import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.DBRefEntryI;
import jalview.api.SiftsClientI;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
try (InputStream in = new FileInputStream(siftFile);
GZIPInputStream gzis = new GZIPInputStream(in);)
{
- // System.out.println("File : " + siftFile.getAbsolutePath());
+ // jalview.bin.Console.outPrintln("File : " + siftFile.getAbsolutePath());
JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.sifts");
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(gzis);
if (siftsFile.exists())
{
// The line below is required for unit testing... don't comment it out!!!
- System.out.println(">>> SIFTS File already downloaded for " + pdbId);
+ jalview.bin.Console.outPrintln(">>> SIFTS File already downloaded for " + pdbId);
if (isFileOlderThanThreshold(siftsFile,
SiftsSettings.getCacheThresholdInDays()))
diffInDays = (int) ((new Date().getTime()
- attr.lastModifiedTime().toMillis())
/ (1000 * 60 * 60 * 24));
- // System.out.println("Diff in days : " + diffInDays);
+ // jalview.bin.Console.outPrintln("Diff in days : " + diffInDays);
} catch (IOException e)
{
e.printStackTrace();
}
}
- // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+ // jalview.bin.Console.outPrintln(">> Download ftp url : " + siftsFileFTPURL);
// long now = System.currentTimeMillis();
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
}
outputStream.close();
inputStream.close();
- // System.out.println(">>> File downloaded : " + downloadedSiftsFile
+ // jalview.bin.Console.outPrintln(">>> File downloaded : " + downloadedSiftsFile
// + " took " + (System.currentTimeMillis() - now) + "ms");
return downloadTo;
}
public static String getDownloadUrlFor(String siftFile)
{
- return SIFTS_SPLIT_FTP_BASE_URL +siftFile.substring(1, 3)+"/"+siftFile;
+ String durl = SIFTS_SPLIT_FTP_BASE_URL+siftFile.substring(1, 3)+"/"+siftFile;
+ Console.trace("SIFTS URL for "+siftFile+" is "+durl);
+ return durl;
+
}
/**
seq = seq.getDatasetSequence();
}
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
- System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+ jalview.bin.Console.outPrintln("Getting SIFTS mapping for " + structId + ": seq "
+ seq.getName());
final StringBuilder mappingDetails = new StringBuilder(128);
{
List<Integer> omitNonObserved = new ArrayList<>();
int nonObservedShiftIndex = 0, pdbeNonObserved = 0;
- // System.out.println("Generating mappings for : " + entityId);
+ // jalview.bin.Console.outPrintln("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
String originalSeq = AlignSeq.extractGaps(
if (mapping.isEmpty())
{
- throw new SiftsException("SIFTS mapping failed");
+ throw new SiftsException("SIFTS mapping failed for "+entityId+" and "+seq.getName());
}
// also construct a mapping object between the seq-coord sys and the PDB
// seq's coord sys
int firstPDBResNum = UNASSIGNED;
for (Segment segment : segments)
{
- // System.out.println("Mapping segments : " + segment.getSegId() + "\\"s
+ // jalview.bin.Console.outPrintln("Mapping segments : " + segment.getSegId() + "\\"s
// + segStartEnd);
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
// Arrays.sort(keys);
int firstIndex = keys[0];
int lastIndex = keys[keys.length - 1];
- // System.out.println("Min value " + firstIndex);
- // System.out.println("Max value " + lastIndex);
+ // jalview.bin.Console.outPrintln("Min value " + firstIndex);
+ // jalview.bin.Console.outPrintln("Max value " + lastIndex);
for (int x = firstIndex; x <= lastIndex; x++)
{
if (!resNumMap.containsKey(x) && !omitNonObserved.contains(x))
*/
public Entity getEntityByMostOptimalMatchedId(String chainId)
{
- // System.out.println("---> advanced greedy entityId matching block
+ // jalview.bin.Console.outPrintln("---> advanced greedy entityId matching block
// entered..");
List<Entity> entities = siftsEntry.getEntity();
SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
++count;
}
Arrays.sort(sPojo, Collections.reverseOrder());
- // System.out.println("highest matched entity : " + sPojo[0].entityId);
- // System.out.println("highest matched pid : " + sPojo[0].pid);
+ // jalview.bin.Console.outPrintln("highest matched entity : " + sPojo[0].entityId);
+ // jalview.bin.Console.outPrintln("highest matched pid : " + sPojo[0].pid);
if (sPojo[0].entityId != null)
{