JAL-3438 spotless for 2.11.2.0

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 1783f37..9b90ca5 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -143,14 +143,16 @@ public class CrossRef
     /*
      * first find seq's xrefs (dna-to-peptide or peptide-to-dna)
      */
-    List<DBRefEntry> rfs = DBRefUtils.selectDbRefs(!fromDna, seq.getDBRefs());
+    List<DBRefEntry> rfs = DBRefUtils.selectDbRefs(!fromDna,
+            seq.getDBRefs());
     addXrefsToSources(rfs, sources);
     if (dataset != null)
     {
       /*
        * find sequence's direct (dna-to-dna, peptide-to-peptide) xrefs
        */
-      List<DBRefEntry> lrfs = DBRefUtils.selectDbRefs(fromDna, seq.getDBRefs());
+      List<DBRefEntry> lrfs = DBRefUtils.selectDbRefs(fromDna,
+              seq.getDBRefs());
       List<SequenceI> foundSeqs = new ArrayList<>();
 
       /*
@@ -370,7 +372,8 @@ public class CrossRef
         {
           // do a bit more work - search for sequences with references matching
           // xrefs on this sequence.
-          found = searchDataset(fromDna, dss, xref, rseqs, cf, false, DBRefUtils.SEARCH_MODE_FULL);
+          found = searchDataset(fromDna, dss, xref, rseqs, cf, false,
+                  DBRefUtils.SEARCH_MODE_FULL);
         }
         if (found)
         {
@@ -443,10 +446,10 @@ public class CrossRef
         addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
                 retrievedDss);
       }
-      // JBPNote: What assumptions are made for dbref structures on 
+      // JBPNote: What assumptions are made for dbref structures on
       // retrieved sequences ?
-      // addedXref will be true means importCrossRefSeq found 
-      // sequences with dbrefs with mappings to sequences congruent with dss 
+      // addedXref will be true means importCrossRefSeq found
+      // sequences with dbrefs with mappings to sequences congruent with dss
 
       if (!addedXref)
       {
@@ -498,11 +501,12 @@ public class CrossRef
       // protein
       if (sq.isProtein() == fromDna)
       {
-       List<DBRefEntry> sqdbrefs = sq.getPrimaryDBRefs();
+        List<DBRefEntry> sqdbrefs = sq.getPrimaryDBRefs();
         for (int idb = 0, ndb = sqdbrefs.size(); idb < ndb; idb++)
         {
-          DBRefEntry dbr = sqdbrefs.get(idb);  
-          List<DBRefEntry> searchrefs = DBRefUtils.searchRefs(dbrSourceSet, dbr, DBRefUtils.SEARCH_MODE_FULL);
+          DBRefEntry dbr = sqdbrefs.get(idb);
+          List<DBRefEntry> searchrefs = DBRefUtils.searchRefs(dbrSourceSet,
+                  dbr, DBRefUtils.SEARCH_MODE_FULL);
           for (int isr = 0, nsr = searchrefs.size(); isr < nsr; isr++)
           {
             sourceRefs.remove(searchrefs.get(isr));
@@ -723,8 +727,9 @@ public class CrossRef
   /**
    * Returns null or the first sequence in the dataset which is identical to
    * xref.mapTo, and has a) a primary dbref matching xref, or if none found, the
-   * first one with an ID source|xrefacc
-   * JBPNote: Could refactor this to AlignmentI/DatasetI
+   * first one with an ID source|xrefacc JBPNote: Could refactor this to
+   * AlignmentI/DatasetI
+   * 
    * @param xref
    *          with map and mapped-to sequence
    * @return
@@ -754,8 +759,8 @@ public class CrossRef
     for (SequenceI seq : dataset.getSequences())
     {
       // first check primary refs.
-      List<DBRefEntry> match = DBRefUtils.searchRefs(
-              seq.getPrimaryDBRefs(), template, DBRefUtils.SEARCH_MODE_FULL);
+      List<DBRefEntry> match = DBRefUtils.searchRefs(seq.getPrimaryDBRefs(),
+              template, DBRefUtils.SEARCH_MODE_FULL);
       if (match != null && match.size() == 1 && sameSequence(seq, dss))
       {
         return seq;
@@ -821,8 +826,9 @@ public class CrossRef
   /**
    * Updates any empty mappings in the cross-references with one to a compatible
    * retrieved sequence if found, and adds any new mappings to the
-   * AlignedCodonFrame
-   * JBPNote: TODO: this relies on sequence IDs like UNIPROT|ACCESSION - which do not always happen.
+   * AlignedCodonFrame JBPNote: TODO: this relies on sequence IDs like
+   * UNIPROT|ACCESSION - which do not always happen.
+   * 
    * @param mapFrom
    * @param xrefs
    * @param retrieved
@@ -972,10 +978,10 @@ public class CrossRef
     }
     for (int i = 0, n = lrfs.size(); i < n; i++)
     {
-//      DBRefEntry xref = new DBRefEntry(lrfs.get(i));
-//      // add in wildcards
-//      xref.setVersion(null);
-//      xref.setMap(null);
+      // DBRefEntry xref = new DBRefEntry(lrfs.get(i));
+      // // add in wildcards
+      // xref.setVersion(null);
+      // xref.setMap(null);
       found |= searchDataset(fromDna, sequenceI, lrfs.get(i), foundSeqs, cf,
               false, DBRefUtils.SEARCH_MODE_NO_MAP_NO_VERSION);
     }
@@ -1008,7 +1014,8 @@ public class CrossRef
    *          sequenceI or all the returned sequences (eg a genomic reference
    *          associated with a locus and one or more transcripts)</li>
    *          </ul>
-   * @param mode   SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
+   * @param mode
+   *          SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
    * @return true if relationship found and sequence added.
    */
   boolean searchDataset(boolean fromDna, SequenceI fromSeq, DBRefEntry xrf,