa.fetch(new AssemblyLocation("22", 20009999, 20011009, 0)).getString();
diff =
(rawSeq.equals(processedSeq))
? "SAME"
: "protected = " + processedSeq + "\nraw = " + rawSeq;
System.out.println("Sequence 10000-11010 = " + diff);
processedSeq = seq.getResidues(1, 12010);
rawSeq = sa.fetch(new AssemblyLocation("22", 20000000, 20012009, 0)).getString();
diff =
(rawSeq.equals(processedSeq))
? "SAME"
: "protected = " + processedSeq + "\nraw = " + rawSeq;
System.out.println("Sequence 1-12010 = " + diff);
processedSeq = seq.getResidues(12010, 1);
rawSeq = sa.fetch(new AssemblyLocation("22", 20000000, 20012009, -1)).getString();
diff =
(rawSeq.equals(processedSeq))
? "SAME"
: "protected = " + processedSeq + "\nraw = " + rawSeq;
System.out.println("Sequence 12010-1 = " + diff);
}
