X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;fp=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=92cb7af43a656462d41bd578d2ad0bf539c45dcf;hb=b122ba188c2ffcbb302809bafc02058e355643ee;hp=24526cfa8a2d6e6e637b4f3c8164a258260268d4;hpb=e91b3bef83f320e13c59ad5d21d69f0abf3d7507;p=jalview.git

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 24526cf..92cb7af 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -189,7 +189,7 @@ public class SiftsClient implements SiftsClientI
     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);
@@ -227,7 +227,7 @@ public class SiftsClient implements SiftsClientI
     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()))
@@ -282,7 +282,7 @@ public class SiftsClient implements SiftsClientI
       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();
@@ -330,7 +330,7 @@ public class SiftsClient implements SiftsClientI
       }
     }
 
-    // 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();
@@ -344,7 +344,7 @@ public class SiftsClient implements SiftsClientI
     }
     outputStream.close();
     inputStream.close();
-    // System.out.println(">>> File downloaded : " + downloadedSiftsFile
+    // jalview.bin.Console.outPrintln(">>> File downloaded : " + downloadedSiftsFile
     // + " took " + (System.currentTimeMillis() - now) + "ms");
     return downloadTo;
   }
@@ -459,7 +459,7 @@ public class SiftsClient implements SiftsClientI
       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);
@@ -492,7 +492,7 @@ public class SiftsClient implements SiftsClientI
   {
     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(
@@ -662,7 +662,7 @@ public class SiftsClient implements SiftsClientI
     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)
@@ -931,8 +931,8 @@ public class SiftsClient implements SiftsClientI
     // 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))
@@ -965,7 +965,7 @@ public class SiftsClient implements SiftsClientI
    */
   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()];
@@ -1001,8 +1001,8 @@ public class SiftsClient implements SiftsClientI
       ++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)
     {