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

[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.java

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 233707b..16b858a 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -137,8 +137,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     // danger: accession separator used as a regex here, a string elsewhere
     // in this case it is ok (it is just a space), but (e.g.) '\' would not be
-    List<String> allIds = Arrays.asList(query
-            .split(getAccessionSeparator()));
+    List<String> allIds = Arrays
+            .asList(query.split(getAccessionSeparator()));
     AlignmentI alignment = null;
     inProgress = true;
 
@@ -236,8 +236,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       }
     } catch (IOException e)
     {
-      System.err.println("Error transferring Ensembl features: "
-              + e.getMessage());
+      System.err.println(
+              "Error transferring Ensembl features: " + e.getMessage());
     }
   }
 
@@ -275,8 +275,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       proteinSeq.createDatasetSequence();
       querySeq.createDatasetSequence();
 
-      MapList mapList = AlignmentUtils
-              .mapCdsToProtein(querySeq, proteinSeq);
+      MapList mapList = AlignmentUtils.mapCdsToProtein(querySeq,
+              proteinSeq);
       if (mapList != null)
       {
         // clunky: ensure Uniprot xref if we have one is on mapped sequence
@@ -287,9 +287,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
                 getEnsemblDataVersion(), proteinSeq.getName(), map);
         querySeq.getDatasetSequence().addDBRef(dbr);
         DBRefEntry[] uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
-                new String[] { DBRefSource.UNIPROT });
+                new String[]
+                { DBRefSource.UNIPROT });
         DBRefEntry[] upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(),
-                new String[] { DBRefSource.UNIPROT });
+                new String[]
+                { DBRefSource.UNIPROT });
         if (uprots != null)
         {
           for (DBRefEntry up : uprots)
@@ -304,8 +306,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
               if (upx.size() > 1)
               {
-                Cache.log
-                        .warn("Implementation issue - multiple uniprot acc on product sequence.");
+                Cache.log.warn(
+                        "Implementation issue - multiple uniprot acc on product sequence.");
               }
             }
             else
@@ -330,8 +332,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
          * copy exon features to protein, compute peptide variants from dna 
          * variants and add as features on the protein sequence ta-da
          */
-        AlignmentUtils
-                .computeProteinFeatures(querySeq, proteinSeq, mapList);
+        AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq,
+                mapList);
       }
     } catch (Exception e)
     {
@@ -364,8 +366,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     /*
      * and add a reference to itself
      */
-    DBRefEntry self = new DBRefEntry(getDbSource(),
-            getEnsemblDataVersion(), seq.getName());
+    DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
+            seq.getName());
     seq.addDBRef(self);
   }
 
@@ -379,8 +381,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
    * @throws JalviewException
    * @throws IOException
    */
-  protected AlignmentI fetchSequences(List<String> ids, AlignmentI alignment)
-          throws JalviewException, IOException
+  protected AlignmentI fetchSequences(List<String> ids,
+          AlignmentI alignment) throws JalviewException, IOException
   {
     if (!isEnsemblAvailable())
     {
@@ -396,15 +398,15 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     FastaFile fr = new FastaFile(fp);
     if (fr.hasWarningMessage())
     {
-      System.out.println(String.format(
-              "Warning when retrieving %d ids %s\n%s", ids.size(),
-              ids.toString(), fr.getWarningMessage()));
+      System.out.println(
+              String.format("Warning when retrieving %d ids %s\n%s",
+                      ids.size(), ids.toString(), fr.getWarningMessage()));
     }
     else if (fr.getSeqs().size() != ids.size())
     {
       System.out.println(String.format(
-              "Only retrieved %d sequences for %d query strings", fr
-                      .getSeqs().size(), ids.size()));
+              "Only retrieved %d sequences for %d query strings",
+              fr.getSeqs().size(), ids.size()));
     }
 
     if (fr.getSeqs().size() == 1 && fr.getSeqs().get(0).getLength() == 0)
@@ -565,8 +567,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         if (directionSet && strand != direction)
         {
           // abort - mix of forward and backward
-          System.err.println("Error: forward and backward strand for "
-                  + accId);
+          System.err.println(
+                  "Error: forward and backward strand for " + accId);
           return null;
         }
         direction = strand;
@@ -609,8 +611,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
      */
     Collections.sort(regions, new RangeComparator(direction == 1));
 
-    List<int[]> to = Arrays.asList(new int[] { start,
-        start + mappedLength - 1 });
+    List<int[]> to = Arrays
+            .asList(new int[]
+            { start, start + mappedLength - 1 });
 
     return new MapList(regions, to, 1, 1);
   }
@@ -671,9 +674,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
        * for sequence_variant on reverse strand, have to convert the allele
        * values to their complements
        */
-      if (!forwardStrand
-              && SequenceOntologyFactory.getInstance().isA(sf.getType(),
-                      SequenceOntologyI.SEQUENCE_VARIANT))
+      if (!forwardStrand && SequenceOntologyFactory.getInstance()
+              .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
       {
         reverseComplementAlleles(copy);
       }