X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=87f854a4fc9eb764886f999dcc82d14173fc5d80;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=104480253703d868a8edffd30614fec6e7d2e519;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 1044802..87f854a 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -142,14 +142,16 @@ 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<>();
 
       /*
@@ -369,7 +371,8 @@ 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)
         {
@@ -441,6 +444,11 @@ 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
@@ -491,11 +499,12 @@ 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));
@@ -514,7 +523,9 @@ 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
@@ -533,10 +544,11 @@ 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)
         {
@@ -548,7 +560,7 @@ 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)
@@ -713,7 +725,8 @@ 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
+   * first one with an ID source|xrefacc JBPNote: Could refactor this to
+   * AlignmentI/DatasetI
    * 
    * @param xref
    *          with map and mapped-to sequence
@@ -744,8 +757,8 @@ 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;
@@ -811,7 +824,8 @@ 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
+   * AlignedCodonFrame JBPNote: TODO: this relies on sequence IDs like
+   * UNIPROT|ACCESSION - which do not always happen.
    * 
    * @param mapFrom
    * @param xrefs
@@ -962,10 +976,10 @@ 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);
     }
@@ -998,7 +1012,8 @@ 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,