import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.util.Format;
import jalview.xml.binding.sifts.Entry;
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 (os != null)
{
MappingOutputPojo mop = new MappingOutputPojo();
- mop.setSeqStart(pdbStart);
- mop.setSeqEnd(pdbEnd);
+ mop.setSeqStart(seqStart);
+ mop.setSeqEnd(seqEnd);
mop.setSeqName(seq.getName());
mop.setSeqResidue(matchedSeq);
- mop.setStrStart(seqStart);
- mop.setStrEnd(seqEnd);
+ mop.setStrStart(pdbStart);
+ mop.setStrEnd(pdbEnd);
mop.setStrName(structId);
mop.setStrResidue(targetStrucSeqs.toString());
{
if ((i + (j * len)) < seqRes.length())
{
- if (seqRes.charAt(i + (j * len)) == strRes
- .charAt(i + (j * len))
+ boolean sameChar = Comparison.isSameResidue(
+ seqRes.charAt(i + (j * len)),
+ strRes.charAt(i + (j * len)), false);
+ if (sameChar
&& !jalview.util.Comparison.isGap(seqRes.charAt(i
+ (j * len))))
{