JAL-2154 JAL-2106 transfer primary refs to CDS for makeCDS

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index c4e51b1..cc80384 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -22,7 +22,6 @@ package jalview.analysis;
 
 import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE;
 
-import jalview.api.DBRefEntryI;
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
@@ -1682,6 +1681,10 @@ public class AlignmentUtils
            * its dataset sequence to the dataset
            */
           cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping);
+          // cdsSeq has a name constructed as CDS|<dbref>
+          // <dbref> will be either the accession for the coding sequence,
+          // marked in the /via/ dbref to the protein product accession
+          // or it will be the original nucleotide accession.
           SequenceI cdsSeqDss = cdsSeq.createDatasetSequence();
           cdsSeqs.add(cdsSeq);
           if (!dataset.getSequences().contains(cdsSeqDss))
@@ -1731,12 +1734,37 @@ public class AlignmentUtils
            * same source and accession, so need a different accession for
            * the CDS from the dna sequence
            */
-          DBRefEntryI dnaRef = dnaDss.getSourceDBRef();
-          if (dnaRef != null)
+          
+          // specific use case:
+          // Genomic contig ENSCHR:1, contains coding regions for ENSG01,
+          // ENSG02, ENSG03, with transcripts and products similarly named.
+          // cannot add distinct dbrefs mapping location on ENSCHR:1 to ENSG01
+          
+          // JBPNote: ?? can't actually create an example that demonstrates we
+          // need to
+          // synthesize an xref.
+          
+          for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs())
           {
+            // creates a complementary cross-reference to the source sequence's
+            // primary reference.
+
+            DBRefEntry cdsCrossRef = new DBRefEntry(primRef.getSource(),
+                    primRef.getSource() + ":" + primRef.getVersion(),
+                    primRef.getAccessionId());
+            cdsCrossRef
+                    .setMap(new Mapping(dnaDss, new MapList(dnaToCdsMap)));
+            cdsSeqDss.addDBRef(cdsCrossRef);
+
+            // problem here is that the cross-reference is synthesized -
+            // cdsSeq.getName() may be like 'CDS|dnaaccession' or
+            // 'CDS|emblcdsacc'
             // assuming cds version same as dna ?!?
-            DBRefEntry proteinToCdsRef = new DBRefEntry(dnaRef.getSource(),
-                    dnaRef.getVersion(), cdsSeq.getName());
+
+            DBRefEntry proteinToCdsRef = new DBRefEntry(
+                    primRef.getSource(), primRef.getVersion(),
+                    cdsSeq.getName());
+            //
             proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap
                     .getInverse()));
             proteinProduct.addDBRef(proteinToCdsRef);