X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=1783f376c2a2f0a735e90114babd3430932c760c;hb=b1f3e3bac931d7f309f60e50b18c435c65586de8;hp=00bb63ac01bb6d1dd5a791060384876065bd5301;hpb=beff7ac7ab7be2c24ccb179be16b8816d2c18610;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 00bb63a..1783f37 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -443,6 +443,11 @@ public class CrossRef
         addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
                 retrievedDss);
       }
+      // 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 
+
       if (!addedXref)
       {
         // try again, after looking for matching IDs
@@ -483,7 +488,7 @@ public class CrossRef
   private void removeAlreadyRetrievedSeqs(List<DBRefEntry> sourceRefs,
           boolean fromDna)
   {
-    List<DBRefEntry> dbrSourceSet = new ArrayList<DBRefEntry>(sourceRefs);
+    List<DBRefEntry> dbrSourceSet = new ArrayList<>(sourceRefs);
     List<SequenceI> dsSeqs = dataset.getSequences();
     for (int ids = 0, nds = dsSeqs.size(); ids < nds; ids++)
     {
@@ -516,7 +521,9 @@ public class CrossRef
 
   /**
    * process sequence retrieved via a dbref on source sequence to resolve and
-   * transfer data
+   * transfer data JBPNote: as of 2022-02-03 - this assumes retrievedSequence
+   * has dbRefs with Mapping references to a sequence congruent with
+   * sourceSequence
    * 
    * @param cf
    * @param sourceSequence
@@ -535,10 +542,11 @@ public class CrossRef
     List<DBRefEntry> dbr = retrievedSequence.getDBRefs();
     if (dbr != null)
     {
-    	for (int ib = 0, nb = dbr.size(); ib < nb; ib++)
+      for (int ib = 0, nb = dbr.size(); ib < nb; ib++)
       {
 
-    	DBRefEntry dbref = dbr.get(ib);
+        DBRefEntry dbref = dbr.get(ib);
+        // matched will return null if the dbref has no map
         SequenceI matched = findInDataset(dbref);
         if (matched == sourceSequence)
         {
@@ -550,7 +558,7 @@ public class CrossRef
         Mapping map = dbref.getMap();
         if (map != null)
         {
-        	SequenceI ms = map.getTo();
+          SequenceI ms = map.getTo();
           if (ms != null && map.getMap() != null)
           {
             if (ms == sourceSequence)
@@ -716,7 +724,7 @@ 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
    * @param xref
    *          with map and mapped-to sequence
    * @return
@@ -814,7 +822,7 @@ 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.
    * @param mapFrom
    * @param xrefs
    * @param retrieved
@@ -929,7 +937,7 @@ public class CrossRef
 
     if (fromDna)
     {
-      AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
+      // AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
       mappings.addMap(mapFrom, mapTo, mapping);
     }
     else