JAL-4090 JAL-1551 spotlessApply

[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!!!
-      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()))
@@ -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();
@@ -344,17 +346,19 @@ public class SiftsClient implements SiftsClientI
     }
     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)
   {
-    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;
-    
+
   }
 
   /**
@@ -459,8 +463,8 @@ public class SiftsClient implements SiftsClientI
       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)
@@ -544,7 +548,8 @@ public class SiftsClient implements SiftsClientI
 
     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
@@ -662,7 +667,8 @@ public class SiftsClient implements SiftsClientI
     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)
@@ -965,7 +971,8 @@ public class SiftsClient implements SiftsClientI
    */
   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()];
@@ -1001,7 +1008,8 @@ public class SiftsClient implements SiftsClientI
       ++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)