return new File(siftsFileName);
}
}
+ else
+ {
+ return siftsFile;
+ }
}
try
{
siftsDownloadDir.mkdirs();
}
// System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+ // long now = System.currentTimeMillis();
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
InputStream inputStream = conn.getInputStream();
}
outputStream.close();
inputStream.close();
- // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
+// System.out.println(">>> File downloaded : " + downloadedSiftsFile
+// + " took " + (System.currentTimeMillis() - now) + "ms");
return new File(downloadedSiftsFile);
}
{
if ((i + (j * len)) < seqRes.length())
{
- boolean sameChar = Comparison.compareChars(
+ boolean sameChar = Comparison.isSameResidue(
seqRes.charAt(i + (j * len)),
strRes.charAt(i + (j * len)), false);
if (sameChar