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JAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is...
[jalview.git]
/
src
/
jalview
/
ws
/
sifts
/
SiftsClient.java
diff --git
a/src/jalview/ws/sifts/SiftsClient.java
b/src/jalview/ws/sifts/SiftsClient.java
index
92cb7af
..
58e0b29
100644
(file)
--- a/
src/jalview/ws/sifts/SiftsClient.java
+++ b/
src/jalview/ws/sifts/SiftsClient.java
@@
-227,7
+227,8
@@
public class SiftsClient implements SiftsClientI
if (siftsFile.exists())
{
// The line below is required for unit testing... don't comment it out!!!
if (siftsFile.exists())
{
// The line below is required for unit testing... don't comment it out!!!
- jalview.bin.Console.outPrintln(">>> SIFTS File already downloaded for " + pdbId);
+ jalview.bin.Console
+ .outPrintln(">>> SIFTS File already downloaded for " + pdbId);
if (isFileOlderThanThreshold(siftsFile,
SiftsSettings.getCacheThresholdInDays()))
if (isFileOlderThanThreshold(siftsFile,
SiftsSettings.getCacheThresholdInDays()))
@@
-330,7
+331,8
@@
public class SiftsClient implements SiftsClientI
}
}
}
}
- // jalview.bin.Console.outPrintln(">> 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();
// long now = System.currentTimeMillis();
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
@@
-344,17
+346,19
@@
public class SiftsClient implements SiftsClientI
}
outputStream.close();
inputStream.close();
}
outputStream.close();
inputStream.close();
- // jalview.bin.Console.outPrintln(">>> File downloaded : " + downloadedSiftsFile
+ // jalview.bin.Console.outPrintln(">>> File downloaded : " +
+ // downloadedSiftsFile
// + " took " + (System.currentTimeMillis() - now) + "ms");
return downloadTo;
}
public static String getDownloadUrlFor(String siftFile)
{
// + " took " + (System.currentTimeMillis() - now) + "ms");
return downloadTo;
}
public static String getDownloadUrlFor(String siftFile)
{
- String durl = SIFTS_SPLIT_FTP_BASE_URL+siftFile.substring(1, 3)+"/"+siftFile;
- Console.trace("SIFTS URL for "+siftFile+" is "+durl);
+ String durl = SIFTS_SPLIT_FTP_BASE_URL + siftFile.substring(1, 3) + "/"
+ + siftFile;
+ Console.trace("SIFTS URL for " + siftFile + " is " + durl);
return durl;
return durl;
-
+
}
/**
}
/**
@@
-459,8
+463,8
@@
public class SiftsClient implements SiftsClientI
seq = seq.getDatasetSequence();
}
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
seq = seq.getDatasetSequence();
}
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
- jalview.bin.Console.outPrintln("Getting SIFTS mapping for " + structId + ": seq "
- + seq.getName());
+ jalview.bin.Console.outPrintln("Getting SIFTS mapping for " + structId
+ + ": seq " + seq.getName());
final StringBuilder mappingDetails = new StringBuilder(128);
PrintStream ps = new PrintStream(System.out)
final StringBuilder mappingDetails = new StringBuilder(128);
PrintStream ps = new PrintStream(System.out)
@@
-544,7
+548,8
@@
public class SiftsClient implements SiftsClientI
if (mapping.isEmpty())
{
if (mapping.isEmpty())
{
- throw new SiftsException("SIFTS mapping failed for "+entityId+" and "+seq.getName());
+ 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
}
// also construct a mapping object between the seq-coord sys and the PDB
// seq's coord sys
@@
-662,7
+667,8
@@
public class SiftsClient implements SiftsClientI
int firstPDBResNum = UNASSIGNED;
for (Segment segment : segments)
{
int firstPDBResNum = UNASSIGNED;
for (Segment segment : segments)
{
- // jalview.bin.Console.outPrintln("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)
// + segStartEnd);
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
@@
-965,7
+971,8
@@
public class SiftsClient implements SiftsClientI
*/
public Entity getEntityByMostOptimalMatchedId(String chainId)
{
*/
public Entity getEntityByMostOptimalMatchedId(String chainId)
{
- // jalview.bin.Console.outPrintln("---> 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()];
// entered..");
List<Entity> entities = siftsEntry.getEntity();
SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
@@
-1001,7
+1008,8
@@
public class SiftsClient implements SiftsClientI
++count;
}
Arrays.sort(sPojo, Collections.reverseOrder());
++count;
}
Arrays.sort(sPojo, Collections.reverseOrder());
- // jalview.bin.Console.outPrintln("highest matched entity : " + sPojo[0].entityId);
+ // 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)
// jalview.bin.Console.outPrintln("highest matched pid : " + sPojo[0].pid);
if (sPojo[0].entityId != null)