Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'

[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 2ff4a8b..68af7c3 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -128,8 +128,8 @@ public class SiftsClient implements SiftsClientI
 
   private enum ResidueDetailType
   {
-    NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE(
-            "codeSecondaryStructure"), ANNOTATION("Annotation");
+    NAME_SEC_STRUCTURE("nameSecondaryStructure"),
+    CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation");
     private String code;
 
     private ResidueDetailType(String code)
@@ -261,8 +261,9 @@ public class SiftsClient implements SiftsClientI
     try
     {
       attr = Files.readAttributes(filePath, BasicFileAttributes.class);
-      diffInDays = (int) ((new Date().getTime() - attr.lastModifiedTime()
-              .toMillis()) / (1000 * 60 * 60 * 24));
+      diffInDays = (int) ((new Date().getTime()
+              - attr.lastModifiedTime().toMillis())
+              / (1000 * 60 * 60 * 24));
       // System.out.println("Diff in days : " + diffInDays);
     } catch (IOException e)
     {
@@ -279,8 +280,8 @@ public class SiftsClient implements SiftsClientI
    * @throws SiftsException
    * @throws IOException
    */
-  public static File downloadSiftsFile(String pdbId) throws SiftsException,
-          IOException
+  public static File downloadSiftsFile(String pdbId)
+          throws SiftsException, IOException
   {
     if (pdbId.contains(".cif"))
     {
@@ -311,8 +312,8 @@ public class SiftsClient implements SiftsClientI
     }
     outputStream.close();
     inputStream.close();
-//    System.out.println(">>> File downloaded : " + downloadedSiftsFile
-//            + " took " + (System.currentTimeMillis() - now) + "ms");
+    // System.out.println(">>> File downloaded : " + downloadedSiftsFile
+    // + " took " + (System.currentTimeMillis() - now) + "ms");
     return new File(downloadedSiftsFile);
   }
 
@@ -360,11 +361,11 @@ public class SiftsClient implements SiftsClientI
       {
         continue;
       }
-      String canonicalSource = DBRefUtils.getCanonicalName(dbRef
-              .getSource());
+      String canonicalSource = DBRefUtils
+              .getCanonicalName(dbRef.getSource());
       if (isValidDBRefEntry(dbRef)
-              && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT) || canonicalSource
-                      .equalsIgnoreCase(DBRefSource.PDB)))
+              && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT)
+                      || canonicalSource.equalsIgnoreCase(DBRefSource.PDB)))
       {
         return dbRef;
       }
@@ -511,8 +512,9 @@ public class SiftsClient implements SiftsClientI
       int orignalSeqStart = seq.getStart();
       if (orignalSeqStart >= 1)
       {
-        int subSeqStart = (seqStart >= orignalSeqStart) ? seqStart
-                - orignalSeqStart : 0;
+        int subSeqStart = (seqStart >= orignalSeqStart)
+                ? seqStart - orignalSeqStart
+                : 0;
         int subSeqEnd = seqEnd - (orignalSeqStart - 1);
         subSeqEnd = originalSeq.length() < subSeqEnd ? originalSeq.length()
                 : subSeqEnd;
@@ -573,12 +575,11 @@ public class SiftsClient implements SiftsClientI
           {
             pdbRefDb = cRefDb;
           }
-          if (cRefDb.getDbCoordSys()
-                  .equalsIgnoreCase(seqCoordSys.getName())
+          if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys.getName())
                   && isAccessionMatched(cRefDb.getDbAccessionId()))
           {
-            currSeqIndex = getLeadingIntegerValue(
-                    cRefDb.getDbResNum(), UNASSIGNED);
+            currSeqIndex = getLeadingIntegerValue(cRefDb.getDbResNum(),
+                    UNASSIGNED);
             if (pdbRefDb != null)
             {
               break;// exit loop if pdb and uniprot are already found
@@ -592,8 +593,9 @@ public class SiftsClient implements SiftsClientI
         if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
         {
 
-          int resNum = (pdbRefDb == null) ? getLeadingIntegerValue(
-                  residue.getDbResNum(), UNASSIGNED)
+          int resNum = (pdbRefDb == null)
+                  ? getLeadingIntegerValue(residue.getDbResNum(),
+                          UNASSIGNED)
                   : getLeadingIntegerValue(pdbRefDb.getDbResNum(),
                           UNASSIGNED);
 
@@ -610,8 +612,9 @@ public class SiftsClient implements SiftsClientI
             omitNonObserved.add(currSeqIndex);
             ++nonObservedShiftIndex;
           }
-          mapping.put(currSeqIndex - nonObservedShiftIndex, new int[] {
-              Integer.valueOf(resNum), UNASSIGNED });
+          mapping.put(currSeqIndex - nonObservedShiftIndex,
+                  new int[]
+                  { Integer.valueOf(resNum), UNASSIGNED });
         }
       }
     }
@@ -640,7 +643,6 @@ public class SiftsClient implements SiftsClientI
     return failValue;
   }
 
-
   /**
    * 
    * @param chainId
@@ -815,7 +817,8 @@ public class SiftsClient implements SiftsClientI
    */
   public Entity getEntityByMostOptimalMatchedId(String chainId)
   {
-    // System.out.println("---> advanced greedy entityId matching block entered..");
+    // System.out.println("---> advanced greedy entityId matching block
+    // entered..");
     List<Entity> entities = siftsEntry.getEntity();
     SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
     int count = 0;
@@ -871,8 +874,8 @@ public class SiftsClient implements SiftsClientI
     return null;
   }
 
-  private class SiftsEntitySortPojo implements
-          Comparable<SiftsEntitySortPojo>
+  private class SiftsEntitySortPojo
+          implements Comparable<SiftsEntitySortPojo>
   {
     public String entityId;
 
@@ -901,8 +904,7 @@ public class SiftsClient implements SiftsClientI
 
     private int nonObservedShiftIndex;
 
-    public SegmentHelperPojo(SequenceI seq,
-            HashMap<Integer, int[]> mapping,
+    public SegmentHelperPojo(SequenceI seq, HashMap<Integer, int[]> mapping,
             TreeMap<Integer, String> resNumMap,
             List<Integer> omitNonObserved, int nonObservedShiftIndex)
     {
@@ -989,8 +991,8 @@ public class SiftsClient implements SiftsClientI
     // output mappings
     StringBuilder output = new StringBuilder(512);
     output.append(NEWLINE);
-    output.append("Sequence \u27f7 Structure mapping details").append(
-            NEWLINE);
+    output.append("Sequence \u27f7 Structure mapping details")
+            .append(NEWLINE);
     output.append("Method: SIFTS");
     output.append(NEWLINE).append(NEWLINE);
 
@@ -1013,8 +1015,8 @@ public class SiftsClient implements SiftsClientI
     for (int j = 0; j < nochunks; j++)
     {
       // Print the first aligned sequence
-      output.append(new Format("%" + (maxid) + "s").form(seqName)).append(
-              " ");
+      output.append(new Format("%" + (maxid) + "s").form(seqName))
+              .append(" ");
 
       for (int i = 0; i < len; i++)
       {
@@ -1086,8 +1088,8 @@ public class SiftsClient implements SiftsClientI
     {
       throw new SiftsException(">>> Low PID detected for SIFTs mapping...");
     }
-    output.append("Length of alignment = " + seqRes.length()).append(
-            NEWLINE);
+    output.append("Length of alignment = " + seqRes.length())
+            .append(NEWLINE);
     output.append(new Format("Percentage ID = %2.2f").form(pid));
     return output;
   }